BACKGROUND OF THE INVENTION The cellular processes regulating modification and maintenance of protein molecules coordinate their function, conformation, stabilization, and degradation. Each of these processes is mediated by key enzymes or proteins such as kinases, phosphatases, proteases, protease inhibitors, isomerases, transferases, and molecular chaperones.

Kinases Kinases catalyze the transfer of high-energy phosphate groups from adenosine triphosphate (ATP) to target proteins on the hydroxyamino acid residues serine, threonine, or tyrosine. Addition of a phosphate group alters the local charge on the acceptor molecule, causing internal conformational changes and potentially influencing intermolecular contacts. Reversible protein phosphorylation is the ubiquitous strategy used to control many of the intracellular events in eukaryotic cells. It is estimated that more than ten percent of proteins active in a typical mammalian cell are phosphorylated.

Extracellular signals including hormones, neurotransmitters, and growth and differentiation factors can activate kinases, which can occur as cell surface receptors or as the activators of the final effector protein, as well as elsewhere along the signal transduction pathway. Kinases are involved in all aspects of a cell's function, from basic metabolic processes, such as glycolysis, to cell-cycle regulation, differentiation, and communication with the extracellular environment through signal transduction cascades. Inappropriate phosphorylation of proteins in cells has been linked to changes in cell cycle progression and cell differentiation. Changes in the cell cycle have been linked to induction of apoptosis or cancer. Changes in cell differentiation have been linked to diseases and disorders of the reproductive system, immune system, and skeletal muscle.

There are two classes of protein kinases. One class, protein tyrosine kinases (PTKs), phosphorylates tyrosine residues, and the other class, protein serine/threonine kinases (STKs),

phosphorylates serine and threonine residues. Some PTKs and STKs possess structural characteristics of both families and have dual specificity for both tyrosine and serine/threonine residues. Almost all kinases contain a conserved 250-300 amino acid catalytic domain containing specific residues and sequence motifs characteristic of the kinase family. (Reviewed in Hardie, G. and S. Hanks (1995) The Protein Kinase Facts Book, Vol I, Academic Press, San Diego, CA, pp. 17- 20).

Phosphatases Phosphatases hydrolytically remove phosphate groups from proteins. Phosphatases are essential in determining the extent of phosphorylation in the cell and, together with kinases, regulate key cellular processes such as metabolic enzyme activity, proliferation, cell growth and differentiation, cell adhesion, and cell cycle progression. Protein phosphatases are characterized as either serine/threonine-or tyrosine-specific based on their preferred phospho-amino acid substrate. Some phosphatases (DSPs, for dual specificity phosphatases) can act on phosphorylated tyrosine, serine, or threonine residues. The protein serine/threonine phosphatases (PSPs) are important regulators of many cAMP-mediated hormone responses in cells. Protein tyrosine phosphatases (PTPs) play a significant role in cell cycle and cell signaling processes.

Proteases Proteases cleave proteins and peptides at the peptide bond that forms the backbone of the protein or peptide chain. Proteolysis is one of the most important and frequent enzymatic reactions that occurs both within and outside of cells. Proteolysis is responsible for the activation and maturation of nascent polypeptides, the degradation of misfolded and damaged proteins, and the controlled turnover of peptides within the cell. Proteases participate in digestion, endocrine function, tissue remodeling during embryonic development, wound healing, and normal growth. Proteases can play a role in regulatory processes by affecting the half life of regulatory proteins. Proteases are involved in the etiology or progression of disease states such as inflammation, angiogenesis, tumor dispersion and metastasis, cardiovascular disease, neurological disease, and bacterial, parasitic, and viral infections.

Proteases can be categorized on the basis of where they cleave their substrates.

Exopeptidases, which include aminopeptidases, dipeptidyl peptidases, tripeptidases, carboxypeptidases, peptidyl-di-peptidases, dipeptidases, and omega peptidases, cleave residues at the termini of their substrates. Endopeptidases, including serine proteases, cysteine proteases, and metalloproteases, cleave at residues within the peptide. Four principal categories of mammalian proteases have been identified based on active site structure, mechanism of action, and overall three-dimensional structure.

(See Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes: A Practical Approach, Oxford University Press, New York NY, pp. 1-5.) Serine Proteases The serine proteases (SPs) are a large, widespread family of proteolytic enzymes that include the digestive enzymes trypsin and chymotrypsin, components of the complement and blood-clotting cascades, and enzymes that control the degradation and turnover of macromolecules within the cell and in the extracellular matrix. Most of the more than 20 subfamilies can be grouped into six clans, each with a common ancestor. These six clans are hypothesized to have descended from at least four evolutionarily distinct ancestors. SPs are named for the presence of a serine residue found in the active catalytic site of most families. The active site is defined by the catalytic triad, a set of conserved asparagine, histidine, and serine residues critical for catalysis. These residues form a charge relay network that facilitates substrate binding. Other residues outside the active site form an oxyanion hole that stabilizes the tetrahedral transition intermediate formed during catalysis. SPs have a wide range of substrates and can be subdivided into subfamilies on the basis of their substrate specificity. The main subfamilies are named for the residue (s) after which they cleave: trypases (after arginine or lysine), aspases (after aspartate), chymases (after phenylalanine or leucine), metases (methionine), and serases (after serine) (Rawlings, N. D. and A. J. Barrett (1994) Methods Enzymol.

244: 19-61).

Most mammalian serine proteases are synthesized as zymogens, inactive precursors that are activated by proteolysis. For example, trypsinogen is converted to its active form, trypsin, by enteropeptidase. Enteropeptidase is an intestinal protease that removes an N-terminal fragment from trypsinogen. The remaining active fragment is trypsin, which in turn activates the precursors of the other pancreatic enzymes. Likewise, proteolysis of prothrombin, the precursor of thrombin, generates three separate polypeptide fragments. The N-terminal fragment is released while the other two fragments, which comprise active thrombin, remain associated through disulfide bonds.

The two largest SP subfamilies are the chymotrypsin (Sl) and subtilisin (S8) families. Some members of the chymotrypsin family contain two structural domains unique to this family. Kringle domains are triple-looped, disulfide cross-linked domains found in varying copy number. Kringle domains are thought to play a role in binding mediators such as membranes, other proteins or phospholipids, and in the regulation of proteolytic activity (PROSITE PDOC00020). Apple domains are 90 amino-acid repeated domains, each containing six conserved cysteines. Three disulfide bonds link the first and sixth, second and fifth, and third and fourth cysteines (PROSITE PDOC00376).

Apple domains are involved in protein-protein interactions. Sl family members include trypsin,

chymotrypsin, coagulation factors IX-XII, complement factors B, C, and D, granzymes, kallikrein, and tissue-and urokinase-plasminogen activators. The subtilisin family has members found in the eubacteria, archaebacteria, eukaryotes, and viruses. Subtilisins include the proprotein-processing endopeptidases kexin and furin and the pituitary prohormone convertases PC1, PC2, PC3, PC6, and PACE4 (Rawlings and Barrett, supra).

SPs have functions in many normal processes and some have been implicated in the etiology or treatment of disease. Enterokinase, the initiator of intestinal digestion, is found in the intestinal brush border, where it cleaves the acidic propeptide from trypsinogen to yield active trypsin (Kitamoto, Y. et al. (1994) Proc. Natl. Acad. Sci. USA 91: 7588-7592). Prolylcarboxypeptidase, a lysosomal serine peptidase that cleaves peptides such as angiotensin II and III and [des-Arg9] bradykinin, shares sequence homology with members of both the serine carboxypeptidase and prolylendopeptidase families (Tan, F. et al. (1993) J. Biol. Chem. 268: 16631-16638). The protease neuropsin may influence synapse formation and neuronal connectivity in the hippocampus in response to neural <BR> <BR> signaling (Chen, Z. -L. et al. (1995) J. Neurosci. 15: 5088-5097). Tissue plasminogen activator is useful for acute management of stroke (Zivin, J. A. (1999) Neurology 53: 14-19) and myocardial infarction (Ross, A. M. (1999) Clin. Cardiol. 22: 165-171). Some receptors (PAR, for proteinase-activated receptor), highly expressed throughout the digestive tract, are activated by proteolytic cleavage of an extracellular domain. The major agonists for PARs, thrombin, trypsin, and mast cell tryptase, are released in allergy and inflammatory conditions. Control of PAR activation by proteases has been suggested as a promising therapeutic target (Vergnolle, N. (2000) Aliment. Pharmacol. Ther. 14: 257- 266; Rice, K. D. et al. (1998) Curr. Pharm. Des. 4: 381-396). Prostate-specific antigen (PSA) is a kallikrein-like serine protease synthesized and secreted exclusively by epithelial cells in the prostate gland. Serum PSA is elevated in prostate cancer and is the most sensitive physiological marker for monitoring cancer progression and response to therapy. PSA can also identify the prostate as the origin of a metastatic tumor (Brawer, M. K. and P. H. Lange (1989) Urology 33: 11-16).

The signal peptidase is a specialized class of SP found in all prokaryotic and eukaryotic cell types that serves in the processing of signal peptides from certain proteins. Signal peptides are amino-terminal domains of a protein which direct the protein from its ribosomal assembly site to a particular cellular or extracellular location. Once the protein has been exported, removal of the signal <BR> <BR> sequence by a signal peptidase and posttranslational processing, e. g. , glycosylation or phosphorylation, activate the protein. Signal peptidases exist as multi-subunit complexes in both yeast and mammals.

The canine signal peptidase complex is composed of five subunits, all associated with the microsomal membrane and containing hydrophobic regions that span the membrane one or more times (Shelness,

G. S. and G. Blobel (1990) J. Biol. Chem. 265: 9512-9519). Some of these subunits serve to fix the complex in its proper position on the membrane while others contain the actual catalytic activity.

Thrombin is a serine protease with an essential role in the process of blood coagulation.

Prothrombin, synthesized in the liver, is converted to active thrombin by Factor Xa. Activated thrombin then cleaves soluble fibrinogen to polymer-forming fibrin, a primary component of blood clots. In addition, thrombin activates Factor XIIIa, which plays a role in cross-linking fibrin.

Thrombin also stimulates platelet aggregation through proteolytic processing of a 41-residue amino-terminal peptide from protease-activated receptor 1 (PAR-1), formerly known as the thrombin receptor. The cleavage of the amino-terminal peptide exposes a new amino terminus and may also be associated with PAR-1 internalization (Stubbs, M. T. and W. Bode (1994) Curr. Opin. Struct. Biol.

4: 823-832; and Ofoso, F. A. et al. (1998) Biochem. J. 336: 283-285). In addition to stimulating platelet activation through cleavage of the PAR-1 receptor, thrombin also induces platelet aggregation following cleavage of glycoprotein V, also on the surface of platelets. Glycoprotein V appears to be the major thrombin substrate on intact platelets. Platelets deficient for glycoprotein V are hypersensitive to thrombin, which is still required to cleave PAR-1. While platelet aggregation is required for normal hemostasis in mammals, excessive platelet aggregation can result in arterial thrombosis, atherosclerotic arteries, acute myocardial infarction, and stroke (Ramakrishnan, V. et al.

(1999) Proc. Natl. Acad. Sci. U. S. A. 96: 13336-13341 and references within).

Proteases in another family have a serine in their active site and are dependent on the hydrolysis of ATP for their activity. These proteases contain proteolytic core domains and regulatory ATPase domains which can be identified by the presence of the P-loop, an ATP/GTP-binding motif (PROSITE PDOC00803). Members of this family include the eukaryotic mitochondrial matrix proteases, Clp protease and the proteasome. Clp protease was originally found in plant chloroplasts but is believed to be widespread in both prokaryotic and eukaryotic cells. The gene for early-onset torsion dystonia encodes a protein related to Clp protease (Ozelius, L. J. et al. (1998) Adv. Neurol.

78: 93-105).

The proteasome is an intracellular protease complex found in some bacteria and in all eukaryotic cells, and plays an important role in cellular physiology. The proteasome is a large (-2000 kDa) multisubunit complex composed of a central catalytic core containing a variety of proteases arranged in four seven-membered rings with the active sites facing inwards into the central cavity, and terminal ATPase subunits covering the outer port of the cavity and regulating substrate entry (for review, see Schmidt, M. et al. (1999) Curr. Opin. Chem. Biol. 3: 584-591). Proteasomes are associated with the ubiquitin conjugation system (UCS), a major pathway for the degradation of

cellular proteins of all types, including proteins that function to activate or repress cellular processes such as transcription and cell cycle progression (Ciechanover, A. (1994) Cell 79: 13-21). In the UCS pathway, proteins targeted for degradation are conjugated to ubiquitin, a small heat stable protein. The ubiquitinated protein is then recognized and degraded by the proteasome. The resultant ubiquitin- peptide complex is hydrolyzed by a ubiquitin carboxyl terminal hydrolase, and free ubiquitin is released for reutilization by the UCS. Ubiquitin-proteasome systems are implicated in the degradation of mitotic cyclic kinases, oncoproteins, tumor suppressor genes (p53), cell surface receptors associated with signal transduction, transcriptional regulators, and mutated or damaged proteins (Ciechanover, supra). This pathway has been implicated in a number of diseases, including cystic fibrosis, Angelman's syndrome, and Liddle syndrome (reviewed in Schwartz, A. L. and A. Ciechanover (1999) Annu. Rev. Med. 50: 57-74). A murine proto-oncogene, Unp, encodes a nuclear ubiquitin protease whose overexpression leads to oncogenic transformation of NIH3T3 cells. The human homolog of this gene is consistently elevated in small cell tumors and adenocarcinomas of the lung (Gray, D. A.

(1995) Oncogene 10: 2179-2183). Ubiquitin carboxyl terminal hydrolase is involved in the differentiation of a lymphoblastic leukemia cell line to a non-dividing mature state (Maki, A. et al.

(1996) Differentiation 60: 59-66). In neurons, ubiquitin carboxyl terminal hydrolase (PGP 9.5) expression is strong in the abnormal structures that occur in human neurodegenerative diseases (Lowe, J. et al. (1990) J. Pathol. 161: 153-160).

Cysteine Proteases Cysteine proteases (CPs) are involved in diverse cellular processes ranging from the processing of precursor proteins to intracellular degradation. Nearly half of the CPs known are present only in viruses. CPs have a cysteine as the major catalytic residue at the active site where catalysis proceeds via a thioester intermediate and is facilitated by nearby histidine and asparagine residues. A glutamine residue is also important, as it helps to form an oxyanion hole. Two important CP families include the papain-like enzymes (C1) and the calpains (C2). Papain-like family members are generally lysosomal or secreted and therefore are synthesized with signal peptides as well as propeptides. Most members bear a conserved motif in the propeptide that may have structural significance (Karrer, K. M. et al. (1993) Proc. Natl. Acad. Sci. USA 90: 3063-3067). Three- dimensional structures of papain family members show a bilobed molecule with the catalytic site located between the two lobes. Papains include cathepsins B, C, H, L, and S, certain plant allergens and dipeptidyl peptidase (for a review, see Rawlings, N. D. and A. J. Barrett (1994) Methods Enzymol.

244: 461-486).

Some CPs are expressed ubiquitously, while others are produced only by cells of the immune system. Of particular note, CPs are produced by monocytes, macrophages and other cells which migrate to sites of inflammation and secrete molecules involved in tissue repair. Overabundance of these repair molecules plays a role in certain disorders. In autoimmune diseases such as rheumatoid arthritis, secretion of the cysteine peptidase cathepsin C degrades collagen, laminin, elastin and other structural proteins found in the extracellular matrix of bones. Bone weakened by such degradation is also more susceptible to tumor invasion and metastasis. Cathepsin L expression may also contribute to the influx of mononuclear cells which exacerbates the destruction of the rheumatoid synovium (Keyszer, G. M. (1995) Arthritis Rheum. 38: 976-984).

Calpains are calcium-dependent cytosolic endopeptidases which contain both an N-terminal catalytic domain and a C-terminal calcium-binding domain. Calpain is expressed as a proenzyme heterodimer consisting of a catalytic subunit unique to each isoform and a regulatory subunit common to different isoforms. Each subunit bears a calcium-binding EF-hand domain. The regulatory subunit also contains a hydrophobic glycine-rich domain that allows the enzyme to associate with cell membranes. Calpains are activated by increased intracellular calcium concentration, which induces a change in conformation and limited autolysis. The resultant active molecule requires a lower calcium concentration for its activity (Chan, S. L. and M. P. Mattson (1999) J. Neurosci. Res. 58: 167-190).

Calpain expression is predominantly neuronal, although it is present in other tissues. Several chronic neurodegenerative disorders, including ALS, Parkinson's disease and Alzheimer's disease are associated with increased calpain expression (Chan and Mattson, supra). Calpain-mediated breakdown of the cytoskeleton has been proposed to contribute to brain damage resulting from head injury (McCracken, E. et al. (1999) J. Neurotrauma 16: 749-761). Calpain-3 is predominantly expressed in skeletal muscle, and is responsible for limb-girdle muscular dystrophy type 2A (Minami, N. et al. (1999) J. Neurol. Sci. 171: 31-37).

Another family of thiol proteases is the caspases, which are involved in the initiation and execution phases of apoptosis. A pro-apoptotic signal can activate initiator caspases that trigger a proteolytic caspase cascade, leading to the hydrolysis of target proteins and the classic apoptotic death of the cell. Two active site residues, a cysteine and a histidine, have been implicated in the catalytic mechanism. Caspases are among the most specific endopeptidases, cleaving after aspartate residues.

Caspases are synthesized as inactive zymogens consisting of one large (p20) and one small (plO) subunit separated by a small spacer region, and a variable N-terminal prodomain. This prodomain interacts with cofactors that can positively or negatively affect apoptosis. An activating signal causes autoproteolytic cleavage of a specific aspartate residue (D297 in the caspase-1 numbering convention)

and removal of the spacer and prodomain, leaving a plO/p20 heterodimer. Two of these heterodimers interact via their small subunits to form the catalytically active tetramer. The long prodomains of some caspase family members have been shown to promote dimerization and auto-processing of procaspases. Some caspases contain a"death effector domain"in their prodomain by which they can be recruited into self-activating complexes with other caspases and FADD protein associated death receptors or the TNF receptor complex. In addition, two dimers from different caspase family members can associate, changing the substrate specificity of the resultant tetramer. Endogenous caspase inhibitors (inhibitor of apoptosis proteins, or IAPs) also exist. All these interactions have clear effects on the control of apoptosis (reviewed in Chan and Mattson, supra ; Salveson, G. S. and V. M.

Dixit (1999) Proc. Natl. Acad. Sci. USA 96: 10964-10967).

Caspases have been implicated in a number of diseases. Mice lacking some caspases have severe nervous system defects due to failed apoptosis in the neuroepithelium and suffer early lethality.

Others show severe defects in the inflammatory response, as caspases are responsible for processing IL-lb and possibly other inflammatory cytokines (Chan and Mattson, supra). Cowpox virus and baculoviruses target caspases to avoid the death of their host cell and promote successful infection. In addition, increases in inappropriate apoptosis have been reported in AIDS, neurodegenerative diseases and ischemic injury, while a decrease in cell death is associated with cancer (Salveson and Dixit, supra ; Thompson, C. B. (1995) Science 267: 1456-1462).

Aspartyl proteases Aspartyl proteases (APs) include the lysosomal proteases cathepsins D and E, as well as chymosin, renin, and the gastric pepsins. Most retroviruses encode an AP, usually as part of the pol polyprotein. APs, also called acid proteases, are monomeric enzymes consisting of two domains, each domain containing one half of the active site with its own catalytic aspartic acid residue. APs are most active in the range of pH 2-3, at which one of the aspartate residues is ionized and the other neutral. The pepsin family of APs contains many secreted enzymes, and all are likely to be synthesized with signal peptides and propeptides. Most family members have three disulfide loops, the first-5 residue loop following the first aspartate, the second 5-6 residue loop preceding the second aspartate, and the third and largest loop occurring toward the C terminus. Retropepsins, on the other hand, are analogous to a single domain of pepsin, and become active as homodimers with each retropepsin monomer contributing one half of the active site. Retropepsins are required for processing the viral polyproteins.

APs have roles in various tissues, and some have been associated with disease. Renin mediates the first step in processing the hormone angiotensin, which is responsible for regulating

electrolyte balance and blood pressure (reviewed in Crews, D. E. and S. R. Williams (1999) Hum. Biol.

71: 475-503). Abnormal regulation and expression of cathepsins are evident in various inflammatory disease states. Expression of cathepsin D is elevated in synovial tissues from patients with rheumatoid arthritis and osteoarthritis. The increased expression and differential regulation of the cathepsins are linked to the metastatic potential of a variety of cancers (Chambers, A. F. et al. (1993) Crit. Rev.

Oncol. 4: 95-114).

Metalloproteases Metalloproteases require a metal ion for activity, usually manganese or zinc. Examples of manganese metalloenzymes include aminopeptidase P and human proline dipeptidase (PEPD).

Aminopeptidase P can degrade bradykinin, a nonapeptide activated in a variety of inflammatory responses. Aminopeptidase P has been implicated in coronary ischemia/reperfusion injury.

Administration of aminopeptidase P inhibitors has been shown to have a cardioprotective effect in rats (Ersahin, C. et al (1999) J. Cardiovasc. Pharmacol. 34: 604-611).

Most zinc-dependent metalloproteases share a common sequence in the zinc-binding domain.

The active site is made up of two histidines which act as zinc ligands and a catalytic glutamic acid C- terminal to the first histidine. Proteins containing this signature sequence are known as the metzincins and include aminopeptidase N, angiotensin-converting enzyme, neurolysin, the matrix metalloproteases and the adamalysins (ADAMS). An alternate sequence is found in the zinc carboxypeptidases, in which all three conserved residues-two histidines and a glutamic acid-are involved in zinc binding.

A number of the neutral metalloendopeptidases, including angiotensin converting enzyme and the aminopeptidases, are involved in the metabolism of peptide hormones. High aminopeptidase B activity, for example, is found in the adrenal glands and neurohypophyses of hypertensive rats (Prieto, I. et al. (1998) Horm. Metab. Res. 30 : 246-248). Oligopeptidase M/neurolysin can hydrolyze bradykinin as well as neurotensin (Serizawa, A. et al. (1995) J. Biol. Chem 270: 2092-2098).

Neurotensin is a vasoactive peptide that can act as a neurotransmitter in the brain, where it has been implicated in limiting food intake (Tritos, N. A. et al. (1999) Neuropeptides 33: 339-349).

The matrix metalloproteases (MMPs) are a family of at least 23 enzymes that can degrade components of the extracellular matrix (ECM). They are Zn2+ endopeptidases with an N-terminal catalytic domain. Nearly all members of the family have a hinge peptide and a C-terminal domain which can bind to substrate molecules in the ECM or to inhibitors produced by the tissue (TIMPs, for tissue inhibitor of metalloprotease ; Campbell, I. L. and A. Pagenstecher (1999) Trends Neurosci.

22: 285-287). The presence of fibronectin-like repeats, transmembrane domains, or C-terminal hemopexinase-like domains can be used to separate MMPs into collagenase, gelatinase, stromelysin

and membrane-type MMP subfamilies. In the inactive form, the Zn2+ ion in the active site interacts with a cysteine in the pro-sequence. Activating factors disrupt the Zn2+-cysteine interaction, or <BR> <BR> "cysteine switch, "exposing the active site. This partially activates the enzyme, which then cleaves off its propeptide and becomes fully active. MMPs are often activated by the serine proteases plasmin and furin. MMPs are often regulated by stoichiometric, noncovalent interactions with inhibitors; the balance of protease to inhibitor, then, is very important in tissue homeostasis (reviewed in Yong, V. W. et al. (1998) Trends Neurosci. 21: 75-80).

MMPs are implicated in a number of diseases including osteoarthritis (Mitchell, P. et al.

(1996) J. Clin. Invest. 97: 761-768), atherosclerotic plaque rupture (Sukhova, G. K. et al. (1999) Circulation 99: 2503-2509), aortic aneurysm (Schneiderman, J. et al. (1998) Am. J. Path. 152: 703-710), non-healing wounds (Saarialho-Kere, U. K. et al. (1994) J. Clin. Invest. 94: 79-88), bone resorption (Blavier, L. and J. M. Delaisse (1995) J. Cell Sci. 108: 3649-3659), age-related macular degeneration (Steen, B. et al. (1998) Invest. Ophthalmol. Vis. Sci. 39: 2194-2200), emphysema (Finlay, G. A. et al.

(1997) Thorax 52: 502-506), myocardial infarction (Rohde, L. E. et al. (1999) Circulation 99: 3063-3070) and dilated cardiomyopathy (Thomas, C. V. et al. (1998) Circulation 97: 1708-1715). MMP inhibitors prevent metastasis of mammary carcinoma and experimental tumors in rat, and Lewis lung carcinoma, hemangioma, and human ovarian carcinoma xenografts in mice (Eccles, S. A. et al. (1996) Cancer Res. 56: 2815-2822; Anderson et al. (I996) Cancer Res. 56: 715-718; Volpert, O. V. et al. (1996) J.

Clin. Invest. 98: 671-679; Taraboletti, G. et al. (1995) J. Natl. Cancer Inst. 87: 293-298; Davies, B. et al. (1993) Cancer Res. 53: 2087-2091). MMPs may be active in Alzheimer's disease. A number of MMPs are implicated in multiple sclerosis, and administration of MMP inhibitors can relieve some of its symptoms (reviewed in Yong et al., supra).

Another family of metalloproteases is the ADAMs, for A Disintegrin and Metalloprotease Domain, which they share with their close relatives the adamalysins, snake venom metalloproteases (SVMPs). ADAMs combine features of both cell surface adhesion molecules and proteases, containing a prodomain, a protease domain, a disintegrin domain, a cysteine rich domain, an epidermal growth factor repeat, a transmembrane domain, and a cytoplasmic tail. The first three domains listed above are also found in the SVMPs. The ADAMs possess four potential functions: proteolysis, adhesion, signaling and fusion. The ADAMs share the metzincin zinc binding sequence and are inhibited by some MMP antagonists such as TIMP-1.

ADAMs are implicated in such processes as sperm-egg binding and fusion, myoblast fusion, and protein-ectodomain processing or shedding of cytokines, cytokine receptors, adhesion proteins and other extracellular protein domains (Schlondorff, J. and C. P. Blobel (1999) J. Cell. Sci. 112: 3603-

3617). The Kuzbanian protein cleaves a substrate in the NOTCH pathway (possibly NOTCH itself), activating the program for lateral inhibition in Drosophila neural development. Two ADAMs, TACE (ADAM 17) and ADAM 10, are proposed to have analogous roles in the processing of amyloid precursor protein in the brain (Schlöndorff and Blobel, supra). TACE has also been identified as the TNF activating enzyme (Black, R. A. et al. (1997) Nature 385 : 729-733). TNF is a pleiotropic cytokine that is important in mobilizing host defenses in response to infection or trauma, but can cause severe damage in excess and is often overproduced in autoimmune disease. TACE cleaves membrane- bound pro-TNF to release a soluble form. Other ADAMs may be involved in a similar type of processing of other membrane-bound molecules.

Proteins of the ADAMTS sub-family have all of the features of ADAM family metalloproteases and contain an additional thrombospondin domain (TS). The prototypic ADAMTS was identified in mouse, and found to be expressed in heart and kidney and upregulated by proinflammatory stimuli (Kuno, K. et al. (1997) J. Biol. Chem. 272: 556-562). To date eleven members are recognized by the Human Genome Organization (HUGO; http://www. gene. ucl. ac. uk/users/hester/adamts. html#Approved). Members of this family have the ability to degrade aggrecan, a high molecular weight proteoglycan which provides cartilage with important mechanical properties including compressibility, and which is lost during the development of arthritis. Enzymes which degrade aggrecan are thus considered attractive targets to prevent and slow the degradation of articular cartilage (See, e. g., Tortorella, M. D. (1999) Science 284: 1664-1666; Abbaszade, 1. (1999} J. Biol. Chem. 274 : 23443-23450). Other members are reported to have antiangiogenic potential (Kuno et al., supra) and/or procollagen processing (Colige, A. et al. (1997) Proc. Natl. Acad. Sci. USA 94: 2374-2379).

Protease inhibitors Protease inhibitors and other regulators of protease activity control the activity and effects of proteases. Protease inhibitors have been shown to control pathogenesis in animal models of proteolytic disorders (Murphy, G. (1991) Agents Actions Suppl. 35: 69-76). Low levels of the cystatins, low molecular weight inhibitors of the cysteine proteases, correlate with malignant progression of tumors (Calkins, C. et al. (1995) Biol. Biochem. Hoppe Seyler 376: 71-80). The cystatin superfamily of protease inhibitors is characterized by a particular pattern of linearly arranged and tandemly repeated disulfide loops (Kellermann, J. et al. (1989) J. Biol. Chem. 264: 14121-14128).

Serpins are inhibitors of mammalian plasma serine proteases. Many serpins serve to regulate the blood clotting cascade and/or the complement cascade in mammals. Sp32 is a positive regulator of the mammalian acrosomal protease, acrosin, that binds the proenzyme, proacrosin, and thereby aides in

packaging the enzyme into the acrosomal matrix (Baba, T. et al. (1994) J. Biol. Chem. 269: 10133- 10140). The Kunitz family of serine protease inhibitors are characterized by one or more"Kunitz domains"containing a series of cysteine residues that are regularly spaced over approximately 50 amino acid residues and form three intrachain disulfide bonds. Members of this family include aprotinin, tissue factor pathway inhibitor (TFPI-1 and TFPI-2), inter-a-trypsin inhibitor, and bikunin (Marlor, C. W. et al. (1997) J. Biol. Chem. 272: 12202-12208). Members of this family are potent inhibitors (in the nanomolar range) against serine proteases such as kallikrein and plasmin. Aprotinin has clinical utility in reduction of perioperative blood loss.

A major portion of all proteins synthesized in eukaryotic cells are synthesized on the cytosolic surface of the endoplasmic reticulum (ER). Before these immature proteins are distributed to other organelles in the cell or are secreted, they must be transported into the interior lumen of the ER where post-translational modifications are performed. These modifications include protein folding and the formation of disulfide bonds, and N-linked glycosylations.

Protein Isomerases Protein folding in the ER is aided by two principal types of protein isomerases, protein disulfide isomerase (PDI), and peptidyl-prolyl isomerase (PPI). PDI catalyzes the oxidation of free sulfhydryl groups in cysteine residues to form intramolecular disulfide bonds in proteins. PPI, an enzyme that catalyzes the isomerization of certain proline imidic bonds in oligopeptides and proteins, is considered to govern one of the rate limiting steps in the folding of many proteins to their final functional conformation. The cyclophilins represent a major class of PPI that was originally identified as the major receptor for the immunosuppressive drug cyclosporin A (Handschumacher, R. E. et al. (1984) Science 226: 544-547).

Protein Glycosylation The glycosylation of most soluble secreted and membrane-bound proteins by oligosaccharides linked to asparagine residues in proteins is also performed in the ER. This reaction is catalyzed by a membrane-bound enzyme, oligosaccharyl transferase. Although the exact purpose of this"N-linked" glycosylation is unknown, the presence of oligosaccharides tends to make a glycoprotein resistant to protease digestion. In addition, oligosaccharides attached to cell-surface proteins called selectins are known to function in cell-cell adhesion processes (Alberts, B. et al. (1994) Molecular Biology of the <BR> <BR> Cell Garland Publishing Co. , New York, NY, p. 608)."O-linked"glycosylation of proteins also occurs in the ER by the addition of N-acetylgalactosamine to the hydroxyl group of a serine or threonine residue followed by the sequential addition of other sugar residues to the first. This process is catalyzed by a series of glycosyltransferases, each specific for a particular donor sugar nucleotide and

acceptor molecule (Lodish, H. et al. (1995) Molecular Cell Biology, W. H. Freeman and Co. , New York, NY, pp. 700-708). In many cases, both N-and 0-linked oligosaccharides appear to be required for the secretion of proteins or the movement of plasma membrane glycoproteins to the cell surface.

An additional glycosylation mechanism operates in the ER specifically to target lysosomal enzymes to lysosomes and prevent their secretion. Lysosomal enzymes in the ER receive an N-linked oligosaccharide, like plasma membrane and secreted proteins, but are then phosphorylated on one or two mannose residues. The phosphorylation of mannose residues occurs in two steps, the first step being the addition of an N-acetylglucosamine phosphate residue by N-acetylglucosamine phosphotransferase, and the second the removal of the N-acetylglucosamine group by phosphodiesterase. The phosphorylated mannose residue then targets the lysosomal enzyme to a mannose 6-phosphate receptor which transports it to a lysosome vesicle (Lodish et al. supra, pp. 708- 711).

Chaperones Molecular chaperones are proteins that aid in the proper folding of immature proteins and refolding of improperly folded ones, the assembly of protein subunits, and in the transport of unfolded proteins across membranes. Chaperones are also called heat-shock proteins (hsp) because of their tendency to be expressed in dramatically increased amounts following brief exposure of cells to elevated temperatures. This latter property most likely reflects their need in the folding of proteins that have become denatured by the high temperatures. Chaperones may be divided into several classes according to their location, function, and molecular weight, and include hsp60, TCP1, hsp70, hsp40 (also called DnaJ), and hsp90. For example, hsp90 binds to steroid hormone receptors, represses transcription in the absence of the ligand, and provides proper folding of the ligand-binding domain of the receptor in the presence of the hormone (Burston, S. G. and A. R. Clarke (1995) Essays Biochem. 29: 125-136). Hsp60 and hsp70 chaperones aid in the transport and folding of newly synthesized proteins. Hsp70 acts early in protein folding, binding a newly synthesized protein before it leaves the ribosome and transporting the protein to the mitochondria or ER before releasing the folded protein. Hsp60, along with hsplO, binds misfolded proteins and gives them the opportunity to refold correctly. All chaperones share an affinity for hydrophobic patches on incompletely folded proteins and the ability to hydrolyze ATP. The energy of ATP hydrolysis is used to release the hsp-bound protein in its properly folded state (Alberts et al., supra, pp. 214,571-572).

Expression profiling Microarrays are analytical tools used in bioanalysis. A microarray has a plurality of molecules spatially distributed over, and stably associated with, the surface of a solid support. Microarrays of

polypeptides, polynucleotides, and/or antibodies have been developed and find use in a variety of applications, such as gene sequencing, monitoring gene expression, gene mapping, bacterial identification, drug discovery, and combinatorial chemistry.

One area in particular in which microarrays find use is in gene expression analysis. Array technology can provide a simple way to explore the expression of a single polymorphic gene or the expression profile of a large number of related or unrelated genes. When the expression of a single gene is examined, arrays are employed to detect the expression of a specific gene or its variants.

When an expression profile is examined, arrays provide a platform for identifying genes that are tissue specific, are affected by a substance being tested in a toxicology assay, are part of a signaling cascade, carry out housekeeping functions, or are specifically related to a particular genetic predisposition, condition, disease, or disorder.

Breast Cancer More than 180,000 new cases of breast cancer are diagnosed each year, and the mortality rate for breast cancer approaches 10% of all deaths in females between the ages of 45-54 (Gish, K.

(1999) AWIS Magazine 28: 7-10). However the survival rate based on early diagnosis of localized breast cancer is extremely high (97%), compared with the advanced stage of the disease in which the tumor has spread beyond the breast (22%). Current procedures for clinical breast examination are lacking in sensitivity and specificity, and efforts are underway to develop comprehensive gene expression profiles for breast cancer that may be used in conjunction with conventional screening methods to improve diagnosis and prognosis of this disease (Perou, C. M. et al. (2000) Nature 406: 747-752).

Mutations in two genes, BRCA1 and BRCA2, are known to greatly predispose a woman to breast cancer and may be passed on from parents to children (Gish, supra). However, this type of hereditary breast cancer accounts for only about 5% to 9% of breast cancers, while the vast majority of breast cancer is due to non-inherited mutations that occur in breast epithelial cells.

The relationship between expression of epidermal growth factor (EGF) and its receptor, EGFR, to human mammary carcinoma has been particularly well studied. (See Khazaie, K. et al.

(1993) Cancer and Metastasis Rev. 12: 255-274, and references cited therein for a review of this area. ) Overexpression of EGFR, particularly coupled with down-regulation of the estrogen receptor, is a marker of poor prognosis in breast cancer patients. In addition, EGFR expression in breast tumor metastases is frequently elevated relative to the primary tumor, suggesting that EGFR is involved in

tumor progression and metastasis. This is supported by accumulating evidence that EGF has effects on cell functions related to metastatic potential, such as cell motility, chemotaxis, secretion and differentiation. Changes in expression of other members of the erbB receptor family, of which EGFR is one, have also been implicated in breast cancer. The abundance of erbB receptors, such as HER- 2/neu, HER-3, and HER-4, and their ligands in breast cancer points to their functional importance in the pathogenesis of the disease, and may therefore provide targets for therapy of the disease (Bacus, S. S. et al. (1994) Am. J. Clin. Pathol. 102: S13-S24). Other known markers of breast cancer include a human secreted frizzled protein mRNA that is downregulated in breast tumors; the matrix Gla protein which is overexpressed in human breast carcinoma cells ; Drgl or RTP, a gene whose expression is diminished in colon, breast, and prostate tumors; maspin, a tumor suppressor gene downregulated in invasive breast carcinomas; and CaN19, a member of the S100 protein family, all of which are down- regulated in mammary carcinoma cells relative to normal mammary epithelial cells (Zhou, Z. et al.

(1998) Int. J. Cancer 78 : 95-99; Chen, L. et al. (1990) Oncogene 5: 1391-1395; Ulrix, W. et al (1999) FEBS Lett 455: 23-26; Sager, R. et al. (1996) Curr. Top. Microbiol. Immunol. 213: 51-64; and Lee, S. W. et al. (1992) Proc. Natl. Acad. Sci. USA 89: 2504-2508).

Cell lines derived from human mammary epithelial cells at various stages of breast cancer provide a useful model to study the process of malignant transformation and tumor progression as it has been shown that these cell lines retain many of the properties of their parental tumors for lengthy culture periods (Wistuba, I. I. et al. (1998) Clin. Cancer Res. 4: 2931-2938). Such a model is particularly useful for comparing phenotypic and molecular characteristics of human mammary epithelial cells at various stages of malignant transformation.

Colon Cancer While soft tissue sarcomas are relatively rare, more than 50% of new patients diagnosed with the disease will die from it. The molecular pathways leading to the development of sarcomas are relatively unknown, due to the rarity of the disease and variation in pathology. Colon cancer evolves through a multi-step process whereby pre-malignant colonocytes undergo a relatively defined sequence of events leading to tumor formation. Several factors participate in the process of tumor progression and malignant transformation including genetic factors, mutations, and selection To understand the nature of gene alterations in colorectal cancer, a number of studies have focused on the inherited syndromes. Familial adenomatous polyposis (FAP), is caused by mutations in the adenomatous polyposis coli gene (APC), resulting in truncated or inactive forms of the protein.

This tumor suppressor gene has been mapped to chromosome 5q. Hereditary nonpolyposis colorectal cancer (HNPCC) is caused by mutations in mis-match repair genes. Although hereditary colon

cancer syndromes occur in a small percentage of the population and most colorectal cancers are considered sporadic, knowledge from studies of the hereditary syndromes can be generally applied.

For instance, somatic mutations in APC occur in at least 80% of sporadic colon tumors. APC mutations are thought to be the initiating event in the disease. Other mutations occur subsequently.

Approximately 50% of colorectal cancers contain activating mutations in ras, while 85% contain inactivating mutations in p53. Changes in all of these genes lead to gene expression changes in colon cancer.

Ovarian Cancer Ovarian cancer is the leading cause of death from a gynecologic cancer. The majority of ovarian cancers are derived from epithelial cells, and 70% of patients with epithelial ovarian cancers present with late-stage disease. As a result, the long-term survival rate for this disease is very low.

Identification of early-stage markers for ovarian cancer would significantly increase the survival rate.

Genetic variations involved in ovarian cancer development include mutation of p53 and microsatellite instability. Gene expression patterns likely vary when normal ovary is compared to ovarian tumors.

Prostate Cancer Prostate cancer develops through a multistage progression ultimately resulting in an aggressive tumor phenotype. The initial step in tumor progression involves the hyperproliferation of normal luminal and/or basal epithelial cells. Androgen responsive cells become hyperplastic and evolve into early-stage tumors. Although early-stage tumors are often androgen sensitive and respond to androgen ablation, a population of androgen independent cells evolve from the hyperplastic population.

These cells represent a more advanced form of prostate tumor that may become invasive and potentially become metastatic to the bone, brain, or lung. A variety of genes may be differentially expressed during tumor progression. For example, loss of heterozygosity (LOH) is frequently observed on chromosome 8p in prostate cancer. Fluorescence in situ hybridization (FISH) revealed a deletion for at least 1 locus on 8p in 29 (69%) tumors, with a significantly higher frequency of the deletion on 8p21. 2-p21. 1 in advanced prostate cancer than in localized prostate cancer, implying that deletions on 8p22-p21. 3 play an important role in tumor differentiation, while 8p21. 2-p21. 1 deletion plays a role in progression of prostate cancer (Oba, K. et al. (2001) Cancer Genet. Cytogenet. 124: 20-26).

Lung Cancer Lung cancer is the leading cause of cancer death for men and the second leading cause of cancer death for women in the U. S. Lung cancers are divided into four histopathologically distinct

groups. Three groups (squamous cell carcinoma, adenocarcinoma, and large cell carcinoma) are classified as non-small cell lung cancers (NSCLCs). The fourth group of cancers is referred to as small cell lung cancer (SCLC). Deletions on chromosome 3 are common in this disease and are thought to indicate the presence of a tumor suppressor gene in this region. Activating mutations in K- ras are commonly found in lung cancer and are the basis of one of the mouse models for the disease.

Peroxisome Proliferator-activated Receptor Gamma (PPAR) Agonist Thiazolidinediones (TZDs) act as agonists for the peroxisome-proliferator-activated receptor gamma (PPARy), a member of the nuclear hormone receptor superfamily. TZDs reduce hyperglycemia, hyperinsulinemia, and hypertension, in part by promoting glucose metabolism and inhibiting gluconeogenesis. Roles for PPARy and its agonists have been demonstrated in a wide range of pathological conditions including diabetes, obesity, hypertension, atherosclerosis, polycystic ovarian syndrome, and cancers such as breast, prostate, liposarcoma, and colon cancer.

The mechanism by which TZDs and other PPARy agonists enhance insulin sensitivity is not fully understood, but may involve the ability of PPARy to promote adipogenesis. When ectopically expressed in cultured preadipocytes, PPARy is a potent inducer of adipocyte differentiation. TZDs, in combination with insulin and other factors, can also enhance differentiation of human preadipocytes in culture (Adams et al. (1997) J. Clin. Invest. 100: 3149-3153). The relative potency of different TZDs in promoting adipogenesis in vitro is proportional to both their insulin sensitizing effects in vivo, and their ability to bind and activate PPARy in vitro. Interestingly, adipocytes derived from omental adipose depots are refractory to the effects of TZDs. It has therefore been suggested that the insulin sensitizing effects of TZDs may result from their ability to promote adipogenesis in subcutaneous adipose depots (Adams et al., supra). Further, dominant negative mutations in the PPARy gene have been identified in two non-obese subjects with severe insulin resistance, hypertension, and overt non- insulin dependent diabetes mellitus (NIDDM) (Barroso et al. (1998) Nature 402: 880-883).

NIDDM is the most common form of diabetes mellitus, a chronic metabolic disease that affects 143 million people worldwide. NIDDM is characterized by abnormal glucose and lipid metabolism that results from a combination of peripheral insulin resistance and defective insulin secretion. NIDDM has a complex, progressive etiology and a high degree of heritability. Numerous complications of diabetes including heart disease, stroke, renal failure, retinopathy, and peripheral neuropathy contribute to the high rate of morbidity and mortality.

At the molecular level, PPARy functions as a ligand activated transcription factor. In the presence of ligand, PPARy forms a heterodimer with the retinoid X receptor (RXR) which then activates transcription of target genes containing one or more copies of a PPARy response element

(PPRE). Many genes important in lipid storage and metabolism contain PPREs and have been identified as PPARy targets, including PEPCK, aP2, LPL, ACS, and FAT-P (Auwerx, J. (1999) Diabetologia 42: 1033-1049). Multiple ligands for PPARy have been identified. These include a variety of fatty acid metabolites; synthetic drugs belonging to the TZD class, such as Pioglitazone and Rosiglitazone (BRL49653) ; and certain non-glitazone tyrosine analogs such as GI262570 and GW1929. The prostaglandin derivative 15-dPGJ2 is a potent endogenous ligand for PPARy.

Expression of PPARy is very high in adipose but barely detectable in skeletal muscle, the primary site for insulin stimulated glucose disposal in the body. PPARy is also moderately expressed in large intestine, kidney, liver, vascular smooth muscle, hematopoietic cells, and macrophages. The high expression of PPARy in adipose tissue suggests that the insulin sensitizing effects of TZDs may result from alterations in the expression of one or more PPARy regulated genes in adipose tissue.

Identification of PPARy target genes will contribute to better drug design and the development of novel therapeutic strategies for diabetes, obesity, and other conditions.

Systematic attempts to identify PPARy target genes have been made in several rodent models of obesity and diabetes (Suzuki et al. (2000) Jpn. J. Pharmacol. 84: 113-123 ; Way et al. (2001) Endocrinology 142: 1269-1277). However, a serious drawback of the rodent gene expression studies is that significant differences exist between human and rodent models of adipogenesis, diabetes, and obesity (Taylor (1999) Cell 97: 9-12; Gregoire et al. (1998) Physiol. Reviews 78: 783-809). Therefore, an unbiased approach to identifying TZD regulated genes in primary cultures of human tissues is necessary to fully elucidate the molecular basis for diseases associated with PPARy activity.

Array technology can provide a simple way to explore the expression of a single polymorphic gene or the expression profile of a large number of related or unrelated genes. When the expression of a single gene is examined, arrays are employed to detect the expression of a specific gene or its variants. When an expression profile is examined, arrays provide a platform for examining which genes are tissue specific, carrying out housekeeping functions, parts of a signaling cascade, or specifically related to a particular genetic predisposition, condition, disease, or disorder. The potential application of gene expression profiling is particularly relevant to improving diagnosis, prognosis, and treatment of disease. For example, both the levels and sequences expressed in tissues from subjects with diabetes may be compared with the levels and sequences expressed in normal tissue.

Cells and Cell Lines Human peripheral blood mononuclear cells (PBMCs) represent the major cellular components of the immune system. PBMCs contain about 12% B lymphocytes, 25% CD4+ and 15% CD8+ lymphocytes, 20% NK cells, 25% monocytes, and 3% various cells that include dendritic cells and

progenitor cells. The proportions, as well as the biology of these cellular components tend to vary slightly between healthy individuals, depending on factors such as age, gender, past medical history, and genetic background.

The human C3A cell line is a clonal derivative of HepG2/C3 (hepatoma cell line, isolated from a 15-year-old male with liver tumor), which was selected for strong contact inhibition of growth. The use of a clonal population enhances the reproducibility of the cells. C3A cells have many characteristics of primary human hepatocytes in culture: i) expression of insulin receptor and insulin- like growth factor II receptor; ii) secretion of a high ratio of serum albumin compared with a- fetoprotein; iii) conversion of ammonia to urea and glutamine; iv) metabolism of aromatic amino acids; and v) proliferation in glucose-free and insulin-free medium. The C3A cell line is now well established as an in vitro model of the mature human liver (Mickelson et al. (1995) Hepatology 22: 866-875; Nagendra et al. (1997) Am. J. Physiol. 272: G408-G416).

Interleukin 3 (IL-3) is a pleiotropic factor produced primarily by activated T cells that can stimulate the proliferation and differentiation of pluripotent hematopoietic stem cells and various lineage committed progenitors. IL-3 also affects the functional activity of mature mast cells, basophils, eosinophils, and macrophages. Because of its multiple functions and targets, IL-3 was originally studied under different names, including mast cell growth factor, P-cell stimulating factor, burst promoting activity, multi-colony stimulating factor, thy-1 inducing factor, and WEHI-3 growth factor.

In addition to activated T cells, other cell types such as human thymic epithelial cells, activated murine mast cells, murine keratinocytes, and neurons/astrocytes can also produce IL-3. IL-3 exerts its biological activities by binding to specific cell surface receptors. The high affinity receptor responsible for IL-3 signaling is composed of at least two subunits, an IL-3 specific a-chain that binds IL-3 with low affinity and a common P-chain that is shared by the IL-5 and GM-CSF highaffinity receptors.

Although the-chain itself does not bind IL-3, it confers high-affinity IL-3 binding in the presence of the a-chain. Receptors for IL-3 are present on bone marrow progenitors, macrophages, mast cells, eosinophils, megakaryocytes, basophils, and various myeloid leukemic cells.

Interleukin 4 (IL-4) is a pleiotropic cytokine produced by activated T cells, mast cells, and basophils. It was initially identified as a B cell differentiation factor (BCDF) and a B cell stimulatory factor (BSF1). Subsequent to the molecular cloning and expression of both human and mouse IL-4, numerous other functions have been ascribed to B cells and other hematopoietic and non- hematopoietic cells including T lymphocytes, monocytes, macrophages, mast cells, myeloid and erythroid progenitors, fibroblasts, endothelial cells, etc. IL-4 exhibits anti-tumor effects both in vivo and in vitro. Recently, IL-4 was identified as an important regulator for the CD4+ subset (Thl-like

vs. Th2-like) development. The biological effects of IL-4 are mediated by the binding of IL-4 to specific cell surface receptors. The functional high-affinity receptor for IL-4 consists of a ligand- binding subunit (IL-4 R) and a second subunit ( (3 chain) that can modulate the ligand binding affinity of the receptor complex. In certain cell types, the gamma chain of the IL-2 receptor complex is a functional p chain of the IL-4 receptor complex. Signaling of IL-4 through its receptor leads to the activation of Signal Transducer and Activator of Transcription 6 (STAT6).

Interleukin 5 (IL-5) is a T cell-derived factor that promotes the proliferation, differentiation, and activation of eosinophils. IL-5 has also been known as T cell replacing factor (TRF), B cell growth factor II (BCGFII), B cell differentiation factor m (BCDF m), eosinophil differentiation factor (EDF), and eosinophil colony-stimulating factor (Eo-CSF). IL-5 exerts its activity on target cells by binding to specific cell surface receptors. The functional high-affinity receptor for human IL-5 is composed of a low-affinity IL-5 binding a-subunit and a non-binding common p-subunit that is shared with the high-affinity receptors for GM-CSF and IL-3.

Interleukin 7 (IL-7), previously known as pre-B-cell growth factor and lymphopoietin-l, was originally purified on the basis of its ability to promote the proliferation of precursor B-cells. It has been shown that IL-7 can also stimulate the proliferation of thymocytes, T cell progenitors, and mature CD4 + and CD8 + T cells. IL-7 can induce the formation of lymphokine-activated killer (LAK) cells as well as the development of cytotoxic T lymphocytes (CTL). Among myeloid lineage cells, IL-7 can upregulate the production of pro-inflammatory cytokines and stimulate the tumoricidal activity of monocytes/macrophages. IL-7 is expressed by adherent stromal cells from various tissues. IL-7 bioactivities are mediated by the binding of IL-7 to functional high-affinity receptor complexes. The ligand binding subunit (IL-7 R) of the IL-7 receptor complex has been cloned from human and mouse sources. Recently, they chain of the IL-2 receptor complex has been shown to be an essential component for IL-7 signal transduction. Both IL-7 R and IL-2 R y are members of the hematopoietin receptor superfamily. Cells known to express IL-7 receptors include pre-B cells, T cells, and bone marrow cells.

Interleukin 10 (IL-10), initially designated cytokine synthesis inhibitory factor (CSIF), was originally identified as a product of murine T helper 2 (Th2) clones that inhibited the cytokine production by Thl clones, which are dependent upon stimulation with antigen in the presence of antigen presenting cells (APC). The human homolog of murine IL-10 was subsequently cloned by cross-hybridization. Human IL-10 is produced by CD4 + T cell clones as well as by some CD8 + T cell clones. In addition, human B cells, EBV-transformed lymphoblastoid cell lines, and monocytes can also produce IL-10 upon activation. IL-10 is a pleiotrophic cytokine that can exert either

immunostimulatory or immunosupressive effects on a variety of cell types. It is a potent immunosuppressant of macrophage functions. In vitro, 1L-10 can inhibit the accessory function and antigen-presenting capacity of monocytes by, among other effects, downregulating class II MHC expression. Thus, IL-10 can inhibit monocyte/macrophage-dependent, antigen-specific proliferation of mouse Thl clones as well as human ThO-, Thl-, and Th2-like T cells. IL-10 can also inhibit the monocyte/macrophage-dependent, antigen stimulated cytokine synthesis (especially IFN-y) by human PBMC and NK cells. Additionally, IL-10 is a potent inhibitor of monocyte/macrophage activation and its resultant cytotoxic effects. It can suppress the production of numerous cytokines including TNF-a, IL-1, IL-6, and IL-10, as well as the synthesis of superoxide anion, reactive oxygen intermediates, and reactive nitrogen intermediates by activated monocytes/macrophages. As an immunostimulatory cytokine, IL-10 can act on B cells to enhance their viability, cell proliferation, Ig secretion, and class II MHC expression. Aside from B lymphocytes, IL-10 is also a growth co-stimulator for thymocytes and mast cells, as well as an enhancer of cytotoxic T cell development.

Granulocyte Colony Stimulating Factor (G-CSF) is a pleiotropic cytokine best known for its specific effects on the proliferation, differentiation, and activation of hematopoietic cells of the neutrophilic granulocyte lineage. Activated monocytes and macrophages are the primary sources of G-CSF in the body. Fibroblasts, endothelial cells, astrocytes, and bone marrow stromal cells can also produce this cytokine upon activation. In vitro, G-CSF stimulates growth, differentiation, and functions of cells from the neutrophil lineage. Consistent with its in vitro functions, G-CSF plays important roles in defending against infection, in inflammation and repair, and in maintaining steady state hematopoiesis.

Granulocyte-monocyte colony stimulating factor (GM-CSF) was first described as a factor that can support the in vitro colony formation of granulocyte-macrophage progenitors. In addition, GM-CSF is a growth factor for erythroid, megakaryocyte, and eosinophil progenitors. Lymphocytes (T and B), monocytes, macrophages, mast cells, endothelial cells, and fibroblasts can produce GM- CSF upon activation. GM-CSF exerts its biological effects by binding to specific cell surface receptors. The high affinity receptors required for human GM-CSF signal transduction are heterodimers consisting of a GM-CSF-specific a chain and a common p chain that is shared by the high-affinity receptors for IL-3 and IL-5.

Leptin is a protein product of the mouse obesity gene. Mice with mutations in the obesity gene that block the synthesis of leptin tend to be obese and diabetic and exhibit reduced activity, metabolism, and body temperature. Human leptin shares approximately 84% sequence identity with the mouse protein. Human leptin cDNA encodes a 167 amino acid residue protein with a 21 amino

acid residue signal sequence that is cleaved to yield the 146 amino acid residue mature protein. The expression of leptin mRNA is restricted to adipose tissue. A high-affinity receptor for leptin (OB-R) with homology to gpl30 and the G-CSF receptor has recently been cloned. OB-R mRNA is expressed in the choroid plexus and in the hypothalamus. OB-R is also an isoform of B219, a sequence that is expressed in at least four isoforms in very primitive hematopoietic cell populations and in a variety of lymphohematopoietic cell lines. The possible roles of leptin in body weight regulation, hematopoiesis, and reproduction are being investigated.

Leukemia inhibitory factor (LIF) was initially identified as a factor that inhibits the proliferation and induces the differentiation to macrophages of the murine myeloid leukemic cell line MI.

Subsequent to its purification and molecular cloning, LIF was recognized to be a pleiotropic factor with multiple effects on both hematopoietic and non-hematopoietic cells. LIF has overlapping biological functions with OSM, IL-6, IL-11, and CNTF. All these cytokines use gpl30 as a component in their signal transducing receptor complexes. Human LIF cDNA encodes a 202 amino acid residue polypeptide with a 22 amino acid residue signal peptide that is cleaved to yield a 180 amino acid residue mature human LIF.

Tumor Growth Factor beta (TGF-ß) is a stable, multifunctional polypeptide growth factor.

While specific receptors for this protein have been found on almost all mammalian cell types thus far examined, the effect of the molecule varies depending on the cell type and growth conditions.

Generally, TGF-P is stimulatory for cells of mesenchymal origin and inhibitory for cells of epithelial or neuroectodermal origin. TGF-ß has been found in the highest concentration in human platelets and mammalian bone, but is produced by many cell types in smaller amounts.

Tumor necrosis factor-alpha (TNF-a) is a pleiotropic cytokine that plays a central role in mediation of the inflammatory response through activation of multiple signal transduction pathways.

TNF-a is produced by activated lymphocytes, macrophages, and other white blood cells, and is known to activate endothelial cells. Monitoring the endothelial cell response to TNF-a at the level of mRNA expression can provide information necessary for better understanding of both TNF-a signaling and endothelial cell biology.

Interferon-gamma (IFN-r), also known as Type I1 interferon or immune interferon, is a cytokine produced primarily, by T-lymphocytes and natural killer cells. The protein shares no significant homology with IFN-or the various IFN-a family proteins. Mature IFN-y exists as noncovalently-linked homodimers. IFN-y was originally characterized based on its antiviral activities.

The protein also exerts antiproliferative, immunoregulatory, and proinflammatory activities and is important in host defense mechanisms. IFN-y induces the production of cytokines; upregulates the

expression of class I and II MHC antigens, Fc receptor, and leukocyte adhesion molecule; modulates macrophage effector functions; influences isotype switching; potentiates the secretion of immunoglobulins by B cells; augments TH1 cell expansion; and may be required for TH1 cell differentiation. IFN-y exerts its biological activities by binding to specific cell surface receptors, which display high affinity binding sites. The IFN-y receptor has been cloned and characterized and is present on almost all cell types except mature erythrocytes. Upon binding to its receptor, IFN-y triggers the activation of JAK-1 and JAK-2 kinases resulting in the phosphorylation of STATI.

Both IFN-y and TNF-a are considered proinflammatory cytokines. Cross-talk can exist between the signal transduction pathways of two cytokines ; for example, signal transduction cascades initiated by two different cytokines lead to the activation of NFkB. Experiments using both IFN-y and TNF-a can help evaluate the transcriptional effects of such cross-talk.

Phorbol myrstate acetate (PMA) is a broad activator of the protein kinase C-dependent pathways. Ionomycin is a calcium ionophore that permits the entry of calcium in the cell, hence increasing the cytosolic calcium concentration. The combination of PMA and ionomycin activates two of the major signaling pathways used by mammalian cells to interact with their environment. In PBMCs, the combination of PMA and ionomycin mimics the secondary signaling events elicited during activation of lymphocytes, NK cells, and monocytes.

Steroid Hormones Steroids are a class of lipid-soluble molecules, including cholesterol, bile acids, vitamin D, and hormones, that share a common four-ring structure based on cyclopentanoperhydrophenanthrene and that carrry out a wide variety of functions. Cholesterol, for example, is a component of cell membranes that controls membrane fluidity. It is also a precursor for bile acids which solubilize lipids and facilitate absorption in the small intestine during digestion. Vitamin D regulates the absorption of calcium in the small intestine and controls the concentration of calcium in plasma. Steroid hormones, produced by the adrenal cortex, ovaries, and testes, include glucocorticoids, mineralocorticoids, androgens, and estrogens. They control various biological processes by binding to intracellular receptors that regulate transcription of specific genes in the nucleus. Glucocorticoids, for example, increase blood glucose concentrations by regulation of gluconeogenesis in the liver, increase blood concentrations of fatty acids by promoting lipolysis in adipose tissues, modulate sensitivity to catcholamines in the central nervous system, and reduce inflammation. The principal mineralocorticoid, aldosterone, is produced by the adrenal cortex and acts on cells of the distal tubules of the kidney to enhance sodium ion reabsorption. Androgens, produced by the interstitial cells of Leydig in the testis, include the male sex hormone testosterone, which triggers changes at puberty, the

production of sperm and maintenance of secondary sexual characteristics. Female sex hormones, estrogen and progesterone, are produced by the ovaries and also by the placenta and adrenal cortex of the fetus during pregnancy. Estrogen regulates female reproductive processes and secondary sexual characteristics. Progesterone regulates changes in the endometrium during the menstrual cycle and pregnancy.

Steroid hormones are widely used for fertility control and in anti-inflammatory treatments for physical injuries and diseases such as arthritis, asthma, and autoimmune disorders. Progesterone, a naturally occurring progestin, is primarily used to treat amenorrhea, abnormal uterine bleeding, or as a contraceptive. Endogenous progesterone is responsible for inducing secretory activity in the endometrium of the estrogen-primed uterus in preparation for the implantation of a fertilized egg and for the maintenance of pregnancy. It is secreted from the corpus luteum in response to luteinizing hormone (LH). The primary contraceptive effect of exogenous progestins involves the suppression of the midcycle surge of LH. At the cellular level, progestins diffuse freely into target cells and bind to the progesterone receptor. Target cells include the female reproductive tract, the mammary gland, the hypothalamus, and the pituitary. Once bound to the receptor, progestins slow the frequency of release of gonadotropin releasing hormone from the hypothalamus and blunt the pre-ovulatory LH surge, thereby preventing follicular maturation and ovulation. Progesterone has minimal estrogenic and androgenic activity. Progesterone is metabolized hepatically to pregnanediol and conjugated with glucuronic acid.

Medroxyprogesterone (MAH), also known as 60c-methyl-17-hydroxyprogesterone, is a synthetic progestin with a pharmacological activity about 15 times greater than progesterone. MAH is used for the treatment of renal and endometrial carcinomas, amenorrhea, abnormal uterine bleeding, and endometriosis associated with hormonal imbalance. MAH has a stimulatory effect on respiratory centers and has been used in cases of low blood oxygenation caused by sleep apnea, chronic obstructive pulmonary disease, or hypercapnia.

Mifepristone, also known as RU-486, is an antiprogesterone drug that blocks receptors of progesterone. It counteracts the effects of progesterone, which is needed to sustain pregnancy.

Mifepristone induces spontaneous abortion when administered in early pregnancy followed by treatment with the prostaglandin misoprostol. Further studies show that mifepristone at a substantially lower dose can be highly effective as a postcoital contraceptive when administered within five days after unprotected intercourse, thus providing women with a"morning-after pill"in case of contraceptive failure or sexual assault. Mifepristone also has potential uses in the treatment of breast and ovarian cancers in cases in which tumors are progesterone-dependent. It interferes with steroid-

dependent growth of brain meningiomas, and may be useful in treatment of endometriosis where it blocks the estrogen-dependent growth of endometrial tissues. It may also be useful in treatment of uterine fibroid tumors and Cushing's Syndrome. Mifepristone binds to glucocorticoid receptors and interferes with cortisol binding. Mifepristone also may act as an anti-glucocorticoid and be effective for treating conditions where cortisol levels are elevated such as AIDS, anorexia nervosa, ulcers, diabetes, Parkinson's disease, multiple sclerosis, and Alzheimer's disease.

Danazol is a synthetic steroid derived from ethinyl testosterone. Danazol indirectly reduces estrogen production by lowering pituitary synthesis of follicle-stimulating hormone and LH. Danazol also binds to sex hormone receptors in target tissues, thereby exhibiting anabolic, antiestrognic, and weakly androgenic activity. Danazol does not possess any progestogenic activity, and does not suppress normal pituitary release of corticotropin or release of cortisol by the adrenal glands. Danazol is used in the treatment of endometriosis to relieve pain and inhibit endometrial cell growth. It is also used to treat fibrocystic breast disease and hereditary angioedema.

Corticosteroids are used to relieve inflammation and to suppress the immune response. They inhibit eosinophil, basophil, and airway epithelial cell function by regulation of cytokines that mediate the inflammatory response. They inhibit leukocyte infiltration at the site of inflammation, interfere in the function of mediators of the inflammatory response, and suppress the humoral immune response.

Corticosteroids are used to treat allergies, asthma, arthritis, and skin conditions. Beclomethasone is a synthetic glucocorticoid that is used to treat steroid-dependent asthma, to relieve symptoms associated with allergic or nonallergic (vasomotor) rhinitis, or to prevent recurrent nasal polyps following surgical removal. The anti-inflammatory and vasoconstrictive effects of intranasal beclomethasone are 5000 times greater than those produced by hydrocortisone. Budesonide is a corticosteroid used to control symptoms associated with allergic rhinitis or asthma. Budesonide has high topical anti-inflammatory activity but low systemic activity. Dexamethasone is a synthetic glucocorticoid used in anti- inflammatory or immunosuppressive compositions. It is also used in inhalants to prevent symptoms of asthma. Due to its greater ability to reach the central nervous system, dexamethasone is usually the treatment of choice to control cerebral edema. Dexamethasone is approximately 20-30 times more potent than hydrocortisone and 5-7 times more potent than prednisone. Prednisone is metabolized in the liver to its active form, prednisolone, a glucocorticoid with anti-inflammatory properties.

Prednisone is approximately 4 times more potent than hydrocortisone and the duration of action of prednisone is intermediate between hydrocortisone and dexamethasone. Prednisone is used to treat allograft rejection, asthma, systemic lupus erythematosus, arthritis, ulcerative colitis, and other inflammatory conditions. Betamethasone is a synthetic glucocorticoid with antiinflammatory and

immunosuppressive activity and is used to treat psoriasis and fungal infections, such as athlete's foot and ringworm.

The anti-inflammatory actions of corticosteroids are thought to involve phospholipase A2 inhibitory proteins, collectively called lipocortins. Lipocortins, in turn, control the biosynthesis of potent mediators of inflammation such as prostaglandins and leukotrienes by inhibiting the release of the precursor molecule arachidonic acid. Proposed mechanisms of action include decreased IgE synthesis, increased number of p-adrenergic receptors on leukocytes, and decreased arachidonic acid metabolism. During an immediate allergic reaction, such as in chronic bronchial asthma, allergens bridge the IgE antibodies on the surface of mast cells, which triggers these cells to release chemotactic substances. Mast cell influx and activation, therefore, is partially responsible for the inflammation and hyperirritability of the oral mucosa in asthmatic patients. This inflammation can be retarded by administration of corticosteroids.

Umbilical Vein Endothelium Human umbilical vein endothelial cells (HUVECs) are a primary cell line derived from the endothelium of the human umbilical vein. HUVECs have been used extensively to study the functional biology of human endothelial cells iii vitro. Activation of vascular endothelium is considered a central event in a wide range of both physiological and pathophysiological processes, such as vascular tone regulation, coagulation and thrombosis, atherosclerosis, and inflammation.

T Cell Activation T cells can be subdivided into two classes according to their main function and the surface- antigens they express. First, CD4 positive (+) T cells, also known as T Helper cells, primarily regulate the immune response by producing soluble factors that, in turn, regulate the activity of effector cells such as B lymphocytes, NK cells, and macrophages. Second, CD8 positive (+) T cells, also known as cytotoxic T cells, primarily kill"abnormal"cells such as tumor cells or cells infected by viruses.

In the blood of a healthy adult, CD4+ T cells and CD8+ T cells represent 25% and 15% of the mononuclear cells, respectively. These two T cell populations can be readily expanded out of blood by incubating bulk peripheral blood mononuclear cells (PBMCs) in the presence of phytohemagglutinin (PHA) and interleukin 2 (IL-2). After 8 to 10 days of treatment, both CD4+ and CD8+ T cells expand roughly 5 to 10 fold, yielding a cell population composed of >90% T cells, also known as PHA blasts. T cell expansion occurs during the first 5 days of PHA stimulation; after 8 to 10 days in culture, most PHA blasts have returned to a resting state.

T cells require two distinct signals to achieve optimal activation. First, the"antigenic"signal delivered through the binding of the TCR-CD3 complex. Second, the costimulatory signal delivered

through the binding of the CD28 molecules. Upon binding of the TCR-CD3 complex alone, T cells only achieve a partial state of activation. However, it is important to note that the signaling requirements of T cells depend greatly on the cycling state of those cells.

Jurkat is an acute T cell leukemia cell line that grows actively in the absence of external stimuli. Jurkat has been extensively used to study signaling in human T cells. PMA (phorbol myristate acetate) is a broad activator of the protein kinase C-dependent pathways. Ionomycin is a calcium ionophore that permits the entry of calcium into the cell, hence increasing the cytosolic calcium concentration. The combination of PMA and ionomycin activates two of the major signaling pathways used by mammalian cells to interact with their environment. In T cells, the combination of PMA and ionomycin mimics the type of secondary signaling events elicited during optimal B cell activation.

Staphylococcal exotoxins specifically activate human T cells, expressing an appropriate TCR- Vbetachain. Although polyclonal in nature, T cells activated by Staphylococcal exotoxins require antigen presenting cells (APCs) to present the exotoxin molecules to the T cells and deliver the costimulatory signals required for optimum T cell activation. Although staphylococcal exotoxins must be presented to T cells by APCs, these molecules are not required to be processed by APC. Indeed, Staphylococcal exotoxins directly bind to a non-polymorphic portion of the human MHC class II molecules, bypassing the need for capture, cleavage, and binding of the peptides to the polymorphic antigenic groove of the MHC class II molecules.

There is a need in the art for new compositions, including nucleic acids and proteins, for the diagnosis, prevention, and treatment of gastrointestinal, cardiovascular, autoimmunelinflarnmatory, cell proliferative, developmental, epithelial, neurological, and reproductive disorders.

SUMMARY OF THE INVENTION Various embodiments of the invention provide purified polypeptides, protein modification and maintenance molecules, referred to collectively as'PMMM'and individually as'PMMM-1,'

58,''PMMM-59,''PMMM-60,''PMMM-61,'and PMMM-62'and methods for using these proteins and their encoding polynucleotides for the detection, diagnosis, and treatment of diseases and medical conditions. Embodiments also provide methods for utilizing the purified protein modification and maintenance molecules and/or their encoding polynucleotides for facilitating the drug discovery process, including determination of efficacy, dosage, toxicity, and pharmacology. Related embodiments provide methods for utilizing the purified protein modification and maintenance molecules and/or their encoding polynucleotides for investigating the pathogenesis of diseases and medical conditions.

An embodiment provides an isolated polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1- 62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62. Another embodiment provides an isolated polypeptide comprising an amino acid sequence of SEQ ID NO : 1-62.

Still another embodiment provides an isolated polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62. In another embodiment, the polynucleotide encodes a polypeptide selected from the group consisting of SEQ ID NO : 1-62. In an alternative embodiment, the polynucleotide is selected from the group consisting of SEQ ID NO : 63-124.

Still another embodiment provides a recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide encoding a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO: 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of

a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62.

Another embodiment provides a cell transformed with the recombinant polynucleotide. Yet another embodiment provides a transgenic organism comprising the recombinant polynucleotide.

Another embodiment provides a method for producing a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62.

The method comprises a) culturing a cell under conditions suitable for expression of the polypeptide, wherein said cell is transformed with a recombinant polynucleotide comprising a promoter sequence operably linked to a polynucleotide encoding the polypeptide, and b) recovering the polypeptide so expressed.

Yet another embodiment provides an isolated antibody which specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62.

Still yet another embodiment provides an isolated polynucleotide selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA <BR> <BR> equivalent of a) -d). In other embodiments, the polynucleotide can comprise at least about 20,30, 40, 60,80, or 100 contiguous nucleotides.

Yet another embodiment provides a method for detecting a target polynucleotide in a sample, said target polynucleotide being selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, b) a polynucleotide

comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a) -d). The method comprises a) hybridizing the sample with a probe comprising at least 20 contiguous nucleotides comprising a sequence complementary to said target polynucleotide in the sample, and which probe specifically hybridizes to said target polynucleotide, under conditions whereby a hybridization complex is formed between said probe and said target polynucleotide or fragments thereof, and b) detecting the presence or absence of said hybridization complex. In a related embodiment, the method can include detecting the amount of the hybridization complex. In still other embodiments, the probe can comprise at least about 20,30, 40,60, 80, or 100 contiguous nucleotides.

Still yet another embodiment provides a method for detecting a target polynucleotide in a sample, said target polynucleotide being selected from the group consisting of a) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, b) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, c) a polynucleotide complementary to the polynucleotide of a), d) a polynucleotide complementary to the polynucleotide of b), and e) an RNA equivalent of a) -d). The method comprises a) amplifying said target polynucleotide or fragment thereof using polymerase chain reaction amplification, and b) detecting the presence or absence of said amplified target polynucleotide or fragment thereof. In a related embodiment, the method can include detecting the amount of the amplified target polynucleotide or fragment thereof.

Another embodiment provides a composition comprising an effective amount of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and a pharmaceutically acceptable excipient. In one embodiment, the composition can comprise an amino acid sequence selected from the group consisting of SEQ ID NO: 1-62. Other embodiments provide a method of treating a disease or condition

associated with decreased or abnormal expression of functional PMMM, comprising administering to a patient in need of such treatment the composition.

Yet another embodiment provides a method for screening a compound for effectiveness as an agonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ 7D NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62. The method comprises a) contacting a sample comprising the polypeptide with a compound, and b) detecting agonist activity in the sample.

Another embodiment provides a composition comprising an agonist compound identified by the method and a pharmaceutically acceptable excipient. Yet another embodiment provides a method of treating a disease or condition associated with decreased expression of functional PMMM, comprising administering to a patient in need of such treatment the composition.

Still yet another embodiment provides a method for screening a compound for effectiveness as an antagonist of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 1-62. The method comprises a) contacting a sample comprising the polypeptide with a compound, and b) detecting antagonist activity in the sample. Another embodiment provides a composition comprising an antagonist compound identified by the method and a pharmaceutically acceptable excipient. Yet another embodiment provides a method of treating a disease or condition associated with overexpression of functional PMMM, comprising administering to a patient in need of such treatment the composition.

Another embodiment provides a method of screening for a compound that specifically binds to a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active

fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62. The method comprises a) combining the polypeptide with at least one test compound under suitable conditions, and b) detecting binding of the polypeptide to the test compound, thereby identifying a compound that specifically binds to the polypeptide.

Yet another embodiment provides a method of screening for a compound that modulates the activity of a polypeptide selected from the group consisting of a) a polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 1-62, b) a polypeptide comprising a naturally occurring amino acid sequence at least 90% identical or at least about 90% identical to an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, c) a biologically active fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO : 1-62, and d) an immunogenic fragment of a polypeptide having an amino acid sequence selected from the group consisting of SEQ ID NO: 1-62. The method comprises a) combining the polypeptide with at least one test compound under conditions permissive for the activity of the polypeptide, b) assessing the activity of the polypeptide in the presence of the test compound, and c) comparing the activity of the polypeptide in the presence of the test compound with the activity of the polypeptide in the absence of the test compound, wherein a change in the activity of the polypeptide in the presence of the test compound is indicative of a compound that modulates the activity of the polypeptide.

Still yet another embodiment provides a method for screening a compound for effectiveness in altering expression of a target polynucleotide, wherein said target polynucleotide comprises a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, the method comprising a) contacting a sample comprising the target polynucleotide with a compound, b) detecting altered expression of the target polynucleotide, and c) comparing the expression of the target polynucleotide in the presence of varying amounts of the compound and in the absence of the compound.

Another embodiment provides a method for assessing toxicity of a test compound, said method comprising a) treating a biological sample containing nucleic acids with the test compound; b) hybridizing the nucleic acids of the treated biological sample with a probe comprising at least 20 contiguous nucleotides of a polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at

least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO : G3-124, iii) a polynucleotide having a sequence complementary to i), iv) a polynucleotide complementary to the polynucleotide of ii), and v) an RNA equivalent of i) -iv). Hybridization occurs under conditions whereby a specific hybridization complex is formed between said probe and a target polynucleotide in the biological sample, said target polynucleotide selected from the group consisting of i) a polynucleotide comprising a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, ii) a polynucleotide comprising a naturally occurring polynucleotide sequence at least 90% identical or at least about 90% identical to a polynucleotide sequence selected from the group consisting of SEQ ID NO : 63-124, iii) a polynucleotide complementary to the polynucleotide of i), iv) a polynucleotide complementary to the polynucleotide of ii), and v) an RNA equivalent of i)-iv).

Alternatively, the target polynucleotide can comprise a fragment of a polynucleotide selected from the group consisting of i) -v) above; c) quantifying the amount of hybridization complex; and d) comparing the amount of hybridization complex in the treated biological sample with the amount of hybridization complex in an untreated biological sample, wherein a difference in the amount of hybridization complex in the treated biological sample is indicative of toxicity of the test compound.

BRIEF DESCRIPTION OF THE TABLES Table 1 summarizes the nomenclature for full length polynucleotide and polypeptide embodiments of the invention.

Table 2 shows the GenBank identification number and annotation of the nearest GenBank homolog, and the PROTEOME database identification numbers and annotations of PROTEOME database homologs, for polypeptide embodiments of the invention. The probability scores for the matches between each polypeptide and its homolog (s) are also shown.

Table 3 shows structural features of polypeptide embodiments, including predicted motifs and domains, along with the methods, algorithms, and searchable databases used for analysis of the polypeptides.

Table 4 lists the cDNA and/or genomic DNA fragments which were used to assemble polynucleotide embodiments, along with selected fragments of the polynucleotides.

Table 5 shows representative cDNA libraries for polynucleotide embodiments.

Table 6 provides an appendix which describes the tissues and vectors used for construction of the cDNA libraries shown in Table 5.

Table 7 shows the tools, programs, and algorithms used to analyze polynucleotides and polypeptides, along with applicable descriptions, references, and threshold parameters.

Table 8 shows single nucleotide polymorphisms found in polynucleotide sequences of the invention, along with allele frequencies in different human populations.

DESCRIPTION OF THE INVENTION Before the present proteins, nucleic acids, and methods are described, it is understood that embodiments of the invention are not limited to the particular machines, instruments, materials, and methods described, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the invention.

As used herein and in the appended claims, the singular forms"a,""an,"and"the"include plural reference unless the context clearly dictates otherwise. Thus, for example, a reference to"a host cell"includes a plurality of such host cells, and a reference to"an antibody"is a reference to one or more antibodies and equivalents thereof known to those skilled in the art, and so forth.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs.

Although any machines, materials, and methods similar or equivalent to those described herein can be used to practice or test the present invention, the preferred machines, materials and methods are now described. All publications mentioned herein are cited for the purpose of describing and disclosing the cell lines, protocols, reagents and vectors which are reported in the publications and which might be used in connection with various embodiments of the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

DEFINITIONS "PMMM"refers to the amino acid sequences of substantially purified PMMM obtained from any species, particularly a mammalian species, including bovine, ovine, porcine, murine, equine, and human, and from any source, whether natural, synthetic, semi-synthetic, or recombinant.

The term"agonist"refers to a molecule which intensifies or mimics the biological activity of PMMM. Agonists may include proteins, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of PMMM either by directly interacting with PMMM or by acting on components of the biological pathway in which PMMM participates.

An"allelic variant"is an alternative form of the gene encoding PMMM. Allelic variants may result from at least one mutation in the nucleic acid sequence and may result in altered mRNAs or in polypeptides whose structure or function may or may not be altered. A gene may have none, one, or many allelic variants of its naturally occurring form. Common mutational changes which give rise to

allelic variants are generally ascribed to natural deletions, additions, or substitutions of nucleotides.

Each of these types of changes may occur alone, or in combination with the others, one or more times in a given sequence.

"Altered"nucleic acid sequences encoding PMMM include those sequences with deletions, insertions, or substitutions of different nucleotides, resulting in a polypeptide the same as PMMM or a polypeptide with at least one functional characteristic of PMMM. Included within this definition are polymorphisms which may or may not be readily detectable using a particular oligonucleotide probe of the polynucleotide encoding PMMM, and improper or unexpected hybridization to allelic variants, with a locus other than the normal chromosomal locus for the polynucleotide encoding PMMM. The <BR> <BR> encoded protein may also be"altered, "and may contain deletions, insertions, or substitutions of amino acid residues which produce a silent change and result in a functionally equivalent PMMM.

Deliberate amino acid substitutions may be made on the basis of one or more similarities in polarity, charge, solubility, hydrophobicity, hydrophilicity, and/or the amphipathic nature of the residues, as long as the biological or immunological activity of PMMM is retained. For example, negatively charged amino acids may include aspartic acid and glutamic acid, and positively charged amino acids may include lysine and arginine. Amino acids with uncharged polar side chains having similar hydrophilicity values may include : asparagine and glutamine ; and serine and threonine. Amino acids with uncharged side chains having similar hydrophilicity values may include : leucine, isoleucine, and valine ; glycine and alanine; and phenylalanine and tyrosine.

The terms"amino acid"and"amino acid sequence"can refer to an oligopeptide, a peptide, a polypeptide, or a protein sequence, or a fragment of any of these, and to naturally occurring or synthetic molecules. Where"amino acid sequence"is recited to refer to a sequence of a naturally <BR> <BR> occurring protein molecule, "amino acid sequence"and like terms are not meant to limit the amino acid sequence to the complete native amino acid sequence associated with the recited protein molecule.

"Amplification"relates to the production of additional copies of a nucleic acid. Amplification may be carried out using polymerase chain reaction (PCR) technologies or other nucleic acid amplification technologies well known in the art.

The term"antagonist"refers to a molecule which inhibits or attenuates the biological activity of PMMM. Antagonists may include proteins such as antibodies, anticalins, nucleic acids, carbohydrates, small molecules, or any other compound or composition which modulates the activity of PMMM either by directly interacting with PMMM or by acting on components of the biological pathway in which PMMM participates.

The term"antibody"refers to intact immunoglobulin molecules as well as to fragments thereof, such as Fab, F (ab') 2, and Fv fragments, which are capable of binding an epitopic determinant.

Antibodies that bind PMMM polypeptides can be prepared using intact polypeptides or using fragments containing small peptides of interest as the immunizing antigen. The polypeptide or oligopeptide used to immunize an animal (e. g. , a mouse, a rat, or a rabbit) can be derived from the translation of RNA, or synthesized chemically, and can be conjugated to a carrier protein if desired.

Commonly used carriers that are chemically coupled to peptides include bovine serum albumin, thyroglobulin, and keyhole limpet hemocyanin (KLH). The coupled peptide is then used to immunize the animal.

The term"antigenic determinant"refers to that region of a molecule (i. e. , an epitope) that makes contact with a particular antibody. When a protein or a fragment of a protein is used to immunize a host animal, numerous regions of the protein may induce the production of antibodies which bind specifically to antigenic determinants (particular regions or three-dimensional structures on <BR> <BR> the protein). An antigenic determinant may compete with the intact antigen (i. e. , the immunogen used to elicit the immune response) for binding to an antibody.

The term"aptamer"refers to a nucleic acid or oligonucleotide molecule that binds to a <BR> <BR> specific molecular target. Aptamers are derived from an in vitro evolutionary process (e. g. , SELEX (Systematic Evolution of Ligands by EXponential Enrichment), described in U. S. Patent No.

5,270, 163), which selects for target-specific aptamer sequences from large combinatorial libraries.

Aptamer compositions may be double-stranded or single-stranded, and may include deoxyribonucleotides, ribonucleotides, nucleotide derivatives, or other nucleotide-like molecules. The nucleotide components of an aptamer may have modified sugar groups (e. g. , the 2'-OH group of a ribonucleotide may be replaced by 2'-F or 2'-NH2), which may improve a desired property, e. g., resistance to nucleases or longer lifetime in blood. Aptamers may be conjugated to other molecules, <BR> <BR> e. g. , a high molecular weight carrier to slow clearance of the aptamer from the circulatory system.<BR> <P>Aptamers may be specifically cross-linked to their cognate ligands, e. g. , by photo-activation of a cross-linker (Brody, E. N. and L. Gold (2000) J. Biotechnol. 74: 5-13).

The term"intramer"refers to an aptamer which is expressed in vivo. For example, a vaccinia virus-based RNA expression system has been used to express specific RNA aptamers at high levels in the cytoplasm of leukocytes (Blind, M. et al. (1999) Proc. Natl. Acad. Sci. USA 96: 3606-3610).

The term"spiegelmer"refers to an aptamer which includes L-DNA, L-RNA, or other left- handed nucleotide derivatives or nucleotide-like molecules. Aptamers containing left-handed

nucleotides are resistant to degradation by naturally occurring enzymes, which normally act on substrates containing right-handed nucleotides.

The term"antisense"refers to any composition capable of base-pairing with the"sense" (coding) strand of a polynucleotide having a specific nucleic acid sequence. Antisense compositions may include DNA; RNA; peptide nucleic acid (PNA); oligonucleotides having modified backbone linkages such as phosphorothioates, methylphosphonates, or benzylphosphonates; oligonucleotides having modified sugar groups such as 2'-methoxyethyl sugars or 2'-methoxyethoxy sugars; or oligonucleotides having modified bases such as 5-methyl cytosine, 2'-deoxyuracil, or 7-deaza-2'- deoxyguanosine. Antisense molecules may be produced by any method including chemical synthesis or transcription. Once introduced into a cell, the complementary antisense molecule base-pairs with a naturally occurring nucleic acid sequence produced by the cell to form duplexes which block either transcription or translation. The designation"negative"or"minus"can refer to the antisense strand, and the designation"positive"or"plus"can refer to the sense strand of a reference DNA molecule.

The term"biologically active"refers to a protein having structural, regulatory, or biochemical functions of a naturally occurring molecule. Likewise,"immunologically active"or"inununot, enic',' refers to the capability of the natural, recombinant, or synthetic PMMM, or of any oligopeptide thereof, to induce a specific immune response in appropriate animals or cells and to bind with specific antibodies.

"Complementary"describes the relationship between two single-stranded nucleic acid sequences that anneal by base-pairing. For example, 5'-AGT-3'pairs with its complement, 3'-TCA-5'.

A"composition comprising a given polynucleotide"and a"composition comprising a given polypeptide"can refer to any composition containing the given polynucleotide or polypeptide. The composition may comprise a dry formulation or an aqueous solution. Compositions comprising polynucleotides encoding PMMM or fragments of PMMM may be employed as hybridization probes.

The probes may be stored in freeze-dried form and may be associated with a stabilizing agent such as a carbohydrate. In hybridizations, the probe may be deployed in an aqueous solution containing salts <BR> (e. g., NaCI), detergents (e. g. , sodium dodecyl sulfate; SDS), and other components (e. g. , Denhardt's solution, dry milk, salmon sperm DNA, etc.).

"Consensus sequence"refers to a nucleic acid sequence which has been subjected to repeated DNA sequence analysis to resolve uncalled bases, extended using the XL-PCR kit (Applied Biosystems, Foster City CA) in the 5'and/or the 3'direction, and resequenced, or which has been assembled from one or more overlapping cDNA, EST, or genomic DNA fragments using a computer

program for fragment assembly, such as the GELVIEW fragment assembly system (Accelrys, Burlington MA) or Phrap (University of Washington, Seattle WA). Some sequences have been both extended and assembled to produce the consensus sequence.

"Conservative amino acid substitutions"are those substitutions that are predicted to least interfere with the properties of the original protein, i. e. , the structure and especially the function of the protein is conserved and not significantly changed by such substitutions. The table below shows amino acids which may be substituted for an original amino acid in a protein and which are regarded as conservative amino acid substitutions.

Conservative amino acid substitutions generally maintain (a) the structure of the polypeptide backbone in the area of the substitution, for example, as a beta sheet or alpha helical conformation, (b) the charge or hydrophobicity of the molecule at the site of the substitution, and/or (c) the bulk of the side chain.

A"deletion"refers to a change in the amino acid or nucleotide sequence that results in the absence of one or more amino acid residues or nucleotides.

The term"derivative"refers to a chemically modified polynucleotide or polypeptide.

Chemical modifications of a polynucleotide can include, for example, replacement of hydrogen by an alkyl, acyl, hydroxyl, or amino group. A derivative polynucleotide encodes a polypeptide which retains at least one biological or immunological function of the natural molecule. A derivative polypeptide is

one modified by glycosylation, pegylation, or any similar process that retains at least one biological or immunological function of the polypeptide from which it was derived.

A"detectable label"refers to a reporter molecule or enzyme that is capable of generating a measurable signal and is covalently or noncovalently joined to a polynucleotide or polypeptide.

"Differential expression"refers to increased or upregulated; or decreased, downregulated, or absent gene or protein expression, determined by comparing at least two different samples. Such comparisons may be carried out between, for example, a treated and an untreated sample, or a diseased and a normal sample.

"Exon shuffling"refers to the recombination of different coding regions (exons). Since an exon may represent a structural or functional domain of the encoded protein, new proteins may be assembled through the novel reassortment of stable substructures, thus allowing acceleration of the evolution of new protein functions.

A"fragment"is a unique portion of PMMM or a polynucleotide encoding PMMM which can be identical in sequence to, but shorter in length than, the parent sequence. A fragment may comprise up to the entire length of the defined sequence, minus one nucleotide/amino acid residue. For example, a fragment may comprise from about 5 to about 1000 contiguous nucleotides or amino acid residues. A fragment used as a probe, primer, antigen, therapeutic molecule, or for other purposes, may be at least 5, 10, 15,16, 20, 25, 3A, 40, 50, 60,75, 100,150, 250 or at least 500 contiguous nucleotides or amino acid residues in length. Fragments may be preferentially selected from certain regions of a molecule. For example, a polypeptide fragment may comprise a certain length of contiguous amino acids selected from the first 250 or 500 amino acids (or first 25% or 50%) of a polypeptide as shown in a certain defined sequence. Clearly these lengths are exemplary, and any length that is supported by the specification, including the Sequence Listing, tables, and figures, may be encompassed by the present embodiments.

A fragment of SEQ ID NO : 63-124 can comprise a region of unique polynucleotide sequence that specifically identifies SEQ ID NO : 63-124, for example, as distinct from any other sequence in the genome from which the fragment was obtained. A fragment of SEQ ID NO : 63-124 can be employed in one or more embodiments of methods of the invention, for example, in hybridization and amplification technologies and in analogous methods that distinguish SEQ ID NO : 63-124 from related polynucleotides. The precise length of a fragment of SEQ ID NO : 63-124 and the region of SEQ ID NO : 63-124 to which the fragment corresponds are routinely determinable by one of ordinary skill in the art based on the intended purpose for the fragment.

A fragment of SEQ ID NO : 1-62 is encoded by a fragment of SEQ ID NO : 63-124. A fragment of SEQ ID NO : 1-62 can comprise a region of unique amino acid sequence that specifically identifies SEQ ID NO: 1-62. For example, a fragment of SEQ ID NO: 1-62 can be used as an immunogenic peptide for the development of antibodies that specifically recognize SEQ ID NO : 1-62.

The precise length of a fragment of SEQ ID NO : 1-62 and the region of SEQ ID NO : 1-62 to which the fragment corresponds can be determined based on the intended purpose for the fragment using one or more analytical methods described herein or otherwise known in the art.

A"full length"polynucleotide is one containing at least a translation initiation codon (e. g., methionine) followed by an open reading frame and a translation termination codon. A"full length" polynucleotide sequence encodes a"full length"polypeptide sequence.

"Homology"refers to sequence similarity or, alternatively, sequence identity, between two or more polynucleotide sequences or two or more polypeptide sequences.

The terms"percent identity"and"% identity, "as applied to polynucleotide sequences, refer to the percentage of identical nucleotide matches between at least two polynucleotide sequences aligned using a standardized algorithm. Such an algorithm may insert, in a standardized and reproducible way, gaps in the sequences being compared in order to optimize alignment between two sequences, and therefore achieve a more meaningful comparison of the two sequences.

Percent identity between polynucleotide sequences may be determined using one or more computer algorithms or programs known in the art or described herein. For example, percent identity can be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3.12e sequence alignment program. This program is part of the LASERGENE software package, a suite of molecular biological analysis programs (DNASTAR, Madison WI). CLUSTAL V is described in Higgins, D. G. and P. M. Sharp (1989 ; CABIOS 5: 151- 153) and in Higgins, D. G. et al. (1992; CABIOS 8: 189-191). For pairwise alignments of polynucleotide sequences, the default parameters are set as follows: Ktuple=2, gap penalty=5, window=4, and"diagonals saved"=4. The"weighted"residue weight table is selected as the default.

Alternatively, a suite of commonly used and freely available sequence comparison algorithms which can be used is provided by the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST) (Altschul, S. F. et al. (1990) J. Mol. Biol. 215: 403-410}, which is available from several sources, including the NCBI, Bethesda, MD, and on the Internet at http://www. ncbi. nlm. nih. gov/BLAST/. The BLAST software suite includes various sequence analysis programs including"blastn, "that is used to align a known polynucleotide sequence with other polynucleotide sequences from a variety of databases. Also available is a tool called"BLAST 2

Sequences"that is used for direct pairwise comparison of two nucleotide sequences. "BLAST 2 Sequences"can be accessed and used interactively at http ://www. ncbi. nlm. nih. gov/gorf/bl2. html. The "BLAST 2 Sequences"tool can be used for both blastn and blastp (discussed below). BLAST programs are commonly used with gap and other parameters set to default settings. For example, to compare two nucleotide sequences, one may use blastn with the"BLAST 2 Sequences"tool Version 2.0. 12 (April-21-2000) set at default parameters. Such default parameters may be, for example: Matrix : BLOSUM62 Rewardfor rnatclz : 1<BR> Pertaltyfor mismatch :-2 Open Gap : 5 and Extension Gap : 2 penalties Gap x drop-off.-50 Expect : 10 Word Size : 11 Filter : on Percent identity may be measured over the length of an entire defined sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined sequence, for instance, a fragment of at least 20, at least 30, at least 40, at least 50, at least 70, at least 100, or at least 200 contiguous nucleotides. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures, or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

Nucleic acid sequences that do not show a high degree of identity may nevertheless encode similar amino acid sequences due to the degeneracy of the genetic code. It is understood that changes in a nucleic acid sequence can be made using this degeneracy to produce multiple nucleic acid sequences that all encode substantially the same protein.

The phrases"percent identity"and"% identity, "as applied to polypeptide sequences, refer to the percentage of identical residue matches between at least two polypeptide sequences aligned using a standardized algorithm. Methods of polypeptide sequence alignment are well-known. Some alignment methods take into account conservative amino acid substitutions. Such conservative substitutions, explained in more detail above, generally preserve the charge and hydrophobicity at the site of substitution, thus preserving the structure (and therefore function) of the polypeptide. The phrases"percent similarity"and"% similarity, "as applied to polypeptide sequences, refer to the percentage of residue matches, including identical residue matches and conservative substitutions,

between at least two polypeptide sequences aligned using a standardized algorithm. In contrast, conservative substitutions are not included in the calculation of percent identity between polypeptide sequences.

Percent identity between polypeptide sequences may be determined using the default parameters of the CLUSTAL V algorithm as incorporated into the MEGALIGN version 3. 12e sequence alignment program (described and referenced above). For pairwise alignments of polypeptide sequences using CLUSTAL V, the default parameters are set as follows: Ktuple=l, gap penalty=3, window=5, and"diagonals saved"=5. The PAM250 matrix is selected as the default residue weight table.

Alternatively the NCBI BLAST software suite may be used. For example, for a pairwise comparison of two polypeptide sequences, one may use the"BLAST 2 Sequences"tool Version 2. 0. 12 (April-21-2000) with blastp set at default parameters. Such default parameters may be, for example: Matrix : BLOSUM62 Open Gap : I I and Extension Gap : I penalties Gap x drop-off.-50 Expect : 10 Word Size: 3 Filter : on Percent identity may be measured over the length of an entire defined polypeptide sequence, for example, as defined by a particular SEQ ID number, or may be measured over a shorter length, for example, over the length of a fragment taken from a larger, defined polypeptide sequence, for instance, a fragment of at least 15, at least 20, at least 30, at least 40, at least 50, at least 70 or at least 150 contiguous residues. Such lengths are exemplary only, and it is understood that any fragment length supported by the sequences shown herein, in the tables, figures or Sequence Listing, may be used to describe a length over which percentage identity may be measured.

"Human artificial chromosomes" (HACs) are linear microchromosomes which may contain DNA sequences of about 6 kb to 10 Mb in size and which contain all of the elements required for chromosome replication, segregation and maintenance.

The term"humanized antibody"refers to an antibody molecule in which the amino acid sequence in the non-antigen binding regions has been altered so that the antibody more closely resembles a human antibody, and still retains its original binding ability.

"Hybridization"refers to the process by which a polynucleotide strand anneals with a complementary strand through base pairing under defined hybridization conditions. Specific hybridization is an indication that two nucleic acid sequences share a high degree of complementarity.

Specific hybridization complexes form under permissive annealing conditions and remain hybridized after the"washing"step (s). The washing step (s) is particularly important in determining the stringency of the hybridization process, with more stringent conditions allowing less non-specific <BR> <BR> binding, i. e. , binding between pairs of nucleic acid strands that are not perfectly matched. Permissive conditions for annealing of nucleic acid sequences are routinely determinable by one of ordinary skill in the art and may be consistent among hybridization experiments, whereas wash conditions may be varied among experiments to achieve the desired stringency, and therefore hybridization specificity.

Permissive annealing conditions occur, for example, at 68°C in the presence of about 6 x SSC, about 1% (w/v) SDS, and about 100 yglml sheared, denatured salmon sperm DNA.

Generally, stringency of hybridization is expressed, in part, with reference to the temperature under which the wash step is carried out. Such wash temperatures are typically selected to be about 5°C to 20°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. The Tm is the temperature (under defined ionic strength and pH) at which 50% of the target sequence hybridizes to a perfectly matched probe. An equation for calculating Tm and conditions for nucleic acid hybridization are well known and can be found in Sambrook, J. and D. W.

Russell (2001; Molecular Cloning : A Laboratory Manual, 3rd ed. , vol. 1-3, Cold Spring Harbor Press, Cold Spring Harbor NY, ch. 9).

High stringency conditions for hybridization between polynucleotides of the present invention include wash conditions of 68°C in the presence of about 0.2 x SSC and about 0. 1% SDS, for 1 hour.

Alternatively, temperatures of about 65°C, 60°C, 55°C, or 42°C may be used. SSC concentration may be varied from about 0.1 to 2 x SSC, with SDS being present at about 0. 1 %. Typically, blocking reagents are used to block non-specific hybridization. Such blocking reagents include, for instance, sheared and denatured salmon sperm DNA at about 100-200 yg/ml. Organic solvent, such as formamide at a concentration of about 35-50% v/v, may also be used under particular circumstances, such as for RNA: DNA hybridizations. Useful variations on these wash conditions will be readily apparent to those of ordinary skill in the art. Hybridization, particularly under high stringency conditions, may be suggestive of evolutionary similarity between the nucleotides. Such similarity is strongly indicative of a similar role for the nucleotides and their encoded polypeptides.

The term"hybridization complex"refers to a complex formed between two nucleic acids by virtue of the formation of hydrogen bonds between complementary bases. A hybridization complex

may be formed in solution (e. g. , Cot or Rot analysis) or formed between one nucleic acid present in<BR> solution and another nucleic acid immobilized on a solid support (e. g. , paper, membranes, filters, chips, pins or glass slides, or any other appropriate substrate to which cells or their nucleic acids have been fixed).

The words"insertion"and"addition"refer to changes in an amino acid or polynucleotide sequence resulting in the addition of one or more amino acid residues or nucleotides, respectively.

"Immune response"can refer to conditions associated with inflammation, trauma, immune disorders, or infectious or genetic disease, etc. These conditions can be characterized by expression of various factors, e. g. , cytokines, chemokines, and other signaling molecules, which may affect cellular and systemic defense systems.

An"immunogenic fragment"is a polypeptide or oligopeptide fragment of PMMM which is capable of eliciting an immune response when introduced into a living organism, for example, a mammal. The term"immunogenic fragment"also includes any polypeptide or oligopeptide fragment of PMMM which is useful in any of the antibody production methods disclosed herein or known in the art.

The term"microarray"refers to an arrangement of a plurality of polynucleotides, polypeptides, antibodies, or other chemical compounds on a substrate.

The terms"element"and"array element"refer to a polynucleotide, polypeptide, antibody, or other chemical compound having a unique and defined position on a microarray.

The term"modulate"refers to a change in the activity of PMMM. For example, modulation may cause an increase or a decrease in protein activity, binding characteristics, or any other biological, functional, or immunological properties of PMMM.

The phrases"nucleic acid"and"nucleic acid sequence"refer to a nucleotide, oligonucleotide, polynucleotide, or any fragment thereof. These phrases also refer to DNA or RNA of genomic or synthetic origin which may be single-stranded or double-stranded and may represent the sense or the antisense strand, to peptide nucleic acid (PNA), or to any DNA-like or RNA-like material.

"Operably linked"refers to the situation in which a first nucleic acid sequence is placed in a functional relationship with a second nucleic acid sequence. For instance, a promoter is operably linked to a coding sequence if the promoter affects the transcription or expression of the coding sequence. Operably linked DNA sequences may be in close proximity or contiguous and, where necessary to join two protein coding regions, in the same reading frame.

"Peptide nucleic acid" (PNA) refers to an antisense molecule or anti-gene agent which comprises an oligonucleotide of at least about 5 nucleotides in length linked to a peptide backbone of

amino acid residues ending in lysine. The terminal lysine confers solubility to the composition. PNAs preferentially bind complementary single stranded DNA or RNA and stop transcript elongation, and may be pegylated to extend their lifespan in the cell.

"Post-translational modification"of an PMMM may involve lipidation, glycosylation, phosphorylation, acetylation, racemization, proteolytic cleavage, and other modifications known in the art. These processes may occur synthetically or biochemically. Biochemical modifications will vary by cell type depending on the enzymatic milieu of PMMM.

"Probe"refers to nucleic acids encoding PMMM, their complements, or fragments thereof, which are used to detect identical, allelic or related nucleic acids. Probes are isolated oligonucleotides or polynucleotides attached to a detectable label or reporter molecule. Typical labels include radioactive isotopes, ligands, chemiluminescent agents, and enzymes."Primers"are short nucleic acids, usually DNA oligonucleotides, which may be annealed to a target polynucleotide by complementary base-pairing. The primer may then be extended along the target DNA strand by a DNA polymerase enzyme. Primer pairs can be used for amplification (and identification) of a nucleic acid, e. g. , by the polymerase chain reaction (PCR).

Probes and primers as used in the present invention typically comprise at least 15 contiguous nucleotides of a known sequence. In order to enhance specificity, longer probes and primers may also be employed, such as probes and primers that comprise at least 20,25, 30,40, 50,60, 70,80, 90,100, or at least 150 consecutive nucleotides of the disclosed nucleic acid sequences. Probes and primers may be considerably longer than these examples, and it is understood that any length supported by the specification, including the tables, figures, and Sequence Listing, may be used.

Methods for preparing and using probes and primers are described in, for example, Sambrook, <BR> J. and D. W. Russell (2001 ; Molecular Cloning: A Laboratory Manual, 3rd ed. , vol. 1-3, Cold Spring Harbor Press, Cold Spring Harbor NY), Ausubel, F. M. et al. (1999; Short Protocols in Molecular Biology. 4 ed., John Wiley & Sons, New York NY), and Innis, M. et al. (1990; PCR Protocols, A Guide to Methods and Applications, Academic Press, San Diego CA). PCR primer pairs can be derived from a known sequence, for example, by using computer programs intended for that purpose such as Primer (Version 0. 5, 1991, Whitehead Institute for Biomedical Research, Cambridge MA).

Oligonucleotides for use as primers are selected using software known in the art for such purpose. For example, OLIGO 4.06 software is useful for the selection of PCR primer pairs of up to 100 nucleotides each, and for the analysis of oligonucleotides and larger polynucleotides of up to 5,000 nucleotides from an input polynucleotide sequence of up to 32 kilobases. Similar primer selection programs have incorporated additional features for expanded capabilities. For example, the PrimOU

primer selection program (available to the public from the Genome Center at University of Texas South West Medical Center, Dallas TX) is capable of choosing specific primers from megabase sequences and is thus useful for designing primers on a genome-wide scope. The Primer3 primer selection program (available to the public from the Whitehead Institute/MIT Center for Genome Research, Cambridge MA) allows the user to input a"mispriming library, "in which sequences to avoid as primer binding sites are user-specified. Primer3 is useful, in particular, for the selection of oligonucleotides for microarrays. (The source code for the latter two primer selection programs may also be obtained from their respective sources and modified to meet the user's specific needs. ) The PrimeGen program (available to the public from the UK Human Genome Mapping Project Resource Centre, Cambridge UK) designs primers based on multiple sequence alignments, thereby allowing selection of primers that hybridize to either the most conserved or least conserved regions of aligned nucleic acid sequences. Hence, this program is useful for identification of both unique and conserved oligonucleotides and polynucleotide fragments. The oligonucleotides and polynucleotide fragments identified by any of the above selection methods are useful in hybridization technologies, for example, as PCR or sequencing primers, microarray elements, or specific probes to identify fully or partially complementary polynucleotides in a sample of nucleic acids. Methods of oligonucleotide selection are not limited to those described above.

A"recombinant nucleic acid"is a nucleic acid that is not naturally occurring or has a sequence that is made by an artificial combination of two or more otherwise separated segments of sequence. This artificial combination is often accomplished by chemical synthesis or, more commonly, by the artificial manipulation of isolated segments of nucleic acids, e. g. , by genetic engineering techniques such as those described in Sambrook and Russell (supra). The term recombinant includes nucleic acids that have been altered solely by addition, substitution, or deletion of a portion of the nucleic acid. Frequently, a recombinant nucleic acid may include a nucleic acid sequence operably linked to a promoter sequence. Such a recombinant nucleic acid may be part of a vector that is used, for example, to transform a cell.

Alternatively, such recombinant nucleic acids may be part of a viral vector, e. g. , based on a vaccinia virus, that could be use to vaccinate a mammal wherein the recombinant nucleic acid is expressed, inducing a protective immunological response in the mammal.

A"regulatory element"refers to a nucleic acid sequence usually derived from untranslated regions of a gene and includes enhancers, promoters, introns, and 5'and 3'untranslated regions (UTRs). Regulatory elements interact with host or viral proteins which control transcription, translation, or RNA stability.

"Reporter molecules"are chemical or biochemical moieties used for labeling a nucleic acid, amino acid, or antibody. Reporter molecules include radionuclides; enzymes; fluorescent, chemiluminescent, or chromogenic agents; substrates; cofactors; inhibitors; magnetic particles; and other moieties known in the art.

An"RNA equivalent, "in reference to a DNA molecule, is composed of the same linear sequence of nucleotides as the reference DNA molecule with the exception that all occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

The tenn"sample"is used in its broadest sense. A sample suspected of containing PMMM, nucleic acids encoding PMMM, or fragments thereof may comprise a bodily fluid; an extract from a cell, chromosome, organelle, or membrane isolated from a cell; a cell; genomic DNA, RNA, or cDNA, in solution or bound to a substrate; a tissue; a tissue print; etc.

The terms"specific binding"and"specifically binding"refer to that interaction between a protein or peptide and an agonist, an antibody, an antagonist, a small molecule, or any natural or synthetic binding composition. The interaction is dependent upon the presence of a particular structure <BR> <BR> of the protein, e. g. , the antigenic determinant or epitope, recognized by the binding molecule. For<BR> example, if an antibody is specific for epitope"A, "the presence of a polypeptide comprising the epitope A, or the presence of free labeled A, in a reaction containing free labeled A and the antibody will reduce the amount of labeled A that binds to the antibody.

The term"substantially purified"refers to nucleic acid or amino acid sequences that are removed from their natural environment and are isolated or separated, and are at least about 60% free, preferably at least about 75% free, and most preferably at least about 90% free from other components with which they are naturally associated.

A"substitution"refers to the replacement of one or more amino acid residues or nucleotides by different amino acid residues or nucleotides, respectively.

"Substrate"refers to any suitable rigid or semi-rigid support including membranes, filters, chips, slides, wafers, fibers, magnetic or nonmagnetic beads, gels, tubing, plates, polymers, microparticles and capillaries. The substrate can have a variety of surface forms, such as wells, trenches, pins, channels and pores, to which polynucleotides or polypeptides are bound.

A"transcript image"or"expression profile"refers to the collective pattern of gene expression by a particular cell type or tissue under given conditions at a given time.

"Transformation"describes a process by which exogenous DNA is introduced into a recipient cell. Transformation may occur under natural or artificial conditions according to various methods

well known in the art, and may rely on any known method for the insertion of foreign nucleic acid sequences into a prokaryotic or eukaryotic host cell. The method for transformation is selected based on the type of host cell being transformed and may include, but is not limited to, bacteriophage or viral infection, electroporation, heat shock, lipofection, and particle bombardment. The term"transformed cells"includes stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as transiently transformed cells which express the inserted DNA or RNA for limited periods of time.

A"transgenic organism, "as used herein, is any organism, including but not limited to animals and plants, in which one or more of the cells of the organism contains heterologous nucleic acid introduced by way of human intervention, such as by transgenic techniques well known in the art. The nucleic acid is introduced into the cell, directly or indirectly by introduction into a precursor of the cell, by way of deliberate genetic manipulation, such as by microinjection or by infection with a recombinant virus. In another embodiment, the nucleic acid can be introduced by infection with a recombinant viral vector, such as a lentiviral vector (Lois, C. et al. (2002) Science 295: 868-872). The term genetic manipulation does not include classical cross-breeding, or in vitro fertilization, but rather is directed to the introduction of a recombinant DNA molecule. The transgenic organisms contemplated in accordance with the present invention include bacteria, cyanobacteria, fungi, plants and animals. The isolated DNA of the present invention can be introduced into the host by methods known in the art, for example infection, transfection, transformation or transconjugation. Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook and Russell (supra).

A"variant"of a particular nucleic acid sequence is defined as a nucleic acid sequence having at least 40% sequence identity to the particular nucleic acid sequence over a certain length of one of the nucleic acid sequences using blastn with the"BLAST 2 Sequences"tool Version 2.0. 9 (May-07- 1999) set at default parameters. Such a pair of nucleic acids may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity over a certain defined length. A variant may be described as, for example, an "allelic" (as defined above),"splice,""species,"or"polymorphic"variant. A splice variant may have significant identity to a reference molecule, but will generally have a greater or lesser number of polynucleotides due to alternate splicing during mRNA processing. The corresponding polypeptide may possess additional functional domains or lack domains that are present in the reference molecule.

Species variants are polynucleotides that vary from one species to another. The resulting polypeptides

will generally have significant amino acid identity relative to each other. A polymorphic variant is a variation in the polynucleotide sequence of a particular gene between individuals of a given species.

Polymorphic variants also may encompass"single nucleotide polymorphisms" (SNPs) in which the polynucleotide sequence varies by one nucleotide base. The presence of SNPs may be indicative of, for example, a certain population, a disease state, or a propensity for a disease state.

A"variant"of a particular polypeptide sequence is defined as a polypeptide sequence having at least 40% sequence identity or sequence similarity to the particular polypeptide sequence over a certain length of one of the polypeptide sequences using blastp with the"BLAST 2 Sequences"tool Version 2.0. 9 (May-07-1999) set at default parameters. Such a pair of polypeptides may show, for example, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 91%, at least 92%, at least 93%, at least 94%, at least 95%, at least 96%, at least 97%, at least 98%, or at least 99% or greater sequence identity or sequence similarity over a certain defined length of one of the polypeptides.

THE INVENTION Various embodiments of the invention include new human protein modification and maintenance molecules (PMMM), the polynucleotides encoding PMMM, and the use of these compositions for the diagnosis, treatment, or prevention of gastrointestinal, cardiovascular, autoimmune/inflammatory, cell proliferative, developmental, epithelial, neurological, and reproductive disorders.

Table 1 summarizes the nomenclature for the full length polynucleotide and polypeptide embodiments of the invention. Each polynucleotide and its corresponding polypeptide are correlated to a single Incyte project identification number (Incyte Project ID). Each polypeptide sequence is denoted by both a polypeptide sequence identification number (Polypeptide SEQ ID NO:) and an Incyte polypeptide sequence number (Incyte Polypeptide ID) as shown. Each polynucleotide sequence is denoted by both a polynucleotide sequence identification number (Polynucleotide SEQ ID NO:) and an Incyte polynucleotide consensus sequence number (Incyte Polynucleotide ID) as shown.

Column 6 shows the Incyte ID numbers of physical, full length clones corresponding to the polypeptide and polynucleotide sequences of the invention. The full length clones encode polypeptides which have at least 95% sequence identity to the polypeptide sequences shown in column 3.

Table 2 shows sequences with homology to polypeptide embodiments of the invention as identified by BLAST analysis against the GenBank protein (genpept) database and the PROTEOME database. Columns 1 and 2 show the polypeptide sequence identification number (Polypeptide SEQ

ID NO:) and the corresponding Incyte polypeptide sequence number (Incyte Polypeptide ID) for polypeptides of the invention. Column 3 shows the GenBank identification number (GenBank ID NO:) of the nearest GenBank homolog and the PROTEOME database identification numbers (PROTEOME ID NO:) of the nearest PROTEOME database homologs. Column 4 shows the probability scores for the matches between each polypeptide and its homolog (s). Column 5 shows the annotation of the GenBank and PROTEOME database homolog (s) along with relevant citations where applicable, all of which are expressly incorporated by reference herein.

Table 3 shows various structural features of the polypeptides of the invention. Columns 1 and 2 show the polypeptide sequence identification number (SEQ ID NO:) and the corresponding Incyte polypeptide sequence number (Incyte Polypeptide ID) for each polypeptide of the invention. Column 3 shows the number of amino acid residues in each polypeptide. Column 4 shows potential phosphorylation sites, and column 5 shows potential glycosylation sites, as determined by the MOTIFS program of the GCG sequence analysis software package (Accekys, Burlington MA). Column 6 shows amino acid residues comprising signature sequences, domains, and motifs. Column 7 shows analytical methods for protein structure/function analysis and in some cases, searchable databases to which the analytical methods were applied.

Together, Tables 2 and 3 summarize the properties of polypeptides of the invention, and these properties establish that the claimed potypeptides are protein modification and maintenance molecules.

For example, SEQ ID NO : 1 is 98% identical, from residue M1 to residue S269, to human aspartyl protease 3 (GenBank ID g6561816) as determined by the Basic Local Alignment Search Tool <BR> <BR> (BLAST). (See Table 2. ) The BLAST probability score is 1. 6E-143, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO : 1 also has homology to pronapsin A, as determined by BLAST analysis using the PROTEOME database. SEQ ID NO : 1 also contains a eukaryotic aspartyl protease active site domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of <BR> <BR> conserved protein families/domains. (See Table 3. ) Data from BLIMPS and MOTIFS analyses, and BLAST analyses against the PRODOM and DOMO databases, provide further corroborative evidence that SEQ ID NO : 1 is an aspartyl protease. In an alternative example, SEQ ID NO : 22 is a splice variant of human interleukin-lB converting enzyme (GenBank ID g33793), a cysteine protease, as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2.) The BLAST probability score is 5.4e-177, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO : 22 also has homology to proteins which have cysteine protease activity, and are caspases that activate interleukin-1 beta and stimulate apoptosis, as well as

having roles in inflammation, as determined by BLAST analysis using the PROTEOME database.

SEQ ID NO : 22 also contains ICE-like protease (caspase) plO and p20 domains, as well as a caspase, interleukin-1 beta converting enzyme domain, as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM and SMART databases of conserved protein families/domains. (See Table 3. ) Data from BLIMPS and MOTIFS analyses, and BLAST analyses against the PRODOM and DOMO databases, provide further corroborative evidence that SEQ ID NO : 22 is an interleukin-lB converting enzyme. In an alternative example, SEQ ID NO : 35 is 99% identical, from residue G127 to residue F363, to human matrix metalloproteinase-28 precursor (GenBank ID gI2698338) as determined by the Basic Local Alignment Search Tool (BLAST). (See <BR> <BR> Table 2. ) The BLAST probability score is 6.4E-200, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO : 35 also has homology to human matrix metalloproteinase-28, as determined by BLAST analysis using the PROTEOME database.

SEQ ID NO : 35 also contains a hemopexin domain as determined by searching for statistically <BR> <BR> significant matches in the hidden Markov model (HMM) -based PFAM database of conserved protein families/domains, and a hemopexin-like repeat domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based SMART database of conserved <BR> <BR> protein families/domains. (See Table 3. ) Data from BLIMPS and PROFILESCAN analyses provide further corroborative evidence that SEQ ID NO : 35 is a matrix metalloprotease. In an alternative example, SEQ ID NO : 48 is a splice variant of human membrane-type serine protease 1 (GenBank ID g6002714) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2. ) The BLAST probability score is 8.2e-124, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance. SEQ ID NO : 48 also has homology to proteins that are localized to the plasma membrane, function in the degradation of extracellular matrix and the activation of hepatocyte growth factor and urokinase plasminogen activator, and are serine proteases, as determined by BLAST analysis using the PROTEOME database. SEQ ID NO : 48 also contains a trypsin domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM and SMART databases of conserved protein families/domains. (See Table 3. ) Data from BLIMPS, MOTIFS, and PROFILESCAN analyses, and BLAST analyses against the PRODOM and DOMO databases, provide further corroborative evidence that SEQ ID NO : 48 is a serine protease. In an alternative example, SEQ ID NO : 61 is 99% identical, from residue A77 to residue P333, to human beta-tryptase (GenBank ID gl79584) as determined by the Basic Local Alignment Search Tool (BLAST). (See Table 2. ) The BLAST probability score is 9.3E-153, which indicates the probability of obtaining the observed polypeptide sequence alignment by chance.

SEQ ID NO : 61 also has homology to human tryptase beta 1, as determined by BLAST analysis using the PROTEOME database. SEQ ID NO : 61 also contains a trypsin-like serine protease domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)- based SMART database of conserved protein families/domains, and a trypsin domain as determined by searching for statistically significant matches in the hidden Markov model (HMM)-based PFAM database of conserved protein families/domains. (See Table 3. ) Data from BLIMPS, MOTIFS, and PROFILESCAN analyses, and BLAST analyses against the PRODOM and DOMO databases, provide further corroborative evidence that SEQ ID NO : 61 is a beta-tryptase. SEQ ID NO : 2-21, SEQ ID NO : 23-34, SEQ ID NO : 36-47, SEQ ID NO : 49-60, and SEQ ID NO : 62 were analyzed and annotated in a similar manner. The algorithms and parameters for the analysis of SEQ ID NO: 1-62 are described in Table 7.

As shown in Table 4, the full length polynucleotide embodiments were assembled using cDNA sequences or coding (exon) sequences derived from genomic DNA, or any combination of these two types of sequences. Column 1 lists the polynucleotide sequence identification number (Polynucleotide SEQ ID NO:), the corresponding Incyte polynucleotide consensus sequence number (Incyte ID) for each polynucleotide of the invention, and the length of each polynucleotide sequence in basepairs.

Column 2 shows the nucleotide start (5') and stop (3') positions of the cDNA and/or genomic sequences used to assemble the full length polynucleotide embodiments, and of fragments of the polynucleotides which are useful, for example, in hybridization or amplification technologies that identify SEQ ID NO : 63-124 or that distinguish between SEQ ID NO : 63-124 and related polynucleotides.

The polynucleotide fragments described in Column 2 of Table 4 may refer specifically, for example, to Incyte cDNAs derived from tissue-specific cDNA libraries or from pooled cDNA libraries. Alternatively, the polynucleotide fragments described in column 2 may refer to GenBank cDNAs or ESTs which contributed to the assembly of the full length polynucleotides. In addition, the polynucleotide fragments described in column 2 may identify sequences derived from the ENSEMBL (The Sanger Centre, Cambridge, UK) database (i. e., those sequences including the designation "ENST"). Alternatively, the polynucleotide fragments described in column 2 may be derived from the NCBI RefSeq Nucleotide Sequence Records Database (i. e. , those sequences including the designation"NM"or"NT") or the NCBI RefSeq Protein Sequence Records (i. e., those sequences including the designation"NP"). Alternatively, the polynucleotide fragments described in column 2 may refer to assemblages of both cDNA and Genscan-predicted exons brought together by an"exon stitching"algorithm. For example, a polynucleotide sequence identified as

FL_XMX_N, _N2_YYYYY N3_N4 represents a"stitched"sequence in which'00= is the identification number of the cluster of sequences to which the algorithm was applied, and YYYYY is the number of the prediction generated by the algorithm, and N, z, 3... if present, represent specific exons that may have been manually edited during analysis (See Example V). Alternatively, the polynucleotide fragments in column 2 may refer to assemblages of exons brought together by an "exon-stretching"algorithm. For example, a polynucleotide sequence identified as FLXXXXXXgAAAAAgBjBBBBlJV is a"stretched"sequence, with XXNXX being the Incyte project identification number, gAAAAA being the GenBank identification number of the human genomic sequence to which the"exon-stretching"algorithm was applied, gBBBBB being the GenBank identification number or NCBI RefSeq identification number of the nearest GenBank protein homolog, and N referring to specific exons (See Example V). In instances where a RefSeq sequence was used as a protein homolog for the"exon-stretching"algorithm, a RefSeq identifier (denoted by"NM," "NP, "or"NT") may be used in place of the GenBank identifier (i. e., gBBBBB).

Alternatively, a prefix identifies component sequences that were hand-edited, predicted from. genomic DNA sequences, or derived from a combination of sequence analysis methods. The following Table lists examples of component sequence prefixes and corresponding sequence analysis methods associated with the prefixes (see Example IV and Example V). Prefix Type of analysis and/or examples of programs GNN, GFG, Exon prediction from genomic sequences using, for example, ENST GENSCAN (Stanford University, CA, USA) or FGENES (Computer Genomics Group, The Sanger Centre, Cambridge, UK). GBI Hand-edited analysis of genomic sequences. FL Stitched or stretched genomic sequences (see Example V). INCY Full length transcript and exon prediction from mapping of EST sequences to the genome. Genomic location and EST composition data are combined to predict the exons and resulting transcript.

In some cases, Incyte cDNA coverage redundant with the sequence coverage shown in Table 4 was obtained to confirm the final consensus polynucleotide sequence, but the relevant Incyte cDNA identification numbers are not shown.

Table 5 shows the representative cDNA libraries for those full length polynucleotides which were assembled using Incyte cDNA sequences. The representative cDNA library is the Incyte cDNA library which is most frequently represented by the Incyte cDNA sequences which were used

to assemble and confirm the above polynucleotides. The tissues and vectors which were used to construct the cDNA libraries shown in Table 5 are described in Table 6.

Table 8 shows single nucleotide polymorphisms (SNPs) found in polynucleotide sequences of the invention, along with allele frequencies in different human populations. Columns 1 and 2 show the polynucleotide sequence identification number (SEQ ID NO:) and the corresponding Incyte project identification number (PID) for polynucleotides of the invention. Column 3 shows the Incyte identification number for the EST in which the SNP was detected (EST ID), and column 4 shows the identification number for the SNP (SNP ID). Column 5 shows the position within the EST sequence at which the SNP is located (EST SNP), and column 6 shows the position of the SNP within the full- length polynucleotide sequence (CB1 SNP). Column 7 shows the allele found in the EST sequence.

Columns 8 and 9 show the two alleles found at the SNP site. Column 10 shows the amino acid encoded by the codon including the SNP site, based upon the allele found in the EST. Columns 11-14 show the frequency of allele 1 in four different human populations. An entry of n/d (not detected) indicates that the frequency of allele 1 in the population was too low to be detected, while n/a (not available) indicates that the allele frequency was not determined for the population.

The invention also encompasses PMMM variants. Various embodiments of PMMM variants can have at least about 80%, at least about 90%, or at least about 95% amino acid sequence identity to the PMMM amino acid sequence, and can contain at least one functional or structural characteristic of PMMM.

Various embodiments also encompass polynucleotides which encode PMMM. In a particular embodiment, the invention encompasses a polynucleotide sequence comprising a sequence selected from the group consisting of SEQ ID NO : 63-124, which encodes PMMM. The polynucleotide sequences of SEQ ID NO : 63-124, as presented in the Sequence Listing, embrace the equivalent RNA sequences, wherein occurrences of the nitrogenous base thymine are replaced with uracil, and the sugar backbone is composed of ribose instead of deoxyribose.

The invention also encompasses variants of a polynucleotide encoding PMMM. In particular, such a variant polynucleotide will have at least about 70%, or alternatively at least about 85%, or even at least about 95% polynucleotide sequence identity to a polynucleotide encoding PMMM. A particular aspect of the invention encompasses a variant of a polynucleotide comprising a sequence selected from the group consisting of SEQ ID NO : 63-124 which has at least about 70%, or alternatively at least about 85%, or even at least about 95% polynucleotide sequence identity to a nucleic acid sequence selected from the group consisting of SEQ ID NO : 63-124. Any one of the

polynucleotide variants described above can encode a polypeptide which contains at least one functional or structural characteristic of PMMM.

In addition, or in the alternative, a polynucleotide variant of the invention is a splice variant of a polynucleotide encoding PMMM. A splice variant may have portions which have significant sequence identity to a polynucleotide encoding PMMM, but will generally have a greater or lesser number of nucleotides due to additions or deletions of blocks of sequence arising from alternate splicing during mRNA processing. A splice variant may have less than about 70%, or alternatively less than about 60%, or alternatively less than about 50% polynucleotide sequence identity to a polynucleotide encoding PMMM over its entire length; however, portions of the splice variant will have at least about 70%, or alternatively at least about 85%, or alternatively at least about 95%, or alternatively 100% polynucleotide sequence identity to portions of the polynucleotide encoding PMMM. For example, a polynucleotide comprising a sequence of SEQ ID NO : 65 and a polynucleotide comprising a sequence of SEQ ID NO : 66 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO : 73 and a polynucleotide comprising a sequence of SEQ ID NO : 74 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO : 82, a polynucleotide comprising a sequence of SEQ ID NO : 116 and a polynucleotide comprising a sequence of SEQ ID NO : 117 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO : 86 and a polynucleotide comprising a sequence of SEQ ID NO : 87 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO : 92 and a polynucleotide comprising a sequence of SEQ ID NO: 102 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO : 96 and a polynucleotide comprising a sequence of SEQ ID NO : 108 are splice variants of each other ; a polynucleotide comprising a sequence of SEQ ID NO : 97 and a polynucleotide comprising a sequence of SEQ ID NO : 99 are splice variants of each other; a polynucleotide comprising a sequence of SEQ ID NO : 98, a polynucleotide comprising a sequence of SEQ ID NO : 109 and a polynucleotide comprising a sequence of SEQ ID NO : 123 are splice variants of each other; a polynucleotide comprising a sequence of SEQ II7 N0 : 105 and a polynucleotide comprising a sequence of SEQ ID NO: 111 are splice variants of each other; and a polynucleotide comprising a sequence of SEQ ID NO : 114 and a polynucleotide comprising a sequence of SEQ ID NO : 115 are splice variants of each other. Any one of the splice variants described above can encode a polypeptide which contains at least one functional or structural characteristic of PMMM.

It will be appreciated by those skilled in the art that as a result of the degeneracy of the genetic code, a multitude of polynucleotide sequences encoding PMMM, some bearing minimal similarity to the polynucleotide sequences of any known and naturally occurring gene, may be

produced. Thus, the invention contemplates each and every possible variation of polynucleotide sequence that could be made by selecting combinations based on possible codon choices. These combinations are made in accordance with the standard triplet genetic code as applied to the polynucleotide sequence of naturally occurring PMMM, and all such variations are to be considered as being specifically disclosed.

Although polynucleotides which encode PMMM and its variants are generally capable of hybridizing to polynucleotides encoding naturally occurring PMMM under appropriately selected conditions of stringency, it may be advantageous to produce polynucleotides encoding PMMM or its <BR> <BR> derivatives possessing a substantially different codon usage, e. g. , inclusion of non-naturally occurring codons. Codons may be selected to increase the rate at which expression of the peptide occurs in a particular prokaryotic or eukaryotic host in accordance with the frequency with which particular codons are utilized by the host. Other reasons for substantially altering the nucleotide sequence encoding PMMM and its derivatives without altering the encoded amino acid sequences include the production of RNA transcripts having more desirable properties, such as a greater half-life, than transcripts produced from the naturally occurring sequence.

The invention also encompasses production of polynucleotides which encode PMMM and PMMM derivatives, or fragments thereof, entirely by synthetic chemistry. After production, the synthetic polynucleotide may be inserted into any of the many available expression vectors and cell systems using reagents well known in the art. Moreover, synthetic chemistry may be used to introduce mutations into a polynucleotide encoding PMMM or any fragment thereof.

Embodiments of the invention can also include polynucleotides that are capable of hybridizing to the claimed polynucleotides, and, in particular, to those having the sequences shown in SEQ ID NO : 63-124 and fragments thereof, under various conditions of stringency (Wahl, G. M. and S. L.

Berger (1987) Methods Enzymol. 152: 399-407; Kimmel, A. R. (1987) Methods Enzymol. 152: 507-511).

Hybridization conditions, including annealing and wash conditions, are described in"Definitions." Methods for DNA sequencing are well known in the art and may be used to practice any of the embodiments of the invention. The methods may employ such enzymes as the Klenow fragment of DNA polymerase I, SEQUENASE (US Biochemical, Cleveland OH), Taq polymerase (Applied Biosystems), thermostable T7 polymerase (Amersham Biosciences, Piscataway NJ), or combinations of polymerases and proofreading exonucleases such as those found in the ELONGASE amplification system (Invitrogen, Carlsbad CA). Preferably, sequence preparation is automated with machines such as the MICROLAB 2200 liquid transfer system (Hamilton, Reno NV), PTC200 thermal cycler (MJ Research, Watertown MA) and ABI CATALYST 800 thermal cycler (Applied Biosystems).

Sequencing is then carried out using either the ABI 373 or 377 DNA sequencing system (Applied Biosystems), the MEGABACE 1000 DNA sequencing system (Amersham Biosciences), or other systems known in the art. The resulting sequences are analyzed using a variety of algorithms which are well known in the art (Ausubel et al., supra, ch. 7; Meyers, R. A. (1995) Molecular Biology and Biotechnology, Wiley VCH, New York NY, pp. 856-853).

The nucleic acids encoding PMMM may be extended utilizing a partial nucleotide sequence and employing various PCR-based methods known in the art to detect upstream sequences, such as promoters and regulatory elements. For example, one method which may be employed, restriction-site PCR, uses universal and nested primers to amplify unknown sequence from genomic DNA within a cloning vector (Sarkar, G. (1993) PCR Methods Applic. 2: 318-322). Another method, inverse PCR, uses primers that extend in divergent directions to amplify unknown sequence from a circularized template. The template is derived from restriction fragments comprising a known genomic locus and surrounding sequences (Triglia, T. et al. (1988) Nucleic Acids Res. 16: 8186). A third method, capture PCR, involves PCR amplification of DNA fragments adjacent to known sequences in human and yeast artificial chromosome DNA (Lagerstrom, M. et al. (1991) PCR Methods Applic. 1: 111-119). In this method, multiple restriction enzyme digestions and ligations may be used to insert an engineered double-stranded sequence into a region of unknown sequence before performing PCR. Other methods which may be used to retrieve unknown sequences are known in the art (Parker, J. D. et al.

(1991) Nucleic Acids Res. 19: 3055-3060). Additionally, one may use PCR, nested primers, and PROMOTERFINDER libraries (BD Clontech, Palo Alto CA) to walk genomic DNA. This procedure avoids the need to screen libraries and is useful in finding intron/exon junctions. For all PCR-based methods, primers may be designed using commercially available software, such as OLIGO 4.06 primer analysis software (National Biosciences, Plymouth MN) or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the template at temperatures of about 68°C to 72°C.

When screening for full length cDNAs, it is preferable to use libraries that have been size-selected to include larger cDNAs. In addition, random-primed libraries, which often include sequences containing the 5'regions of genes, are preferable for situations in which an oligo d (T) library does not yield a full-length cDNA. Genomic libraries may be useful for extension of sequence into 5'non-transcribed regulatory regions.

Capillary electrophoresis systems which are commercially available may be used to analyze the size or confirm the nucleotide sequence of sequencing or PCR products. In particular, capillary sequencing may employ flowable polymers for electrophoretic separation, four different nucleotide-

specific, laser-stimulated fluorescent dyes, and a charge coupled device camera for detection of the emitted wavelengths. Output/light intensity may be converted to electrical signal using appropriate <BR> <BR> software (e. g. , GENOTYPER and SEQUENCE NAVIGATOR, Applied Biosystems), and the entire process from loading of samples to computer analysis and electronic data display may be computer controlled. Capillary electrophoresis is especially preferable for sequencing small DNA fragments which may be present in limited amounts in a particular sample.

In another embodiment of the invention, polynucleotides or fragments thereof which encode PMMM may be cloned in recombinant DNA molecules that direct expression of PMMM, or fragments or functional equivalents thereof, in appropriate host cells. Due to the inherent degeneracy of the genetic code, other polynucleotides which encode substantially the same or a functionally equivalent polypeptides may be produced and used to express PMMM.

The polynucleotides of the invention can be engineered using methods generally known in the art in order to alter PMMM-encoding sequences for a variety of purposes including, but not limited to, modification of the cloning, processing, and/or expression of the gene product. DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. For example, oligonucleotide-mediated site-directed mutagenesis may be used to introduce mutations that create new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, and so forth.

The nucleotides of the present invention may be subjected to DNA shuffling techniques such as MOLECULARBREEDING (Maxygen Inc. , Santa Clara CA; described in U. S. Patent No.

5,837, 458; Chang, C.-C. et al. (1999) Nat. Biotechnol. 17: 793-797; Christians, F. C. et al. (1999) Nat.

Biotechnol. 17: 259-264; and Crameri, A. et al. (1996) Nat. Biotechnol. 14: 315-319) to alter or improve the biological properties of PMMM, such as its biological or enzymatic activity or its ability to bind to other molecules or compounds. DNA shuffling is a process by which a library of gene variants is produced using PCR-mediated recombination of gene fragments. The library is then subjected to selection or screening procedures that identify those gene variants with the desired properties. These preferred variants may then be pooled and further subjected to recursive rounds of DNA shuffling and selection/screening. Thus, genetic diversity is created through"artificial"breeding and rapid molecular evolution. For example, fragments of a single gene containing random point mutations may be recombined, screened, and then reshuffled until the desired properties are optimized. Alternatively, fragments of a given gene may be recombined with fragments of homologous genes in the same gene family, either from the same or different species, thereby maximizing the genetic diversity of multiple naturally occurring genes in a directed and controllable manner.

In another embodiment, polynucleotides encoding PMMM may be synthesized, in whole or in part, using one or more chemical methods well known in the art (Caruthers, M. H. et al. (1980) Nucleic Acids Symp. Ser. 7: 215-223; Horn, T. et al. (1980) Nucleic Acids Symp. Ser. 7: 225-232).

Alternatively, PMMM itself or a fragment thereof may be synthesized using chemical methods known in the art. For example, peptide synthesis can be performed using various solution-phase or solid-phase techniques (Creighton, T. (1984) Proteins, Structures and Molecular Properties, WH Freeman, New York NY, pp. 55-60; Roberge, J. Y. et al. (1995) Science 269: 202-204). Automated synthesis may be achieved using the ABI 431A peptide synthesizer (Applied Biosystems).

Additionally, the amino acid sequence of PMMM, or any part thereof, may be altered during direct synthesis and/or combined with sequences from other proteins, or any part thereof, to produce a variant polypeptide or a polypeptide having a sequence of a naturally occurring polypeptide.

The peptide may be substantially purified by preparative high performance liquid chromatography (Chiez, R. M. and F. Z. Regnier (1990) Methods Enzymol. 182: 392-421). The composition of the synthetic peptides may be confirmed by amino acid analysis or by sequencing (Creighton, supra, pp. 28-53).

In order to express a biologically active PMMM, the polynucleotides encoding PMMM or <BR> <BR> derivatives thereof may be inserted into an appropriate expression vector, i. e. , a vector which contains the necessary elements for transcriptional and translational control of the inserted coding sequence in, a suitable host. These elements include regulatory sequences, such as enhancers, constitutive and inducible promoters, and 5'and 3'untranslated regions in the vector and in polynucleotides encoding PMMM. Such elements may vary in their strength and specificity. Specific initiation signals may also be used to achieve more efficient translation of polynucleotides encoding PMMM. Such signals include the ATG initiation codon and adjacent sequences, e. g. the Kozak sequence. In cases where a polynucleotide sequence encoding PMMM and its initiation codon and upstream regulatory sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a fragment thereof, is inserted, exogenous translational control signals including an in-frame ATG initiation codon should be provided by the vector. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers appropriate for the particular host cell system used (Scharf, D. et al. (1994) Results Probl.

Cell Differ. 20: 125-162).

Methods which are well known to those skilled in the art may be used to construct expression vectors containing polynucleotides encoding PMMM and appropriate transcriptional and translational

control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination (Sambrook and Russell, supra, ch. 1-4, and 8; Ausubel et al., supra, ch. 1,3, and 15).

A variety of expression vector/host systems may be utilized to contain and express polynucleotides encoding PMMM. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with viral expression vectors (e. g., baculovirus) ; plant cell systems transformed with viral expression vectors (e. g., cauliflower mosaic virus, CaMV, or tobacco mosaic virus, TMV) or with bacterial expression vectors (e. g. , Ti or pBR322 plasmids); or animal cell systems (Sambrook and Russell, supra ; Ausubel et al., supra ; Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264: 5503-5509; Engelhard, E. K. et al.

(1994) Proc. Natl. Acad. Sci. USA 91 : 3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7: 1937- 1945; Takamatsu, N. (1987) EMBO J. 6: 307-311 ; The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York NY, pp. 191-196; Logan, J. and T. Shenk (1984) Proc.

Natl. Acad. Sci. USA 81 : 3655-3659; Harrington, J. J. et al. (1997) Nat. Genet. 15: 345-355).

Expression vectors derived from retroviruses, adenoviruses, or herpes or vaccinia viruses, or from various bacterial plasmids, may be used for delivery of polynucleotides to the targeted organ, tissue, or cell population (Di Nicola, M. et al. (1998) Cancer Gen. Ther. 5: 350-356; Yu, M. et al. (1993) Proc.

Natl. Acad. Sci. USA 90: 6340-6344; Buller, R. M. et al. (1985) Nature 317: 813-815; McGregor, D. P. et al. (1994) Mol. Immunol. 31: 219-226; Verma, I. M. and N. Somia (1997) Nature 389: 239-242). The invention is not limited by the host cell employed.

In bacterial systems, a number of cloning and expression vectors may be selected depending upon the use intended for polynucleotides encoding PMMM. For example, routine cloning, subcloning, and propagation of polynucleotides encoding PMMM can be achieved using a multifunctional E. coli vector such as PBLUESCRIPT (Stratagene, La Jolla CA) or PSPORT1 plasmid (Invitrogen).

Ligation of polynucleotides encoding PMMM into the vector's multiple cloning site disrupts the lacZ gene, allowing a colorimetric screening procedure for identification of transformed bacteria containing recombinant molecules. In addition, these vectors may be useful for in vitro transcription, dideoxy sequencing, single strand rescue with helper phage, and creation of nested deletions in the cloned sequence (Van Heeke, G. and S. M. Schuster (1989) J. Biol. Chem. 264: 5503-5509). When large quantities of PMMM are needed, e. g. for the production of antibodies, vectors which direct high level expression of PMMM may be used. For example, vectors containing the strong, inducible SP6 or T7 bacteriophage promoter may be used.

Yeast expression systems may be used for production of PMMM. A number of vectors containing constitutive or inducible promoters, such as alpha factor, alcohol oxidase, and PGH promoters, may be used in the yeast Saccharomyces cerevisiae or Pichia pastoris. In addition, such vectors direct either the secretion or intracellular retention of expressed proteins and enable integration of foreign polynucleotide sequences into the host genome for stable propagation (Ausubel et al., supra ; Bitter, G. A. et al. (1987) Methods Enzymol. 153 : 516-544; Scorer, C. A. et al. (1994) Bio/Technology 12: 181-184).

Plant systems may also be used for expression of PMMM. Transcription of polynucleotides encoding PMMM may be driven by viral promoters, e. g. , the 35S and 19S promoters of CaMV used alone or in combination with the omega leader sequence from TMV (Takamatsu, N. (1987) EMBO J.

6: 307-311). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi, G. et al. (1984) EMBO J. 3: 1671-1680 ; Broglie, R. et al. (1984) Science 224: 838-843; Winter, J. et al. (1991) Results Probl. Cell Differ. 17: 85-105). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection (The McGraw Hill Yearbook of Science and Technology (1992) McGraw Hill, New York NY, pp.

191-196).

In mammalian cells, a number of viral-based expression systems may be utilized. In cases where an adenovirus is used as an expression vector, polynucleotides encoding PMMM may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain infective virus which expresses PMMM in host cells (Logan, J. and T. Shenk (1984) Proc.

Natl. Acad. Sci. USA 81: 3655-3659). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells. SV40 or EBV- based vectors may also be used for high-level protein expression.

Human artificial chromosomes (HACs) may also be employed to deliver larger fragments of DNA than can be contained in and expressed from a plasmid. HACs of about 6 kb to 10 Mb are constructed and delivered via conventional delivery methods (liposomes, polycationic amino polymers, or vesicles) for therapeutic purposes (Harrington, J. J. et al. (1997) Nat. Genet. 15: 345-355).

For long term production of recombinant proteins in mammalian systems, stable expression of PMMM in cell lines is preferred. For example, polynucleotides encoding PMMM can be transformed into cell lines using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector.

Following the introduction of the vector, cells may be allowed to grow for about 1 to 2 days in enriched

media before being switched to selective media. The purpose of the selectable marker is to confer resistance to a selective agent, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be propagated using tissue culture techniques appropriate to the cell type.

Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase and adenine phosphoribosyltransferase genes, for use in tk-and apr cells, respectively (Wigler, M. et al. (1977) Cell 11: 223-232; Lowy, I. et al. (1980) Cell 22: 817-823). Also, antimetabolite, antibiotic, or herbicide resistance can be used as the basis for selection. For example, dhfr confers resistance to methotrexate; neo confers resistance to the aminoglycosides neomycin and G-418; and als and pat confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Wigler, M. et al.

(1980) Proc. Natl. Acad. Sci. USA 77: 3567-3570; Colbere-Garapin, F. et al. (1981) J. Mol. Biol.

150: 1-14). Additional selectable genes have been described, e. g., trpB and hisD, which alter cellular requirements for metabolites (Hartman, S. C. and R. C. Mulligan (1988) Proc. Natl. Acad. Sci. USA 85: 8047-8051). Visible markers, e. g. , anthocyanins, green fluorescent proteins (GFP; BD Clontech), p-glucuronidase and its substrate ß-glucuronide, or luciferase and its substrate luciferin may be used.

These markers can be used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes, C. A. (1995) Methods Mol. Biol. 55: 121-131).

Although the presence/absence of marker gene expression suggests that the gene of interest is also present, the presence and expression of the gene may need to be confirmed. For example, if the sequence encoding PMMM is inserted within a marker gene sequence, transformed cells containing polynucleotides encoding PMMM can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a sequence encoding PMMM under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.

In general, host cells that contain the polynucleotide encoding PMMM and that express PMMM may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations, PCR amplification, and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein sequences.

Immunological methods for detecting and measuring the expression of PMMM using either specific polyclonal or monoclonal antibodies are known in the art. Examples of such techniques

include enzyme-linked immunosorbent assays (ELISAs), radioimmunoassays (RIAs), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on PMMM is preferred, but a competitive binding assay may be employed. These and other assays are well known in the art (Hampton, R. et al. (1990) Serological Methods, a Laboratory Manual, APS Press, St. Paul MN, Sect.

IV ; Coligan, J. E. et al. (1997) Current Protocols in Immunology, Greene Pub. Associates and Wiley- Interscience, New York NY ; Pound, J. D. (1998) Immunochemical Protocols, Humana Press, Totowa NJ).

A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides encoding PMMM include oligolabeling, nick translation, end-labeling, or PCR amplification using a labeled nucleotide.

Alternatively, polynucleotides encoding PMMM, or any fragments thereof, may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits, such as those provided by Amersham Biosciences, Promega (Madison WI), and US Biochemical. Suitable reporter molecules or labels which may be used for ease of detection include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents, as well as substrates, cofactors, inhibitors, magnetic particles, and the like.

Host cells transformed with polynucleotides encoding PMMM may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a transformed cell may be secreted or retained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides which encode PMMM may be designed to contain signal sequences which direct secretion of PMMM through a prokaryotic or eukaryotic cell membrane.

In addition, a host cell strain may be chosen for its ability to modulate expression of the inserted polynucleotides or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation, glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a"prepro"or "pro"form of the protein may also be used to specify protein targeting, folding, and/or activity.

Different host cells which have specific cellular machinery and characteristic mechanisms for post-translational activities (e. g., CHO, HeLa, MDCK, HEK293, andWI38) are available from the

American Type Culture Collection (ATCC, Manassas VA) and may be chosen to ensure the correct modification and processing of the foreign protein.

In another embodiment of the invention, natural, modified, or recombinant polynucleotides encoding PMMM may be ligated to a heterologous sequence resulting in translation of a fusion protein in any of the aforementioned host systems. For example, a chimeric PMMM protein containing a heterologous moiety that can be recognized by a commercially available antibody may facilitate the screening of peptide libraries for inhibitors of PMMM activity. Heterologous protein and peptide moieties may also facilitate purification of fusion proteins using commercially available affinity matrices. Such moieties include, but are not limited to, glutathione S-transferase (GST), maltose binding protein (MBP), thioredoxin (Trx), calmodulin binding peptide (CBP), 6-His, FLAG, c-myc, and hemagglutinin (HA). GST, MBP, Trx, CBP, and 6-His enable purification of their cognate fusion proteins on immobilized glutathione, maltose, phenylarsine oxide, calmodulin, and metal-chelate resins, respectively. FLAG, c-myc, and hemagglutinin (HA) enable immunoaffinity purification of fusion proteins using commercially available monoclonal and polyclonal antibodies that specifically recognize these epitope tags. A fusion protein may also be engineered to contain a proteolytic cleavage site located between the PMMM encoding sequence and the heterologous protein sequence, so that PMMM may be cleaved away from the heterologous moiety following purification. Methods for fusion protein expression and purification are discussed in Ausubel et al. (supra, ch. 10 and 16). A variety of commercially available kits may also be used to facilitate expression and purification of fusion proteins.

In another embodiment, synthesis of radiolabeled PMMM may be achieved ion vitro using the TNT rabbit reticulocyte lysate or wheat germ extract system (Promega). These systems couple transcription and translation of protein-coding sequences operably associated with the T7, T3, or SP6 promoters. Translation takes place in the presence of a radiolabeled amino acid precursor, for example, 35S-methionine.

PMMM, fragments of PMMM, or variants of PMMM may be used to screen for compounds that specifically bind to PMMM. One or more test compounds may be screened for specific binding to PMMM. In various embodiments, 1,2, 3,4, 5,10, 20,50, 100, or 200 test compounds can be screened for specific binding to PMMM. Examples of test compounds can include antibodies, anticalins, oligonucleotides, proteins (e. g. , ligands or receptors), or small molecules.

In related embodiments, variants of PMMM can be used to screen for binding of test compounds, such as antibodies, to PMMM, a variant of PMMM, or a combination of PMMM and/or one or more variants PMMM. In an embodiment, a variant of PMMM can be used to screen for

compounds that bind to a variant of PMMM, but riot to PMMM having the exact sequence of a sequence of SEQ ID NO : 1-62. PMMM variants used to perform such screening can have a range of about 50% to about 99% sequence identity to PMMM, with various embodiments having 60%, 70%, 75%, 80%, 85%, 90%, and 95% sequence identity.

In an embodiment, a compound identified in a screen for specific binding to PMMM can be <BR> <BR> closely related to the natural ligand of PMMM, e. g. , a ligand or fragment thereof, a natural substrate, a structural or functional mimetic, or a natural binding partner (Coligan, J. E. et al. (1991) Current Protocols in Immunology 1 (2): Chapter 5). In another embodiment, the compound thus identified can be a natural ligand of a receptor PMMM (Howard, A. D. et al. (2001) Trends Pharmacol. Sci. 22: 132- 140; Wise, A. et al. (2002) Drug Discovery Today 7: 235-246).

In other embodiments, a compound identified in a screen for specific binding to PMMM can be closely related to the natural receptor to which PMMM binds, at least a fragment of the receptor, or a fragment of the receptor including all or a portion of the ligand binding site or binding pocket. For example, the compound may be a receptor for PMMM which is capable of propagating a signal, or a decoy receptor for PMMM which is not capable of propagating a signal (Ashkenazi, A. and V. M.

Divit (1999) Curr. Opin. Cell Biol. 11: 255-260; Mantovani, A. et al. (2001) Trends Immunol. 22: 328- 336). The compound can be rationally designed using known techniques. Examples of such techniques include those used to construct the compound etanercept (ENBREL; Amgen Inc., Thousand Oaks CA), which is efficacious for treating rheumatoid arthritis in humans. Etanercept is an engineered p75 tumor necrosis factor (TNF) receptor dimer linked to the Pc portion of human IgG (Taylor, P. C. et al. (2001) Curr. Opin. Immunol. 13: 611-616).

In, one embodiment, two or more antibodies having similar or, alternatively, different specificities can be screened for specific binding to PMMM, fragments of PMMM, or variants of PMMM. The binding specificity of the antibodies thus screened can thereby be selected to identify particular fragments or variants of PMMM. In one embodiment, an antibody can be selected such that its binding specificity allows for preferential identification of specific fragments or variants of PMMM. In another embodiment, an antibody can be selected such that its binding specificity allows for preferential diagnosis of a specific disease or condition having increased, decreased, or otherwise abnormal production of PMMM.

In an embodiment, anticalins can be screened for specific binding to PMMM, fragments of PMMM, or variants of PMMM. Anticalins are ligand-binding proteins that have been constructed based on a lipocalin scaffold (Weiss, G. A. and H. B. Lowman (2000) Chem. Biol. 7: R177-R184 ; Skerra, A. (2001) J. Biotechnol. 74: 257-275). The protein architecture of lipocalins can include a

beta-barrel having eight antiparallel beta-strands, which supports four loops at its open end. These loops form the natural ligand-binding site of the lipocalins, a site which can be re-engineered iii vitro by amino acid substitutions to impart novel binding specificities. The amino acid substitutions can be made using methods known in the art or described herein, and can include conservative substitutions (e. g. , substitutions that do not alter binding specificity) or substitutions that modestly, moderately, or significantly alter binding specificity.

In one embodiment, screening for compounds which specifically bind to, stimulate, or inhibit PMMM involves producing appropriate cells which express PMMM, either as a secreted protein or on the cell membrane. Preferred cells can include cells from mammals, yeast, Drosop1zila, or E. coli.

Cells expressing PMMM or cell membrane fractions which contain PMMM are then contacted with a test compound and binding, stimulation, or inhibition of activity of either PMMM or the compound is analyzed.

An assay may simply test binding of a test compound to the polypeptide, wherein binding is detected by a fluorophore, radioisotope, enzyme conjugate, or other detectable label. For example, the assay may comprise the steps of combining at least one test compound with PMMM, either in solution or affixed to a solid support, and detecting the binding of PMMM to the compound. Alternatively, the assay may detect or measure binding of a test compound in the presence of a labeled competitor.

Additionally, the assay may be carried out using cell-free preparations, chemical libraries, or natural. product mixtures, and the test compound (s) may be free in solution or affixed to a solid support.

An assay can be used to assess the ability of a compound to bind to its natural ligand and/or to inhibit the binding of its natural ligand to its natural receptors. Examples of such assays include radio- labeling assays such as those described in U. S. Patent No. 5,914, 236 and U. S. Patent No. 6,372, 724.

In a related embodiment, one or more amino acid substitutions can be introduced into a polypeptide compound (such as a receptor) to improve or alter its ability to bind to its natural ligands (Matthews, D. J. and J. A. Wells. (1994) Chem. Biol. 1: 25-30). In another related embodiment, one or more amino acid substitutions can be introduced into a polypeptide compound (such as a ligand) to improve or alter its ability to bind to its natural receptors (Cunningham, B. C. and J. A. Wells (1991) Proc. Natl. Acad.

Sci. USA 88: 3407-3411; Lowman, H. B. et al. (1991) J. Biol. Chem. 266: 10982-10988).

PMMM, fragments of PMMM, or variants of PMMM may be used to screen for compounds that modulate the activity of PMMM. Such compounds may include agonists, antagonists, or partial or inverse agonists. In one embodiment, an assay is performed under conditions permissive for PMMM activity, wherein PMMM is combined with at least one test compound, and the activity of PMMM in the presence of a test compound is compared with the activity of PMMM in the absence of the test

compound. A change in the activity of PMMM in the presence of the test compound is indicative of a compound that modulates the activity of PMMM. Alternatively, a test compound is combined with an in vitro or cell-free system comprising PMMM under conditions suitable for PMMM activity, and the assay is performed. In either of these assays, a test compound which modulates the activity of PMMM may do so indirectly and need not come in direct contact with the test compound. At least one and up to a plurality of test compounds may be screened.

In another embodiment, polynucleotides encoding PMMM or their mammalian homologs may be"knocked out"in an animal model system using homologous recombination in embryonic stem (ES) cells. Such techniques are well known in the art and are useful for the generation of animal models of human disease (see, e. g. , U. S. Patent No. 5,175, 383 and U. S. Patent No. 5,767, 337). For example, mouse ES cells, such as the mouse 129/SvJ cell line, are derived from the early mouse embryo and grown in culture. The ES cells are transformed with a vector containing the gene of interest disrupted <BR> <BR> by a marker gene, e. g. , the neomycin phosphotransferase gene (neo; Capecchi, M. R. (1989) Science 244: 1288-1292). The vector integrates into the corresponding region of the host genome by homologous recombination. Alternatively, homologous recombination takes place using the Cre-loxP system to knockout a gene of interest in a tissue-or developmental stage-specific manner (Marth, J. D.

(1996) Clin. Invest. 97: 1999-2002; Wagner, K. U. et al. (1997) Nucleic Acids Res. 25: 4323-4330).

Transformed ES cells are identified and microinjected into mouse cell blastocysts such as those from the C57BL/6 mouse strain. The blastocysts are surgically transferred to pseudopregnant dams, and the resulting chimeric progeny are genotyped and bred to produce heterozygous or homozygous strains. Transgenic animals thus generated may be tested with potential therapeutic or toxic agents.

Polynucleotides encoding PMMM may also be manipulated in vitro in ES cells derived from human blastocysts. Human ES cells have the potential to differentiate into at least eight separate cell lineages including endoderm, mesoderm, and ectodermal cell types. These cell lineages differentiate into, for example, neural cells, hematopoietic lineages, and cardiomyocytes (Thomson, J. A. et al.

(1998) Science 282: 1145-1147).

Polynucleotides encoding PMMM can also be used to create"knockin"humanized animals (pigs) or transgenic animals (mice or rats) to model human disease. With knockin technology, a region of a polynucleotide encoding PMMM is injected into animal ES cells, and the injected sequence integrates into the animal cell genome. Transformed cells are injected into blastulae, and the blastulae are implanted as described above. Transgenic progeny or inbred lines are studied and treated with potential pharmaceutical agents to obtain information on treatment of a human disease. Alternatively,

a mammal inbred to overexpress PMMM, e. g. , by secreting PMMM in its milk, may also serve as a convenient source of that protein (Janne, J. et al. (1998) Biotechnol. Annu. Rev. 4: 55-74).

THERAPEUTICS Chemical and structural similarity, e. g. , in the context of sequences and motifs, exists between regions of PMMM and protein modification and maintenance molecules. In addition, examples of tissues expressing PMMM can be found in Table 6 and can also be found in Example XI. Therefore, PMMM appears to play a role in gastrointestinal, cardiovascular, autoimmune/inflammatory, cell proliferative, developmental, epithelial, neurological, and reproductive disorders. In the treatment of disorders associated with increased PMMM expression or activity, it is desirable to decrease the expression or activity of PMMM. In the treatment of disorders associated with decreased PMMM expression or activity, it is desirable to increase the expression or activity of PMMM.

Therefore, in one embodiment, PMMM or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of PMMM. Examples of such disorders include, but are not limited to, a gastrointestinal disorder, such as dysphagia, peptic esophagitis, esophageal spasm, esophageal stricture, esophageal carcinoma, dyspepsia, indigestion, gastritis, gastric carcinoma, anorexia, nausea, emesis, gastroparesis, antral or pyloric edema, abdominal angina, pyrosis, gastroenteritis, intestinal obstruction, infections of the intestinal tract, peptic ulcer, cholelithiasis, cholecystitis, cholestasis, pancreatitis, pancreatic carcinoma, biliary tract disease, hepatitis, hyperbilirubinemia, cirrhosis, passive congestion of the liver, hepatoma, infectious colitis, ulcerative colitis, ulcerative proctitis, Crohn's disease, Whipple's disease, Mallory-Weiss syndrome, colonic carcinoma, colonic obstruction, irritable bowel syndrome, short bowel syndrome, diarrhea, constipation, gastrointestinal hemorrhage, acquired immunodeficiency syndrome (AIDS) enteropathy, jaundice, hepatic encephalopathy, hepatorenal syndrome, hepatic steatosis, hemochromatosis, Wilson's disease, alphai-antitrypsin deficiency, Reye's syndrome, primary sclerosing cholangitis, liver infarction, portal vein obstruction and thrombosis, centrilobular necrosis, peliosis hepatis, hepatic vein thrombosis, veno-occlusive disease, preeclampsia, eclampsia, acute fatty liver of pregnancy, intrahepatic cholestasis of pregnancy, and hepatic tumors including nodular hyperplasias, adenomas, and carcinomas; a cardiovascular disorder, such as arteriovenous fistula, atherosclerosis, hypertension, vasculitis, Raynaud's disease, aneurysms, arterial dissections, varicose veins, thrombophlebitis and phlebothrombosis, vascular tumors, and complications of thrombolysis, balloon angioplasty, vascular replacement, and coronary artery bypass graft surgery, congestive heart failure, ischemic heart disease, angina pectoris, myocardial infarction, hypertensive heart disease, degenerative valvular heart disease, calcific aortic valve stenosis, congenitally bicuspid aortic valve,

mitral annular calcification, mitral valve prolapse, rheumatic fever and rheumatic heart disease, infective endocarditis, nonbacterial thrombotic endocarditis, endocarditis of systemic lupus erythematosus, carcinoid heart disease, cardiomyopathy, myocarditis, pericarditis, neoplastic heart disease, congenital heart disease, and complications of cardiac transplantation; an autoimmune/inflammatory disease, such as acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, atherosclerotic plaque rupture, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyendocrinopathy-candidiasis-ectodermal dystrophy (APECED), bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves'disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, degradation of articular cartilage, osteoporosis, pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma; a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphoma, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, colon, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; a developmental disorder, such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, bone resorption, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms'tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida, anencephaly, craniorachischisis, congenital glaucoma, cataract, age-related macular degeneration, and sensorineural hearing loss; an epithelial disorder, such as dyshidrotic eczema, allergic contact dermatitis, keratosis pilaris, melasma, vitiligo, actinic keratosis, basal cell carcinoma, squamous cell

carcinoma, seborrheic keratosis, folliculitis, herpes simplex, herpes zoster, varicella, candidiasis, dermatophytosis, scabies, insect bites, cherry angioma, keloid, dermatofibroma, acrochordons, urticaria, transient acantholytic dermatosis, xerosis, eczema, atopic dermatitis, contact dermatitis, hand eczema, nummular eczema, lichen simplex chronicus, asteatotic eczema, stasis dermatitis and stasis ulceration, seborrheic dermatitis, psoriasis, lichen planus, pityriasis rosea, impetigo, ecthyma, dermatophytosis, tinea versicolor, warts, acne vulgaris, acne rosacea, pemphigus vulgaris, pemphigus foliaceus, paraneoplastic pemphigus, bullous pemphigoid, herpes gestationis, dermatitis herpetiformis, linear IgA disease, epidermolysis bullosa acquisita, dermatomyositis, lupus erythematosus, scleroderma and morphea, erythroderma, alopecia, figurate skin lesions, telangiectasias, hypopigmentation, hyperpigmentation, vesicles/bullae, exanthems, cutaneous drug reactions, papulonodular skin lesions, chronic non-healing wounds, photosensitivity diseases, epidermolysis bullosa simplex, epidermolytic hyperkeratosis, epidermolytic and nonepidermolytic palmoplantar keratoderma, ichthyosis bullosa of Siemens, ichthyosis exfoliativa, keratosis palmaris et plantaris, keratosis palmoplantaris, palmoplantar keratoderma, keratosis punctata, Meesmann's corneal dystrophy, pachyonychia congenita, white sponge nevus, steatocystoma multiplex, epidermal nevi/epidermolytic hyperkeratosis type, monilethrix, trichothiodystrophy, chronic hepatitis/cryptogenic cirrhosis, and colorectal hyperplasia; a neurological disorder, such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorders of the central nervous system including Down syndrome, cerebral palsy, neuroskeletal disorders, autonomic nervous system disorders, cranial nerve disorders, spinal cord diseases, muscular dystrophy and other neuromuscular disorders, peripheral nervous system disorders, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathies, myasthenia gravis, periodic paralysis, mental disorders including mood, anxiety, and schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, Tourette's disorder, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal

dementia; and a reproductive disorder, such as infertility, including tubal disease, ovulatory defects, and endometriosis, a disorder of prolactin production, a disruption of the estrous cycle, a disruption of the menstrual cycle, polycystic ovary syndrome, ovarian hyperstimulation syndrome, an endometrial or ovarian tumor, a uterine fibroid, autoimmune disorders, an ectopic pregnancy, and teratogenesis; cancer of the breast, fibrocystic breast disease, and galactorrhea; a disruption of spennatogenesis, abnormal sperm physiology, cancer of the testis, cancer of the prostate, benign prostatic hyperplasia, prostatitis, Peyronie's disease, impotence, carcinoma of the male breast, and gynecomastia.

In another embodiment, a vector capable of expressing PMMM or a fragment or derivative thereof may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of PMMM including, but not limited to, those described above.

In a further embodiment, a composition comprising a substantially purified PMMM in conjunction with a suitable pharmaceutical carrier may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of PMMM including, but not limited to, those provided above.

In still another embodiment, an agonist which modulates the activity of PMMM may be administered to a subject to treat or prevent a disorder associated with decreased expression or activity of PMMM including, but not limited to, those listed above.

In a further embodiment, an antagonist of PMMM may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of PMMM. Examples of such disorders include, but are not limited to, those gastrointestinal, cardiovascular, autoimmune/inflammatory, cell proliferative, developmental, epithelial, neurological, and reproductive disorders described above. In one aspect, an antibody which specifically binds PMMM may be used directly as an antagonist or indirectly as a targeting or delivery mechanism for bringing a pharmaceutical agent to cells or tissues which express PMMM.

In an additional embodiment, a vector expressing the complement of the polynucleotide encoding PMMM may be administered to a subject to treat or prevent a disorder associated with increased expression or activity of PMMM including, but not limited to, those described above.

In other embodiments, any protein, agonist, antagonist, antibody, complementary sequence, or vector embodiments may be administered in combination with other appropriate therapeutic agents.

Selection of the appropriate agents for use in combination therapy may be made by one of ordinary skill in the art, according to conventional pharmaceutical principles. The combination of therapeutic agents may act synergistically to effect the treatment or prevention of the various disorders described

above. Using this approach, one may be able to achieve therapeutic efficacy with lower dosages of each agent, thus reducing the potential for adverse side effects.

An antagonist of PMMM may be produced using methods which are generally known in the art. In particular, purified PMMM may be used to produce antibodies or to screen libraries of pharmaceutical agents to identify those which specifically bind PMMM. Antibodies to PMMM may also be generated using methods that are well known in the art. Such antibodies may include, but are not limited to, polyclonal, monoclonal, chimeric, and single chain antibodies, Fab fragments, and <BR> <BR> fragments produced by a Fab expression library. In an embodiment, neutralizing antibodies (i. e. , those<BR> which inhibit dimer formation) can be used therapeutically. Single chain antibodies (e. g. , from camels or llamas) may be potent enzyme inhibitors and may have application in the design of peptide mimics, and in the development of immuno-adsorbents and biosensors (Muyldermans, S. (2001) J. Biotechnol.

74: 277-302).

For the production of antibodies, various hosts including goats, rabbits, rats, mice, camels, dromedaries, llamas, humans, and others may be immunized by injection with PMMM or with any fragment or oligopeptide thereof which has immunogenic properties. Depending on the host species, various adjuvants may be used to increase immunological response. Such adjuvants include, but are not limited to, Freund's, mineral gels such as aluminum hydroxide, and surface active substances such as lysolecithin, pluronic polyols, polyanions, peptides, oil emulsions, KLH, and dinitrophenol. Among adjuvants used in humans, BCG (bacilli Calmette-Guerin) and Corynebacteriumpamum are especially preferable.

It is preferred that the oligopeptides, peptides, or fragments used to induce antibodies to PMMM have an amino acid sequence consisting of at least about 5 amino acids, and generally will consist of at least about 10 amino acids. It is also preferable that these oligopeptides, peptides, or fragments are substantially identical to a portion of the amino acid sequence of the natural protein.

Short stretches of PMMM amino acids may be fused with those of another protein, such as KLH, and antibodies to the chimeric molecule may be produced.

Monoclonal antibodies to PMMM may be prepared using any technique which provides for the production of antibody molecules by continuous cell lines in culture. These include, but are not limited to, the hybridoma technique, the human B-cell hybridoma technique, and the EBV-hybridoma technique (Kohler, G. et al. (1975) Nature 256: 495-497; Kozbor, D. et al. (1985) J. Immunol. Methods 81: 31-42; Cote, R. J. et al. (1983) Proc. Natl. Acad. Sci. USA 80 : 2026-2030; Cole, S. P. et al. (1984) Mol. Cell Biol. 62: 109-120).

In addition, techniques developed for the production of"chimeric antibodies, "such as the splicing of mouse antibody genes to human antibody genes to obtain a molecule with appropriate antigen specificity and biological activity, can be used (Morrison, S. L. et al. (1984) Proc. Natl. Acad.

Sci. USA 81: 6851-6855; Neuberger, M. S. et al. (1984) Nature 312: 604-608; Takeda, S. et al. (1985) Nature 314: 452-454). Alternatively, techniques described for the production of single chain antibodies may be adapted, using methods known in the art, to produce PMMM-specific single chain antibodies.

Antibodies with related specificity, but of distinct idiotypic composition, may be generated by chain shuffling from random combinatorial immunoglobulin libraries (Burton, D. R. (1991) Proc. Natl. Acad.

Sci. USA 88: 10134-10137).

Antibodies may also be produced by inducing ire vivo production in the lymphocyte population or by screening immunoglobulin libraries or panels of highly specific binding reagents as disclosed in the literature (Orlandi, R. et al. (1989) Proc. Natl. Acad. Sci. USA 86: 3833-3837; Winter, G. et al.

(1991) Nature 349: 293-299).

Antibody fragments which contain specific binding sites for PMMM may also be generated.

For example, such fragments include, but are not limited to, F (ab') 2 fragments produced by pepsin digestion of the antibody molecule and Fab fragments generated by reducing the disulfide bridges of the F (ab') 2 fragments. Alternatively, Fab expression libraries may be constructed to allow rapid and easy identification of monoclonal Fab fragments with the desired specificity (Huse, W. D. et al. (1989) Science 246: 1275-1281).

Various immunoassays may be used for screening to identify antibodies having the desired specificity. Numerous protocols for competitive binding or immunoradiometric assays using either polyclonal or monoclonal antibodies with established specificities are well known in the art. Such immunoassays typically involve the measurement of complex formation between PMMM and its specific antibody. A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering PMMM epitopes is generally used, but a competitive binding assay may also be employed (Pound, supra).

Various methods such as Scatchard analysis in conjunction with radioimmunoassay techniques may be used to assess the affinity of antibodies for PMMM. Affinity is expressed as an association constant, Ka, which is defined as the molar concentration of PMMM-antibody complex divided by the molar concentrations of free antigen and free antibody under equilibrium conditions. The Ka determined for a preparation of polyclonal antibodies, which are heterogeneous in their affinities for multiple PMMM epitopes, represents the average affinity, or avidity, of the antibodies for PMMM.

The Ka determined for a preparation of monoclonal antibodies, which are monospecific for a particular

PMMM epitope, represents a true measure of affinity. High-affinity antibody preparations with Ka ranging from about 109 to 1012 L/mole are preferred for use in immunoassays in which the PMMM- antibody complex must withstand rigorous manipulations. Low-affinity antibody preparations with ranging from about 106 to 10'L/mole are preferred for use in immunopurification and similar procedures which ultimately require dissociation of PMMM, preferably in active form, from the antibody (Catty, D. (1988) Antibodies, Volume 1 : A Practical Approach. IRL Press, Washington DC; Liddell, J. E. and A. Cryer (1991) A Practical Guide to Monoclonal Antibodies. John Wiley & Sons, New York NY).

The titer and avidity of polyclonal antibody preparations may be further evaluated to determine the quality and suitability of such preparations for certain downstream applications. For example, a polyclonal antibody preparation containing at least 1-2 mg specific antibody/ml, preferably 5-10 mg specific antibody/ml, is generally employed in procedures requiring precipitation of PMMM-antibody complexes. Procedures for evaluating antibody specificity, titer, and avidity, and guidelines for antibody quality and usage in various applications, are generally available (Catty, supra ; Coligan et al., supra).

In another embodiment of the invention, polynucleotides encoding PMMM, or any fragment or complement thereof, may be used for therapeutic purposes. In one aspect, modifications of gene expression can be achieved by designing complementary sequences or antisense molecules (DNA, RNA, PNA, or modified oligonucleotides) to the coding or regulatory regions of the gene encoding PMMM. Such technology is well known in the art, and antisense oligonucleotides or larger fragments can be designed from various locations along the coding or control regions of sequences encoding PMMM (Agrawal, S. , ed. (1996) Antisense Therapeutics, Humana Press, Totawa NJ).

In therapeutic use, any gene delivery system suitable for introduction of the antisense sequences into appropriate target cells can be used. Antisense sequences can be delivered intracellularly in the form of an expression plasmid which, upon transcription, produces a sequence complementary to at least a portion of the cellular sequence encoding the target protein (Slater, J. E. et al. (1998) J. Allergy Clin. Immunol. 102 : 469-475; Scanlon, K. J. et al. (1995) FASEB J. 9: 1288-1296).

Antisense sequences can also be introduced intracellularly through the use of viral vectors, such as retrovirus and adeno-associated virus vectors (Miller, A. D. (1990) Blood 76: 271-278; Ausubel et al., supra ; Uckert, W. and W. Walther (1994) Pharmacol. Ther. 63: 323-347). Other gene delivery mechanisms include liposome-derived systems, artificial viral envelopes, and other systems known in the art (Rossi, J. J. (1995) Br. Med. Bull. 51: 217-225; Boado, R. J. et al. (1998) J. Pharm. Sci. 87: 1308- 1315 ; Morris, M. C. et al. (1997) Nucleic Acids Res. 25: 2730-2736).

In another embodiment of the invention, polynucleotides encoding PMMM may be used for somatic or germline gene therapy. Gene therapy may be performed to (i) correct a genetic deficiency (e. g. , in the cases of severe combined immunodeficiency (SCID)-X1 disease characterized by X- linked inheritance (Cavazzana-Calvo, M. et al. (2000) Science 288 : 669-672), severe combined immunodeficiency syndrome associated with an inherited adenosine deaminase (ADA) deficiency (Blaese, R. M. et al. (1995) Science 270: 475-480; Bordignon, C. et al. (1995) Science 270: 470-475), cystic fibrosis (Zabner, J. et al. (1993) Cell 75: 207-216; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6: 643-666; Crystal, R. G. et al. (1995) Hum. Gene Therapy 6 : 667-703), thalassamias, familial hypercholesterolemia, and hemophilia resulting from Factor VIII or Factor IX deficiencies (Crystal, <BR> <BR> R. G. (1995) Science 270: 404-410; Verma, I. M. and N. Somia (1997) Nature 389: 239-242) ), (ii)<BR> express a conditionally lethal gene product (e. g. , in the case of cancers which result from unregulated cell proliferation), or (iii) express a protein which affords protection against intracellular parasites (e. g., against human retroviruses, such as human immunodeficiency virus (HIV) (Baltimore, D. (1988) Nature 335 : 395-396 ; Poeschla, E. et al. (1996) Proc. Natl. Acad. Sci. USA 93 : 11395-11399), hepatitis B or C virus (HBV, HCV); fungal parasites, such as Candida albicans and Paracoccidioides brasilieflsis ; and protozoan parasites such as Plasmodiunz falciparunz and Trypanosoma cruzi). In the case where a genetic deficiency in PMMM expression or regulation causes disease, the expression of PMMM from an appropriate population of transduced cells may alleviate the clinical manifestations caused by the genetic deficiency.

In a further embodiment of the invention, diseases or disorders caused by deficiencies in PMMM are treated by constructing mammalian expression vectors encoding PMMM and introducing these vectors by mechanical means into PMMM-deficient cells. Mechanical transfer technologies for use with cells in vivo or ex vitro include (i) direct DNA microinjection into individual cells, (ii) ballistic gold particle delivery, (iii) liposome-mediated transfection, (iv) receptor-mediated gene transfer, and (v) the use of DNA transposons (Morgan, R. A. and W. F. Anderson (1993) Annu. Rev. Biochem.

62: 191-217; Ivics, Z. (1997) Cell 91: 501-510; Boulay, J. -L. and H. Récipon (1998) Curr. Opin.

Biotechnol. 9: 445-450).

Expression vectors that may be effective for the expression of PMMM include, but are not limited to, the PCDNA 3.1, EPITAG, PRCCMV2, PREP, PVAX, PCR2-TOPOTA vectors (Invitrogen, Carlsbad CA), PCMV-SCRIPT, PCMV-TAG, PEGSH/PERV (Stratagene, La Jolla CA), and PTET-OFF, PTET-ON, PTRE2, PTRE2-LUC, PTK-HYG (BD Clontech, Palo Alto CA).

PMMM may be expressed using (i) a constitutively active promoter, (e. g. , from cytomegalovirus (CMV), Rous sarcoma virus (RSV), SV40 virus, thymidine kinase (TK), or p-actin genes), (ii) an

inducible promoter (e. g. , the tetracycline-regulated promoter (Gossen, M. and H. Bujard (1992) Proc.

Natl. Acad. Sci. USA 89 : 5547-5551; Gossen, M. et al. (1995) Science 268: 1766-1769; Rossi, F. M. V. and H. M. Blau (1998) Curr. Opin. Biotechnol. 9: 451-456), commercially available in the T-REX plasmid (Invitrogen) ) ; the ecdysone-inducible promoter (available in the plasmids PVGRXR and PIND ; Invitrogen); the FK506/rapamycin inducible promoter; or the RU486/mifepristone inducible promoter (Rossi, F. M. V. and H. M. Blau, supra)), or (iii) a tissue-specific promoter or the native promoter of the endogenous gene encoding PMMM from a normal individual.

Commercially available liposome transformation kits (e. g. , the PERFECT LIPID TRANSFECTION KIT, available from Invitrogen) allow one with ordinary skill in the art to deliver polynucleotides to target cells in culture and require minimal effort to optimize experimental parameters. In the alternative, transformation is performed using the calcium phosphate method (Graham, P. L. and A. J. Eb (1973) Virology 52: 456-467), or by electroporation (Neumann, E. et al.

(1982) EMBO J. 1 : 841-845). The introduction of DNA to primary cells requires modification of these standardized mammalian transfection protocols.

In another embodiment of the invention, diseases or disorders caused by genetic defects with respect to PMMM expression are treated by constructing a retrovirus vector consisting of (i) the polynucleotide encoding PMMM under the control of an independent promoter or the retrovirus long terminal repeat (LTR) promoter, (ii) appropriate RNA packaging signals, and (iii) a Rev-responsive element (RRE) along with additional retrovirus cis-acting RNA sequences and coding sequences required for efficient vector propagation. Retrovirus vectors (e. g. , PFB and PFBNEO) are commercially available (Stratagene) and are based on published data (Riviere, I. et al. (1995) Proc.

Natl. Acad. Sci. USA 92: 6733-6737), incorporated by reference herein. The vector is propagated in an appropriate vector producing cell line (VPCL) that expresses an envelope gene with a tropism for receptors on the target cells or a promiscuous envelope protein such as VSVg (Armentano, D. et al.

(1987) J. Virol. 61: 1647-1650; Bender, M. A. et al. (1987) J. Virol. 61: 1639-1646; Adam, M. A. and A. D. Miller (1988) J. Virol. 62: 3802-3806; Dull, T. et al. (1998) J. Virol. 72: 8463-8471; Zufferey, R. et al. (1998) J. Virol. 72: 9873-9880). U. S. Patent No. 5,910, 434 to Rigg ("Method for obtaining retrovirus packaging cell lines producing high transducing efficiency retroviral supernatant") discloses a method for obtaining retrovirus packaging cell lines and is hereby incorporated by reference.

Propagation of retrovirus vectors, transduction of a population of cells (e. g., CD4+ T-cells), and the return of transduced cells to a patient are procedures well known to persons skilled in the art of gene therapy and have been well documented (Ranga, U. et al. (1997) J. Virol. 71: 7020-7029; Bauer, G. et

al. (1997) Blood 89: 2259-2267; Bonyhadi, M. L. (1997) J. Virol. 71: 4707-4716; Ranga, U. et al. (1998) Proc. Natl. Acad. Sci. USA 95: 1201-1206; Su, L. (1997) Blood 89: 2283-2290).

In an embodiment, an adenovirus-based gene therapy delivery system is used to deliver polynucleotides encoding PMMM to cells which have one or more genetic abnormalities with respect to the expression of PMMM. The construction and packaging of adenovirus-based vectors are well known to those with ordinary skill in the art. Replication defective adenovirus vectors have proven to be versatile for importing genes encoding immunoregulatory proteins into intact islets in the pancreas (Csete, M. E. et al. (1995) Transplantation 27: 263-268). Potentially useful adenoviral vectors are described in U. S. Patent No. 5,707, 618 to Armentano ("Adenovirus vectors for gene therapy"), hereby incorporated by reference. For adenoviral vectors, see also Antinozzi, P. A. et al. (1999; Annu.

Rev. Nutr. 19: 511-544) and Verma, I. M. and N. Somia (1997; Nature 18 : 389 : 239-242).

In another embodiment, a herpes-based, gene therapy delivery system is used to deliver polynucleotides encoding PMMM to target cells which have one or more genetic abnormalities with respect to the expression of PMMM. The use of herpes simplex virus (HSV) -based vectors may be especially valuable for introducing PMMM to cells of the central nervous system, for which HSV has a tropism. The construction and packaging of herpes-based vectors are well known to those with ordinary skill in the art. A replication-competent herpes simplex virus (HSV) type 1-based vector has been used to deliver a reporter gene to the eyes of primates (Liu, X. et al. (1999) Exp. Eye Res.

169: 385-395). The construction of a HSV-1 virus vector has also been disclosed in detail in U. S.

Patent No. 5,804, 413 to DeLuca ("Herpes simplex virus strains for gene transfer"), which is hereby incorporated by reference. U. S. Patent No. 5,804, 413 teaches the use of recombinant HSV d92 which consists of a genome containing at least one exogenous gene to be transferred to a cell under the control of the appropriate promoter for purposes including human gene therapy. Also taught by this patent are the construction and use of recombinant HSV strains deleted for ICP4, ICP27 and ICP22. For HSV vectors, see also Goins, W. F. et al. (1999; J. Virol. 73: 519-532) and Xu, H. et al.

(1994; Dev. Biol. 163: 152-161). The manipulation of cloned herpesvirus sequences, the generation of recombinant virus following the transfection of multiple plasmids containing different segments of the large herpesvirus genomes, the growth and propagation of herpesvirus, and the infection of cells with herpesvirus are techniques well known to those of ordinary skill in the art.

In another embodiment, an alphavirus (positive, single-stranded RNA virus) vector is used to deliver polynucleotides encoding PMMM to target cells. The biology of the prototypic alphavirus, Semliki Forest Virus (SPV), has been studied extensively and gene transfer vectors have been based on the SFV genome (Garoff, H. and K. -J. Li (1998) Curr. Opin. Biotechnol. 9: 464-469). During

alphavirus RNA replication, a subgenomic RNA is generated that normally encodes the viral capsid proteins. This subgenomic RNA replicates to higher levels than the full length genomic RNA, resulting in the overproduction of capsid proteins relative to the viral proteins with enzymatic activity (e. g., protease and polymerase). Similarly, inserting the coding sequence for PMMM into the alphavirus genome in place of the capsid-coding region results in the production of a large number of PMMM-coding RNAs and the synthesis of high levels of PMMM in vector transduced cells. While alphavirus infection is typically associated with cell lysis within a few days, the ability to establish a persistent infection in hamster normal kidney cells (BHK-21) with a variant of Sindbis virus (SIN) indicates that the lytic replication of alphaviruses can be altered to suit the needs of the gene therapy application (Dryga, S. A. et al. (1997) Virology 228: 74-83). The wide host range of alphaviruses will allow the introduction of PMMM into a variety of cell types. The specific transduction of a subset of cells in a population may require the sorting of cells prior to transduction. The methods of manipulating infectious cDNA clones of alphaviruses, performing alphavirus cDNA and RNA transfections, and performing alphavirus infections, are well known to those with ordinary skill in the art.

Oligonucleotides derived from the transcription initiation site, e. g. , between about positions-10 and +10 from the start site, may also be employed to inhibit gene expression. Similarly, inhibition can be achieved using triple helix base-pairing methodology. Triple helix pairing is useful because it causes inhibition of the ability of the double helix to open sufficiently for the binding of polymerases, transcription factors, or regulatory molecules. Recent therapeutic advances using triplex DNA have been described in the literature (Gee, J. E. et al. (1994) in Huber, B. E. and B. I. Carr, Molecular and InmunoloQic Approaches, Futura Publishing, Mt. Kisco NY, pp. 163-177). A complementary sequence or antisense molecule may also be designed to block translation of mRNA by preventing the transcript from binding to ribosomes.

Ribozymes, enzymatic RNA molecules, may also be used to catalyze the specific cleavage of RNA. The mechanism of ribozyme action involves sequence-specific hybridization of the ribozyme molecule to complementary target RNA, followed by endonucleolytic cleavage. For example, engineered hammerhead motif ribozyme molecules may specifically and efficiently catalyze endonucleolytic cleavage of RNA molecules encoding PMMM.

Specific ribozyme cleavage sites within any potential RNA target are initially identified by scanning the target molecule for ribozyme cleavage sites, including the following sequences: GUA, GUU, and GUC. Once identified, short RNA sequences of between 15 and 20 ribonucleotides, corresponding to the region of the target gene containing the cleavage site, may be evaluated for

secondary structural features which may render the oligonucleotide inoperable. The suitability of candidate targets may also be evaluated by testing accessibility to hybridization with complementary oligonucleotides using ribonuclease protection assays.

Complementary ribonucleic acid molecules and ribozymes may be prepared by any method known in the art for the synthesis of nucleic acid molecules. These include techniques for chemically synthesizing oligonucleotides such as solid phase phosphoramidite chemical synthesis. Alternatively, RNA molecules may be generated by in vitro and in vivo transcription of DNA molecules encoding PMMM. Such DNA sequences may be incorporated into a wide variety of vectors with suitable RNA polymerase promoters such as 17 or SP6. Alternatively, these cDNA constructs that synthesize complementary RNA, constitutively or inducibly, can be introduced into cell lines, cells, or tissues.

RNA molecules may be modified to increase intracellular stability and half-life. Possible modifications include, but are not limited to, the addition of flanking sequences at the 5'and/or 3'ends of the molecule, or the use of phosphorothioate or 2'O-methyl rather than phosphodiesterase linkages within the backbone of the molecule. This concept is inherent in the production of PNAs and can be extended in all of these molecules by the inclusion of nontraditional bases such as inosine, queosine, and wybutosine, as well as acetyl-, methyl-, thio-, and similarly modified forms of adenine, cytidine, guanine, thymine, and uridine which are not as easily recognized by endogenous endonucleases.

In other embodiments of the invention, the expression of one or more selected polynucleotides of the present invention can be altered, inhibited, decreased, or silenced using RNA interference (RNAi) or post-transcriptional gene silencing (PTGS) methods known in the art. RNAi is a post- transcriptional mode of gene silencing in which double-stranded RNA (dsRNA) introduced into a <BR> <BR> targeted cell specifically suppresses the expression of the homologous gene (i. e. , the gene bearing the sequence complementary to the dsRNA). This effectively knocks out or substantially reduces the expression of the targeted gene. PTGS can also be accomplished by use of DNA or DNA fragments as well. RNAi methods are described by Fire, A. et al. (1998; Nature 391: 806-811) and Gura, T.

(2000; Nature 404: 804-808). PTGS can also be initiated by introduction of a complementary segment of DNA into the selected tissue using gene delivery and/or viral vector delivery methods described herein or known in the art.

RNAi can be induced in mammalian cells by the use of small interfering RNA also known as siRNA. siRNA are shorter segments of dsRNA (typically about 21 to 23 nucleotides in length) that result in vivo from cleavage of introduced dsRNA by the action of an endogenous ribonuclease. siRNA appear to be the mediators of the RNAi effect in mammals. The most effective siRNAs

appear to be 21 nucleotide dsRNAs with 2 nucleotide 3'overhangs. The use of siRNA for inducing RNAi in mammalian cells is described by Elbashir, S. M. et al. (2001; Nature 411: 494-498). siRNA can be generated indirectly by introduction of dsRNA into the targeted cell.

Alternatively, siRNA can be synthesized directly and introduced into a cell by transfection methods and agents described herein or known in the art (such as liposome-mediated transfection, viral vector methods, or other polynucleotide delivery/introductory methods). Suitable siRNAs can be selected by examining a transcript of the target polynucleotide (e. g., mRNA) for nucleotide sequences downstream from the AUG start codon and recording the occurrence of each nucleotide and the 3' adjacent 19 to 23 nucleotides as potential siRNA target sites, with sequences having a 21 nucleotide length being preferred. Regions to be avoided for target siRNA sites include the 5'and 3'untranslated regions (UTRs) and regions near the start codon (within 75 bases), as these may be richer in regulatory protein binding sites. UTR-binding proteins and/or translation initiation complexes may interfere with binding of the siRNP endonuclease complex. The selected target sites for siRNA can then be compared to the appropriate genome database (e. g. , human, etc. ) using BLAST or other sequence comparison algorithms known in the art. Target sequences with significant homology to other coding sequences can be eliminated from consideration. The selected siRNAs can be produced by chemical synthesis methods known in the art or by in vitro transcription using commercially available methods and kits such as the SILENCER siRNA construction kit (Ambion, Austin TX).

In alternative embodiments, long-term gene silencing and/or RNAi effects can be induced in selected tissue using expression vectors that continuously express siRNA. This can be accomplished using expression vectors that are engineered to express hairpin RNAs (shRNAs) using methods <BR> <BR> known in the art (see, e. g. , Brummelkamp, T. R. et al. (2002) Science 296: 550-553; and Paddison, P. J. et al. (2002) Genes Dev. 16: 948-958). In these and related embodiments, shRNAs can be delivered to target cells using expression vectors known in the art. An example of a suitable expression vector for delivery of siRNA is the PSILENCER1. 0-U6 (circular) plasmid (Ambion). Once delivered to the target tissue, shRNAs are processed in vivo into siRNA-like molecules capable of carrying out gene- specific silencing.

In various embodiments, the expression levels of genes targeted by RNAi or PTGS methods can be determined by assays for mRNA and/or protein analysis. Expression levels of the mRNA of a targeted gene can be determined, for example, by northern analysis methods using the NORTHERNMAX-GLY kit (Ambion) ; by microarray methods; by PCR methods; by real time PCR methods; and by other RNA/polynucleotide assays known in the art or described herein. Expression levels of the protein encoded by the targeted gene can be determined, for example, by microarray

methods; by polyacrylamide gel electrophoresis; and by Western analysis using standard techniques known in the art.

An additional embodiment of the invention encompasses a method for screening for a compound which is effective in altering expression of a polynucleotide encoding PMMM. Compounds which may be effective in altering expression of a specific polynucleotide may include, but are not limited to, oligonucleotides, antisense oligonucleotides, triple helix-forming oligonucleotides, transcription factors and other polypeptide transcriptional regulators, and non-macromolecular chemical entities which are capable of interacting with specific polynucleotide sequences. Effective compounds may alter polynucleotide expression by acting as either inhibitors or promoters of polynucleotide expression. Thus, in the treatment of disorders associated with increased PMMM expression or activity, a compound which specifically inhibits expression of the polynucleotide encoding PMMM may be therapeutically useful, and in the treatment of disorders associated with decreased PMMM expression or activity, a compound which specifically promotes expression of the polynucleotide encoding PMMM may be therapeutically useful.

In various embodiments, one or more test compounds may be screened for effectiveness in altering expression of a specific polynucleotide. A test compound may be obtained by any method commonly known in the art, including chemical modification of a compound known to be effective in altering polynucleotide expression; selection from an existing, commercially-available or proprietary library of naturally-occurring or non-natural chemical compounds; rational design of a compound based on chemical and/or structural properties of the target polynucleotide; and selection from a library of chemical compounds created combinatorially or randomly. A sample comprising a polynucleotide encoding PMMM is exposed to at least one test compound thus obtained. The sample may comprise, for example, an intact or permeabilized cell, or an in vitro cell-free or reconstituted biochemical system. Alterations in the expression of a polynucleotide encoding PMMM are assayed by any method commonly known in the art. Typically, the expression of a specific nucleotide is detected by hybridization with a probe having a nucleotide sequence complementary to the sequence of the polynucleotide encoding PMMM. The amount of hybridization may be quantified, thus forming the basis for a comparison of the expression of the polynucleotide both with and without exposure to one or more test compounds. Detection of a change in the expression of a polynucleotide exposed to a test compound indicates that the test compound is effective in altering the expression of the polynucleotide. A screen for a compound effective in altering expression of a specific polynucleotide can be carried out, for example, using a Schizosaccharootizyces pombe gene expression system (Atkins, D. et al. (1999) U. S. Patent No. 5,932, 435; Arndt, G. M. et al. (2000) Nucleic Acids Res.

28: E15) or a human cell line such as HeLa cell (Clarke, M. L. et al. (2000) Biochem. Biophys. Res.

Commun. 268: 8-13). A particular embodiment of the present invention involves screening a combinatorial library of oligonucleotides (such as deoxyribonucleotides, ribonucleotides, peptide nucleic acids, and modified oligonucleotides) for antisense activity against a specific polynucleotide sequence (Bruice, T. W. et al. (1997) U. S. Patent No. 5,686, 242; Bruice, T. W. et al. (2000) U. S. Patent No.

6,022, 691).

Many methods for introducing vectors into cells or tissues are available and equally suitable for use in vivo, in vitro, and ex vivo. For ex vivo therapy, vectors may be introduced into stem cells taken from the patient and clonally propagated for autologous transplant back into that same patient.

Delivery by transfection, by liposome injections, or by polycationic amino polymers may be achieved using methods which are well known in the art (Goldman, C. K. et al. (1997) Nat. Biotechnol. 15: 462- 466).

Any of the therapeutic methods described above may be applied to any subject in need of such therapy, including, for example, mammals such as humans, dogs, cats, cows, horses, rabbits, and monkeys.

An additional embodiment of the invention relates to the administration of a composition which generally comprises an active ingredient formulated with a pharmaceutically acceptable excipient.

Excipients may include, for example, sugars, starches, celluloses, gums, and proteins. Various formulations are commonly known and are thoroughly discussed in the latest edition of Remington's Pharmaceutical Sciences (Maack Publishing, Easton PA). Such compositions may consist of PMMM, antibodies to PMMM, and mimics, agonists, antagonists, or inhibitors of PMMM.

In various embodiments, the compositions described herein, such as pharmaceutical compositions, may be administered by any number of routes including, but not limited to, oral, intravenous, intramuscular, intra-arterial, intramedullary, intrathecal, intraventricular, pulmonary, transdermal, subcutaneous, intraperitoneal, intranasal, enteral, topical, sublingual, or rectal means.

Compositions for pulmonary administration may be prepared in liquid or dry powder form.

These compositions are generally aerosolized immediately prior to inhalation by the patient. In the case of small molecules (e. g. traditional low molecular weight organic drugs), aerosol delivery of fast- acting formulations is well-known in the art. In the case of macromolecules (e. g. larger peptides and proteins), recent developments in the field of pulmonary delivery via the alveolar region of the lung <BR> <BR> have enabled the practical delivery of drugs such as insulin to blood circulation (see, e. g. , Patton, J. S.<BR> et al. , U. S. Patent No. 5,997, 848). Pulmonary delivery allows administration without needle injection, and obviates the need for potentially toxic penetration enhancers.

Compositions suitable for use in the invention include compositions wherein the active ingredients are contained in an effective amount to achieve the intended purpose. The determination of an effective dose is well within the capability of those skilled in the art.

Specialized forms of compositions may be prepared for direct intracellular delivery of macromolecules comprising PMMM or fragments thereof. For example, liposome preparations containing a cell-impermeable macromolecule may promote cell fusion and intracellular delivery of the macromolecule. Alternatively, PMMM or a fragment thereof may be joined to a short cationic N- terminal portion from the HIV Tat-1 protein. Fusion proteins thus generated have been found to transduce into the cells of all tissues, including the brain, in a mouse model system (Schwarze, S. R. et al. (1999) Science 285: 1569-1572).

For any compound, the therapeutically effective dose can be estimated initially either in cell culture assays, e. g., of neoplastic cells, or in animal models such as mice, rats, rabbits, dogs, monkeys, or pigs. An animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.

A therapeutically effective dose refers to that amount of active ingredient, for example PMMM or fragments thereof, antibodies of PMMM, and agonists, antagonists or inhibitors of PMMM, which ameliorates the symptoms or condition. Therapeutic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or with experimental animals, such as by calculating the ED50 (the dose therapeutically effective in 50% of the population) or LDso (the dose lethal to 50% of the population) statistics. The dose ratio of toxic to therapeutic effects is the therapeutic index, which can be expressed as the LD50 ED50 ratio. Compositions which exhibit large therapeutic indices are preferred. The data obtained from cell culture assays and animal studies are used to formulate a range of dosage for human use. The dosage contained in such compositions is preferably within a range of circulating concentrations that includes the EDso with little or no toxicity.

The dosage varies within this range depending upon the dosage form employed, the sensitivity of the patient, and the route of administration.

The exact dosage will be determined by the practitioner, in light of factors related to the subject requiring treatment. Dosage and administration are adjusted to provide sufficient levels of the active moiety or to maintain the desired effect. Factors which may be taken into account include the severity of the disease state, the general health of the subject, the age, weight, and gender of the subject, time and frequency of administration, drug combination (s), reaction sensitivities, and response

to therapy. Long-acting compositions may be administered every 3 to 4 days, every week, or biweekly depending on the half-life and clearance rate of the particular formulation.

Normal dosage amounts may vary from about 0. 1 mg to 100, 000, ug, up to a total dose of about 1 gram, depending upon the route of administration. Guidance as to particular dosages and methods of delivery is provided in the literature and generally available to practitioners in the art.

Those skilled in the art will employ different formulations for nucleotides than for proteins or their inhibitors. Similarly, delivery of polynucleotides or polypeptides will be specific to particular cells, conditions, locations, etc.

DIAGNOSTICS In another embodiment, antibodies which specifically bind PMMM may be used for the diagnosis of disorders characterized by expression of PMMM, or in assays to monitor patients being treated with PMMM or agonists, antagonists, or inhibitors of PMMM. Antibodies useful for diagnostic purposes may be prepared in the same manner as described above for therapeutics. Diagnostic assays for PMMM include methods which utilize the antibody and a label to detect PMMM in human body fluids or in extracts of cells or tissues. The antibodies may be used with or without modification, and may be labeled by covalent or non-covalent attachment of a reporter molecule. A wide variety of reporter molecules, several of which are described above, are known in the art and may be used.

A variety of protocols for measuring PMMM, including ELISAs, RIAs, and FACS, are known in the art and provide a basis for diagnosing altered or abnormal levels of PMMM expression. Normal or standard values for PMMM expression are established by combining body fluids or cell extracts taken from normal mammalian subjects, for example, human subjects, with antibodies to PMMM under conditions suitable for complex formation. The amount of standard complex formation may be quantitated by various methods, such as photometric means. Quantities of PMMM expressed in subject, control, and disease samples from biopsied tissues are compared with the standard values.

Deviation between standard and subject values establishes the parameters for diagnosing disease.

In another embodiment of the invention, polynucleotides encoding PMMM may be used for diagnostic purposes. The polynucleotides which may be used include oligonucleotides, complementary RNA and DNA molecules, and PNAs. The polynucleotides may be used to detect and quantify gene expression in biopsied tissues in which expression of PMMM may be correlated with disease. The diagnostic assay may be used to determine absence, presence, and excess expression of PMMM, and to monitor regulation of PMMM levels during therapeutic intervention.

In one aspect, hybridization with PCR probes which are capable of detecting polynucleotides, including genomic sequences, encoding PMMM or closely related molecules may be used to identify

nucleic acid sequences which encode PMMM. The specificity of the probe, whether it is made from a highly specific region, e. g. , the 5'regulatory region, or from a less specific region, e. g. , a conserved motif, and the stringency of the hybridization or amplification will determine whether the probe identifies only naturally occurring sequences encoding PMMM, allelic variants, or related sequences.

Probes may also be used for the detection of related sequences, and may have at least 50% sequence identity to any of the PMMM encoding sequences. The hybridization probes of the subject invention may be DNA or RNA and may be derived from the sequence of SEQ ID NO : 63-124 or from genomic sequences including promoters, enhancers, and introns of the PMMM gene.

Means for producing specific hybridization probes for polynucleotides encoding PMMM include the cloning of polynucleotides encoding PMMM or PMMM derivatives into vectors for the production of mRNA probes. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by means of the addition of the appropriate RNA polymerases and the appropriate labeled nucleotides. Hybridization probes may be labeled by a variety of reporter groups, for example, by radionuclides such as 32p or 35S, or by enzymatic labels, such as alkaline phosphatase coupled to the probe via avidin/biotin coupling systems, and the like.

Polynucleotides encoding PMMM may be used for the diagnosis of disorders associated with expression of PMMM. Examples of such disorders include, but are not limited to, a gastrointestinal disorder, such as dysphagia, peptic esophagitis, esophageal spasm, esophageal stricture, esophageal carcinoma, dyspepsia, indigestion, gastritis, gastric carcinoma, anorexia, nausea, emesis, gastroparesis, antral or pyloric edema, abdominal angina, pyrosis, gastroenteritis, intestinal obstruction, infections of the intestinal tract, peptic ulcer, cholelithiasis, cholecystitis, cholestasis, pancreatitis, pancreatic carcinoma, biliary tract disease, hepatitis, hyperbilirubinemia, cirrhosis, passive congestion of the liver, hepatoma, infectious colitis, ulcerative colitis, ulcerative proctitis, Crohn's disease, Whipple's disease, Mallory-Weiss syndrome, colonic carcinoma, colonic obstruction, irritable bowel syndrome, short bowel syndrome, diarrhea, constipation, gastrointestinal hemorrhage, acquired immunodeficiency syndrome (AIDS) enteropathy, jaundice, hepatic encephalopathy, hepatorenal syndrome, hepatic steatosis, hemochromatosis, Wilson's disease, alphal-antitrypsin deficiency, Reye's syndrome, primary sclerosing cholangitis, liver infarction, portal vein obstruction and thrombosis, centrilobular necrosis, peliosis hepatis, hepatic vein thrombosis, veno-occlusive disease, preeclampsia, eclampsia, acute fatty liver of pregnancy, intrahepatic cholestasis of pregnancy, and hepatic tumors including nodular hyperplasias, adenomas, and carcinomas; a cardiovascular disorder, such as arteriovenous fistula, atherosclerosis, hypertension, vasculitis, Raynaud's disease, aneurysms, arterial dissections, varicose veins, thrombophlebitis and phlebothrombosis, vascular tumors, and complications of thrombolysis,

balloon angioplasty, vascular replacement, and coronary artery bypass graft surgery, congestive heart. failure, ischemic heart disease, angina pectoris, myocardial infarction, hypertensive heart disease, degenerative valvular heart disease, calcific aortic valve stenosis, congenitally bicuspid aortic valve, mitral annular calcification, mitral valve prolapse, rheumatic fever and rheumatic heart disease, infective endocarditis, nonbacterial thrombotic endocarditis, endocarditis of systemic lupus erythematosus, carcinoid heart disease, cardiomyopathy, myocarditis, pericarditis, neoplastic heart disease, congenital heart disease, and complications of cardiac transplantation; an autoimmune/inflammatory disease, such as acquired immunodeficiency syndrome (AIDS), Addison's disease, adult respiratory distress syndrome, allergies, ankylosing spondylitis, amyloidosis, anemia, asthma, atherosclerosis, atherosclerotic plaque rupture, autoimmune hemolytic anemia, autoimmune thyroiditis, autoimmune polyendocrinopathy-candidiasis-ectodennal dystrophy (APECED), bronchitis, cholecystitis, contact dermatitis, Crohn's disease, atopic dermatitis, dermatomyositis, diabetes mellitus, emphysema, episodic lymphopenia with lymphocytotoxins, erythroblastosis fetalis, erythema nodosum, atrophic gastritis, glomerulonephritis, Goodpasture's syndrome, gout, Graves'disease, Hashimoto's thyroiditis, hypereosinophilia, irritable bowel syndrome, multiple sclerosis, myasthenia gravis, myocardial or pericardial inflammation, osteoarthritis, degradation of articular cartilage, osteoporosis, pancreatitis, polymyositis, psoriasis, Reiter's syndrome, rheumatoid arthritis, scleroderma, Sjögren's syndrome, systemic anaphylaxis, systemic lupus erythematosus, systemic sclerosis, thrombocytopenic purpura, ulcerative colitis, uveitis, Werner syndrome, complications of cancer, hemodialysis, and extracorporeal circulation, viral, bacterial, fungal, parasitic, protozoal, and helminthic infections, and trauma; a cell proliferative disorder such as actinic keratosis, arteriosclerosis, atherosclerosis, bursitis, cirrhosis, hepatitis, mixed connective tissue disease (MCTD), myelofibrosis, paroxysmal nocturnal hemoglobinuria, polycythemia vera, psoriasis, primary thrombocythemia, and cancers including adenocarcinoma, leukemia, lymphom, melanoma, myeloma, sarcoma, teratocarcinoma, and, in particular, cancers of the adrenal gland, bladder, bone, bone marrow, brain, breast, cervix, colon, gall bladder, ganglia, gastrointestinal tract, heart, kidney, liver, lung, muscle, ovary, pancreas, parathyroid, penis, prostate, salivary glands, skin, spleen, testis, thymus, thyroid, and uterus; a developmental disorder, such as renal tubular acidosis, anemia, Cushing's syndrome, achondroplastic dwarfism, Duchenne and Becker muscular dystrophy, bone resorption, epilepsy, gonadal dysgenesis, WAGR syndrome (Wilms'tumor, aniridia, genitourinary abnormalities, and mental retardation), Smith-Magenis syndrome, myelodysplastic syndrome, hereditary mucoepithelial dysplasia, hereditary keratodermas, hereditary neuropathies such as Charcot-Marie-Tooth disease and neurofibromatosis, hypothyroidism, hydrocephalus, seizure disorders such as Syndenham's chorea and cerebral palsy, spina bifida,

anencephaly, craniorachischisis, congenital glaucoma, cataract, age-related macular degeneration, and sensorineural hearing loss; an epithelial disorder, such as dyshidrotic eczema, allergic contact dermatitis, keratosis pilaris, melasma, vitiligo, actinic keratosis, basal cell carcinoma, squamous cell carcinoma, seborrheic keratosis, folliculitis, herpes simplex, herpes zoster, varicella, candidiasis, dermatophytosis, scabies, insect bites, cherry angioma, keloid, dermatofibroma, acrochordons, urticaria, transient acantholytic dermatosis, xerosis, eczema, atopic dermatitis, contact dermatitis, hand eczema, nummular eczema, lichen simplex chronicus, asteatotic eczema, stasis dermatitis and stasis ulceration, seborrheic dermatitis, psoriasis, lichen planus, pityriasis rosea, impetigo, ecthyma, dermatophytosis, tinea versicolor, warts, acne vulgaris, acne rosacea, pemphigus vulgaris, pemphigus foliaceus, paraneoplastic pemphigus, bullous pemphigoid, herpes gestationis, dermatitis herpetiformis, linear IgA disease, epidermolysis bullosa acquisita, dermatomyositis, lupus erythematosus, scleroderma and morphea, erythroderma, alopecia, figurate skin lesions, telangiectasias, hypopigmentation, hyperpigmentation, vesicles/bullae, exanthems, cutaneous drug reactions, papulonodular skin lesions, chronic non-healing wounds, photosensitivity diseases, epidermolysis bullosa simplex, epidermolytic hyperkeratosis, epidermolytic and nonepidermolytic palmoplantar keratoderma, ichthyosis bullosa of Siemens, ichthyosis exfoliativa, keratosis palmaris et plantaris, keratosis palmoplantaris, palmoplantar keratoderma, keratosis punctata, Meesmann's corneal dystrophy, pachyonychia congenita, white sponge nevus, steatocystoma multiplex, epidermal nevi/epidermolytic hyperkeratosis type, monilethrix, trichothiodystrophy, chronic hepatitis/cryptogenic cirrhosis, and colorectal hyperplasia ; a neurological disorder, such as epilepsy, ischemic cerebrovascular disease, stroke, cerebral neoplasms, Alzheimer's disease, Pick's disease, Huntington's disease, dementia, Parkinson's disease and other extrapyramidal disorders, amyotrophic lateral sclerosis and other motor neuron disorders, progressive neural muscular atrophy, retinitis pigmentosa, hereditary ataxias, multiple sclerosis and other demyelinating diseases, bacterial and viral meningitis, brain abscess, subdural empyema, epidural abscess, suppurative intracranial thrombophlebitis, myelitis and radiculitis, viral central nervous system disease, prion diseases including kuru, Creutzfeldt-Jakob disease, and Gerstmann-Straussler-Scheinker syndrome, fatal familial insomnia, nutritional and metabolic diseases of the nervous system, neurofibromatosis, tuberous sclerosis, cerebelloretinal hemangioblastomatosis, encephalotrigeminal syndrome, mental retardation and other developmental disorders of the central nervous system including Down syndrome, cerebral palsy, neuroskeletal disorders, autonomic nervous system disorders, cranial nerve disorders, spinal cord diseases, muscular dystrophy and other neuromuscular disorders, peripheral nervous system disorders, dermatomyositis and polymyositis, inherited, metabolic, endocrine, and toxic myopathies, myasthenia gravis, periodic paralysis, mental disorders including mood, anxiety, and

schizophrenic disorders, seasonal affective disorder (SAD), akathesia, amnesia, catatonia, diabetic neuropathy, tardive dyskinesia, dystonias, paranoid psychoses, postherpetic neuralgia, Tourette's disorder, progressive supranuclear palsy, corticobasal degeneration, and familial frontotemporal dementia ; and a reproductive disorder, such as infertility, including tubal disease, ovulatory defects, and endometriosis, a disorder of prolactin production, a disruption of the estrous cycle, a disruption of the menstrual cycle, polycystic ovary syndrome, ovarian hyperstimulation syndrome, an endometrial or ovarian tumor, a uterine fibroid, autoimmune disorders, an ectopic pregnancy, and teratogenesis; cancer of the breast, fibrocystic breast disease, and galactorrhea; a disruption of spermatogenesis, abnormal sperm physiology, cancer of the testis, cancer of the prostate, benign prostatic hyperplasia, prostatitis, Peyronie's disease, impotence, carcinoma of the male breast, and gynecomastia.

Polynucleotides encoding PMMM may be used in Southern or northern analysis, dot blot, or other membrane-based technologies; in PCR technologies ; in dipstick, pin, and multiformat ELISA-like assays; and in microarrays utilizing fluids or tissues from patients to detect altered PMMM expression.

Such qualitative or quantitative methods are well known in the art.

In a particular embodiment, polynucleotides encoding PMMM may be used in assays that detect the presence of associated disorders, particularly those mentioned above. Polynucleotides complementary to sequences encoding PMMM may be labeled by standard methods and added to a fluid or tissue sample from a patient under conditions suitable for the formation of hybridization complexes. After a suitable incubation period, the sample is washed and the signal is quantified and compared with a standard value. If the amount of signal in the patient sample is significantly altered in comparison to a control sample then the presence of altered levels of polynucleotides encoding PMMM in the sample indicates the presence of the associated disorder. Such assays may also be used to evaluate the efficacy of a particular therapeutic treatment regimen in animal studies, in clinical trials, or to monitor the treatment of an individual patient.

In order to provide a basis for the diagnosis of a disorder associated with expression of PMMM, a normal or standard profile for expression is established. This may be accomplished by combining body fluids or cell extracts taken from normal subjects, either animal or human, with a sequence, or a fragment thereof, encoding PMMM, under conditions suitable for hybridization or amplification. Standard hybridization may be quantified by comparing the values obtained from normal subjects with values from an experiment in which a known amount of a substantially purified polynucleotide is used. Standard values obtained in this manner may be compared with values obtained from samples from patients who are symptomatic for a disorder. Deviation from standard values is used to establish the presence of a disorder.

Once the presence of a disorder is established and a treatment protocol is initiated, hybridization assays may be repeated on a regular basis to determine if the level of expression in the patient begins to approximate that which is observed in the normal subject. The results obtained from successive assays may be used to show the efficacy of treatment over a period ranging from several days to months.

With respect to cancer, the presence of an abnormal amount of transcript (either under-or overexpressed) in biopsied tissue from an individual may indicate a predisposition for the development of the disease, or may provide a means for detecting the disease prior to the appearance of actual clinical symptoms. A more definitive diagnosis of this type may allow health professionals to employ preventative measures or aggressive treatment earlier, thereby preventing the development or further progression of the cancer.

Additional diagnostic uses for oligonucleotides designed from the sequences encoding PMMM may involve the use of PCR. These oligomers may be chemically synthesized, generated enzymatically, or produced ion vitro. Oligomers will preferably contain a fragment of a polynucleotide encoding PMMM, or a fragment of a polynucleotide complementary to the polynucleotide encoding PMMM, and will be employed under optimized conditions for identification of a specific gene or condition. Oligomers may also be employed under less stringent conditions for detection or quantification of closely related DNA or RNA sequences.

In a particular aspect, oligonucleotide primers derived from polynucleotides encoding PMMM may be used to detect single nucleotide polymorphisms (SNPs). SNPs are substitutions, insertions and deletions that are a frequent cause of inherited or acquired genetic disease in humans. Methods of SNP detection include, but are not limited to, single-stranded conformation polymorphism (SSCP) and fluorescent SSCP (fSSCP) methods. In SSCP, oligonucleotide primers derived from polynucleotides encoding PMMM are used to amplify DNA using the polymerase chain reaction (PCR). The DNA may be derived, for example, from diseased or normal tissue, biopsy samples, bodily fluids, and the like. SNPs in the DNA cause differences in the secondary and tertiary structures of PCR products in single-stranded form, and these differences are detectable using gel electrophoresis in non-denaturing gels. In fSCCP, the oligonucleotide primers are fluorescently labeled, which allows detection of the amplimers in high-throughput equipment such as DNA sequencing machines. Additionally, sequence database analysis methods, termed in silico SNP (isSNP), are capable of identifying polymorphisms by comparing the sequence of individual overlapping DNA fragments which assemble into a common consensus sequence. These computer-based methods filter out sequence variations due to laboratory preparation of DNA and sequencing errors using statistical models and automated analyses of DNA

sequence chromatograms. In the alternative, SNPs may be detected and characterized by mass spectrometry using, for example, the high throughput MASSARRAY system (Sequenom, Inc. , San Diego CA).

SNPs may be used to study the genetic basis of human disease. For example, at least 16 common SNPs have been associated with non-insulin-dependent diabetes mellitus. SNPs are also useful for examining differences in disease outcomes in monogenic disorders, such as cystic fibrosis, sickle cell anemia, or chronic granulomatous disease. For example, variants in the mannose-binding lectin, MBL2, have been shown to be correlated with deleterious pulmonary outcomes in cystic fibrosis. SNPs also have utility in pharmacogenomics, the identification of genetic variants that influence a patient's response to a drug, such as life-threatening toxicity. For example, a variation in N-acetyl transferase is associated with a high incidence of peripheral neuropathy in response to the anti-tuberculosis drug isoniazid, while a variation in the core promoter of the ALOX5 gene results in diminished clinical response to treatment with an anti-asthma drug that targets the 5-lipoxygenase pathway. Analysis of the distribution of SNPs in different populations is useful for investigating genetic drift, mutation, recombination, and selection, as well as for tracing the origins of populations <BR> <BR> and their migrations (Taylor, J. G. et al. (2001) Trends Mol. Med. 7: 507-512; Kwok, P. -Y. and Z. Gu (1999) Mol. Med. Today 5: 538-543; Nowotny, P. et al. (2001) Curr. Opin. Neurobiol. 11: 637-641).

Methods which may also be used to quantify the expression of PMMM include radiolabeling or biotinylating nucleotides, coamplification of a control nucleic acid, and interpolating results from standard curves (Melby, P. C. et al. (1993) J. Immunol. Methods 159: 235-244; Duplaa, C. et al. (1993) Anal. Biochem. 212 : 229-236). The speed of quantitation of multiple samples may be accelerated by running the assay in a high-throughput format where the oligomer or polynucleotide of interest is presented in various dilutions and a spectrophotometric or colorimetric response gives rapid quantitation.

In further embodiments, oligonucleotides or longer fragments derived from any of the polynucleotides described herein may be used as elements on a microarray. The microarray can be used in transcript imaging techniques which monitor the relative expression levels of large numbers of genes simultaneously as described below. The microarray may also be used to identify genetic variants, mutations, and polymorphisms. This information may be used to determine gene function, to understand the genetic basis of a disorder, to diagnose a disorder, to monitor progression/regression of disease as a function of gene expression, and to develop and monitor the activities of therapeutic agents in the treatment of disease. In particular, this information may be used to develop a pharmacogenomic profile of a patient in order to select the most appropriate and effective treatment

regimen for that patient. For example, therapeutic agents which are highly effective and display the fewest side effects may be selected for a patient based on his/her pharmacogenomic profile.

In another embodiment, PMMM, fragments of PMMM, or antibodies specific for PMMM may be used as elements on a microarray. The microarray may be used to monitor or measure protein-protein interactions, drug-target interactions, and gene expression profiles, as described above.

A particular embodiment relates to the use of the polynucleotides of the present invention to generate a transcript image of a tissue or cell type. A transcript image represents the global pattern of gene expression by a particular tissue or cell type. Global gene expression patterns are analyzed by quantifying the number of expressed genes and their relative abundance under given conditions and at <BR> <BR> a given time (Seilhamer et al. ,"Comparative Gene Transcript Analysis, "U. S. Patent No. 5,840, 484; hereby expressly incorporated by reference herein). Thus a transcript image may be generated by hybridizing the polynucleotides of the present invention or their complements to the totality of transcripts or reverse transcripts of a particular tissue or cell type. In one embodiment, the hybridization takes place in high-throughput format, wherein the polynucleotides of the present invention or their complements comprise a subset of a plurality of elements on a microarray. The resultant transcript image would provide a profile of gene activity.

Transcript images may be generated using transcripts isolated from tissues, cell lines, biopsies, or other biological samples. The transcript image may thus reflect gene expression in vivo, as in the case of a tissue or biopsy sample, or in vitro, as in the case of a cell line.

Transcript images which profile the expression of the polynucleotides of the present invention may also be used in conjunction with in vitro model systems and preclinical evaluation of pharmaceuticals, as well as toxicological testing of industrial and naturally-occurring environmental compounds. All compounds induce characteristic gene expression patterns, frequently termed molecular fingerprints or toxicant signatures, which are indicative of mechanisms of action and toxicity (Nuwaysir, E. F. et al. (1999) Mol. Carcinog. 24: 153-159; Steiner, S. and N. L. Anderson (2000) Toxicol. Lett. 112-113: 467-471). If a test compound has a signature similar to that of a compound with known toxicity, it is likely to share those toxic properties. These fingerprints or signatures are most useful and refined when they contain expression information from a large number of genes and gene families. Ideally, a genome-wide measurement of expression provides the highest quality signature. Even genes whose expression is not altered by any tested compounds are important as well, as the levels of expression of these genes are used to normalize the rest of the expression data.

The normalization procedure is useful for comparison of expression data after treatment with different compounds. While the assignment of gene function to elements of a toxicant signature aids in

interpretation of toxicity mechanisms, knowledge of gene function is not necessary for the statistical matching of signatures which leads to prediction of toxicity (see, for example, Press Release 00-02 from the National Institute of Environmental Health Sciences, released February 29,2000, available at http://www. niehs. nih. gov/oc/news/toxchip. htm). Therefore, it is important and desirable in toxicological screening using toxicant signatures to include all expressed gene sequences.

In an embodiment, the toxicity of a test compound can be assessed by treating a biological sample containing nucleic acids with the test compound. Nucleic acids that are expressed in the treated biological sample are hybridized with one or more probes specific to the polynucleotides of the present invention, so that transcript levels corresponding to the polynucleotides of the present invention may be quantified. The transcript levels in the treated biological sample are compared with levels in an untreated biological sample. Differences in the transcript levels between the two samples are indicative of a toxic response caused by the test compound in the treated sample.

Another embodiment relates to the use of the polypeptides disclosed herein to analyze the proteome of a tissue or cell type. The term proteome refers to the global pattern of protein expression in a particular tissue or cell type. Each protein component of a proteome can be subjected individually to further analysis. Proteome expression patterns, or profiles, are analyzed by quantifying the number of expressed proteins and their relative abundance under given conditions and at a given time. A profile of a cell's proteome may thus be generated by separating and analyzing the polypeptides of a particular tissue or cell type. In one embodiment, the separation is achieved using two-dimensional gel electrophoresis, in which proteins from a sample are separated by isoelectric focusing in the first dimension, and then according to molecular weight by sodium dodecyl sulfate slab gel electrophoresis in the second dimension (Steiner and Anderson, supra). The proteins are visualized in the gel as discrete and uniquely positioned spots, typically by staining the gel with an agent such as Coomassie Blue or silver or fluorescent stains. The optical density of each protein spot is generally proportional to the level of the protein in the sample. The optical densities of equivalently positioned protein spots from different samples, for example, from biological samples either treated or untreated with a test compound or therapeutic agent, are compared to identify any changes in protein spot density related to the treatment. The proteins in the spots are partially sequenced using, for example, standard methods employing chemical or enzymatic cleavage followed by mass spectrometry. The identity of the protein in a spot may be determined by comparing its partial sequence, preferably of at least 5 contiguous amino acid residues, to the polypeptide sequences of interest. In some cases, further sequence data may be obtained for definitive protein identification.

A proteomic profile may also be generated using antibodies specific for PMMM to quantify the levels of PMMM expression. In one embodiment, the antibodies are used as elements on a microarray, and protein expression levels are quantified by contacting the microarray with the sample and detecting the levels of protein bound to each array element (Lueking, A. et al. (1999) Anal.

Biochem. 270: 103-111; Mendoze, L. G. et al. (1999) Biotechniques 27: 778-788). Detection may be performed by a variety of methods known in the art, for example, by reacting the proteins in the sample with a thiol-or amino-reactive fluorescent compound and detecting the amount of fluorescence bound at each array element.

Toxicant signatures at the proteome level are also useful for toxicological screening, and should be analyzed in parallel with toxicant signatures at the transcript level. There is a poor correlation between transcript and protein abundances for some proteins in some tissues (Anderson, N. L. and J. Seilhamer (1997) Electrophoresis 18: 533-537), so proteome toxicant signatures may be useful in the analysis of compounds which do not significantly affect the transcript image, but which alter the proteomic profile. In addition, the analysis of transcripts in body fluids is difficult, due to rapid degradation of mRNA, so proteomic profiling may be more reliable and informative in such cases.

In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins that are expressed in the treated biological sample are separated so that the amount of each protein can be quantified. The amount of each protein is compared to the amount of the corresponding protein in an untreated biological sample.

A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample. Individual proteins are identified by sequencing the amino acid residues of the individual proteins and comparing these partial sequences to the polypeptides of the present invention.

In another embodiment, the toxicity of a test compound is assessed by treating a biological sample containing proteins with the test compound. Proteins from the biological sample are incubated with antibodies specific to the polypeptides of the present invention. The amount of protein recognized by the antibodies is quantified. The amount of protein in the treated biological sample is compared with the amount in an untreated biological sample. A difference in the amount of protein between the two samples is indicative of a toxic response to the test compound in the treated sample.

Microarrays may be prepared, used, and analyzed using methods known in the art (Brennan, T. M. et al. (1995) U. S. Patent No. 5,474, 796; Schena, M. et al. (1996) Proc. Natl. Acad. Sci. USA 93: 10614-10619; Baldeschweiler et al. (1995) PCT application W095/25116 ; Shalon, D. et al. (1995) PCT application W095/35505; Heller, R. A. et al. (1997) Proc. Natl. Acad. Sci. USA 94: 2150-2155;

Heller, M. J. et al. (1997) U. S. Patent No. 5,605, 662). Various types of microarrays are well known <BR> <BR> and thoroughly described in Schena, M. , ed. (1999; DNA Microarrays : A Practical Approach, Oxford University Press, London).

In another embodiment of the invention, nucleic acid sequences encoding PMMM may be used to generate hybridization probes useful in mapping the naturally occurring genomic sequence.

Either coding or noncoding sequences may be used, and in some instances, noncoding sequences may be preferable over coding sequences. For example, conservation of a coding sequence among members of a multi-gene family may potentially cause undesired cross hybridization during chromosomal mapping. The sequences may be mapped to a particular chromosome, to a specific <BR> <BR> region of a chromosome, or to artificial chromosome constructions, e. g. , human artificial chromosomes (HACs), yeast artificial chromosomes (YACs), bacterial artificial chromosomes (BACs), bacterial PI constructions, or single chromosome cDNA libraries (Harrington, J. J. et al. (1997) Nat. Genet. 15: 345- 355; Price, C. M. (1993) Blood Rev. 7: 127-134; Trask, B. J. (1991) Trends Genet. 7: 149-154). Once mapped, the nucleic acid sequences may be used to develop genetic linkage maps, for example, which correlate the inheritance of a disease state with the inheritance of a particular chromosome region or restriction fragment length polymorphism (RFLP) (Lander, E. S. and D. Botstein (1986) Proc. Natl.

Acad. Sci. USA 83: 7353-7357).

Fluorescent in situ hybridization (FISH) may be correlated with other physical and genetic map data (Heinz-Ulrich, et al. (1995) in Meyers, supra, pp. 965-968). Examples of genetic map data can be found in various scientific journals or at the Online Mendelian Inheritance in Man (OMIM) World Wide Web site. Correlation between the location of the gene encoding PMMM on a physical map and a specific disorder, or a predisposition to a specific disorder, may help define the region of DNA associated with that disorder and thus may further positional cloning efforts.

In situ hybridization of chromosomal preparations and physical mapping techniques, such as linkage analysis using established chromosomal markers, may be used for extending genetic maps.

Often the placement of a gene on the chromosome of another mammalian species, such as mouse, may reveal associated markers even if the exact chromosomal locus is not known. This information is valuable to investigators searching for disease genes using positional cloning or other gene discovery techniques. Once the gene or genes responsible for a disease or syndrome have been crudely <BR> <BR> localized by genetic linkage to a particular genomic region, e. g. , ataxia-telangiectasia to llq22-23, any sequences mapping to that area may represent associated or regulatory genes for further investigation (Gatti, R. A. et al. (1988) Nature 336: 577-580). The nucleotide sequence of the instant invention may

also be used to detect differences in the chromosomal location due to translocation, inversion, etc., among normal, carrier, or affected individuals.

In another embodiment of the invention, PMMM, its catalytic or immunogenic fragments, or oligopeptides thereof can be used for screening libraries of compounds in any of a variety of drug screening techniques. The fragment employed in such screening may be free in solution, affixed to a solid support, borne on a cell surface, or located intracellularly. The formation of binding complexes between PMMM and the agent being tested may be measured.

Another technique for drug screening provides for high throughput screening of compounds having suitable binding affinity to the protein of interest (Geysen, et al. (1984) PCT application W084/03564). In this method, large numbers of different small test compounds are synthesized on a solid substrate. The test compounds are reacted with PMMM, or fragments thereof, and washed.

Bound PMMM is then detected by methods well known in the art. Purified PMMM can also be coated directly onto plates for use in the aforementioned drug screening techniques. Alternatively, non-neutralizing antibodies can be used to capture the peptide and immobilize it on a solid support.

In another embodiment, one may use competitive drug screening assays in which neutralizing antibodies capable of binding PMMM specifically compete with a test compound for binding PMMM In this manner, antibodies can be used to detect the presence of any peptide which shares one or more antigenic determinants with PMMM.

In additional embodiments, the nucleotide sequences which encode PMMM may be used in any molecular biology techniques that have yet to be developed, provided the new techniques rely on properties of nucleotide sequences that are currently known, including, but not limited to, such properties as the triplet genetic code and specific base pair interactions.

Without further elaboration, it is believed that one skilled in the art can, using the preceding description, utilize the present invention to its fullest extent. The following embodiments are, therefore, to be construed as merely illustrative, and not limitative of the remainder of the disclosure in any way whatsoever.

The disclosures of all patents, applications, and publications mentioned above and below, including U. S. Ser. No. 60/398,143, U. S. Ser. No. 60/402, 458, U. S. Ser. No. 60/403,289, U. S. Ser.

No. 60/406,472, and U. S. Ser. No. 60/409,354, are hereby expressly incorporated by reference.

EXAMPLES I. Construction of cDNA Libraries

Incyte cDNAs are derived from cDNA libraries described in the LIFESEQ database (Incyte, Palo Alto CA). Some tissues are homogenized and lysed in guanidinium isothiocyanate, while others are homogenized and lysed in phenol or in a suitable mixture of denaturants, such as TRIZOL (Invitrogen), a monophasic solution of phenol and guanidine isothiocyanate. The resulting lysates are centrifuged over CsCI cushions or extracted with chloroform. RNA is precipitated from the lysates with either isopropanol or sodium acetate and ethanol, or by other routine methods.

Phenol extraction and precipitation of RNA are repeated as necessary to increase RNA purity. In some cases, RNA is treated with DNase. For most libraries, poly (A) + RNA is isolated using oligo d (T)-coupled paramagnetic particles (Promega), OLIGOTEX latex particles (QIAGEN, Chatsworth CA), or an OLIGOTEX mRNA purification kit (QIAGEN). Alternatively, RNA is <BR> <BR> isolated directly from tissue lysates using other RNA isolation kits, e. g. , the POLY (A) PURE mRNA purification kit (Ambion, Austin TX}.

In some cases, Stratagene is provided with RNA and constructs the corresponding cDNA libraries. Otherwise, cDNA is synthesized and cDNA libraries are constructed with the UNIZAP vector system (Stratagene) or SUPERSCRIPT plasmid system (Invitrogen), using the recommended procedures or similar methods known in the art (Ausubel et al., supra, ch. 5). Reverse transcription is initiated using oligo d (T) or random primers. Synthetic oligonucleotide adapters are ligated to double stranded cDNA, and the cDNA is digested with the appropriate restriction enzyme or enzymes. For most libraries, the cDNA is size-selected (300-1000 bp) using SEPHACRYL S1000, SEPHAROSE CL2B, or SEPHAROSE CL4B column chromatography (Amersham Biosciences) or preparative agarose gel electrophoresis. cDNAs are ligated into compatible restriction enzyme sites of the polylinker of a suitable plasmid, e. g., PBLUESCRIPT plasmid (Stratagene), PSPORT1 plasmid (Invitrogen, Carlsbad CA), PCDNA2.1 plasmid (Invitrogen), PBK-CMV plasmid (Stratagene), PCR2- TOPOTA plasmid (Invitrogen), PCMV-ICIS plasmid (Stratagene), pIGEN (Incyte, Palo Alto CA), pRARE (Incyte), or pINCY (Incyte), or derivatives thereof. Recombinant plasmids are transformed into competent E. coli cells including XLl-Blue, XLl-BlueMRF, or SOLR from Stratagene or DH5a, DH1OB, or ElectroMAX DH10B from Invitrogen.

II. Isolation of cDNA Clones Plasmids obtained as described in Example I are recovered from host cells by in vivo excision using the UNIZAP vector system (Stratagene) or by cell lysis. Plasmids are purified using at least one of the following: a Magic or WIZARD Minipreps DNA purification system (Promega); an AGTC Miniprep purification kit (Edge Biosystems, Gaithersburg MD); and QIAWELL 8 Plasmid, QIAWELL 8 Plus Plasmid, QIAWELL 8 Ultra Plasmid purification systems or the R. E. A. L. PREP

96 plasmid purification kit from QIAGEN. Following precipitation, plasmids are resuspended in 0.1 ml of distilled water and stored, with or without lyophilization, at 4°C.

Alternatively, plasmid DNA is amplified from host cell lysates using direct link PCR in a high- throughput format (Rao, V. B. (1994) Anal. Biochem. 216: 1-14). Host cell lysis and thermal cycling steps are carried out in a single reaction mixture. Samples are processed and stored in 384-well plates, and the concentration of amplified plasmid DNA is quantified fluorometrically using PICOGREEN dye (Molecular Probes, Eugene OR) and a FLUOROSKAN I fluorescence scanner (Labsystems Oy, Helsinki, Finland).

III. Sequencing and Analysis Incyte cDNA recovered in plasmids as described in Example II are sequenced as follows.

Sequencing reactions are processed using standard methods or high-throughput instrumentation such as the ABI CATALYST 800 (Applied Biosystems) thermal cycler or the PTC-200 thermal cycler (MJ Research) in conjunction with the HYDRA microdispenser (Robbins Scientific) or the MICROLAB 2200 (Hamilton) liquid transfer system. cDNA sequencing reactions are prepared using reagents provided by Amersham Biosciences or supplied in ABI sequencing kits such as the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems).

Electrophoretic separation of cDNA sequencing reactions and detection of labeled polynucleotides are carried out using the MEGABACE 1000 DNA sequencing system (Amersham Biosciences) ; the ABI PRISM 373 or 377 sequencing system (Applied Biosystems) in conjunction with standard ABI protocols and base calling software; or other sequence analysis systems known in the art. Reading frames within the cDNA sequences are identified using standard methods (Ausubel et al., supra, ch.

7). Some of the cDNA sequences are selected for extension using the techniques disclosed in Example VIII.

Polynucleotide sequences derived from Incyte cDNAs are validated by removing vector, linker, and poly (A) sequences and by masking ambiguous bases, using algorithms and programs based on BLAST, dynamic programming, and dinucleotide nearest neighbor analysis. The Incyte cDNA sequences or translations thereof are then queried against a selection of public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases, and BLOCKS, PRINTS, 'DOMO, PRODOM; PROTEOME databases with sequences from Homo sapiens, Rattus norvegicus, Mus fzzzzsculus, Caerzorlzabditis elegans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, and Candida albicans (Incyte, Palo Alto CA); hidden Markov model (HMM)-based protein family databases such as PFAM, INCY, and TIGRFAM (Haft, D. H. et al.

(2001) Nucleic Acids Res. 29: 41-43); and HMM-based protein domain databases such as SMART

(Schultz, J. et al. (1998) Proc. Natl. Acad. Sci. USA 95: 5857-5864 ; Letunic, I. et al. (2002) Nucleic Acids Res. 30: 242-244). (HMM is a probabilistic approach which analyzes consensus primary <BR> <BR> structures of gene families ; see, for example, Eddy, S. R. (1996) Curr. Opin. Struct. Biol. 6: 361-365. ) The queries are performed using programs based on BLAST, FASTA, BLIMPS, and HMMER. The Incyte cDNA sequences are assembled to produce full length polynucleotide sequences.

Alternatively, GenBank cDNAs, GenBank ESTs, stitched sequences, stretched sequences, or Genscan-predicted coding sequences (see Examples IV and V) are used to extend Incyte cDNA assemblages to full length. Assembly is performed using programs based on Phred, Phrap, and Consed, and cDNA assemblages are screened for open reading frames using programs based on GeneMark, BLAST, and FASTA. The full length polynucleotide sequences are translated to derive the corresponding full length polypeptide sequences. Alternatively, a polypeptide may begin at any of the methionine residues of the full length translated polypeptide. Full length polypeptide sequences are subsequently analyzed by querying against databases such as the GenBank protein databases ; (genpept), SwissProt, the PROTEOME databases, BLOCKS, PRINTS, DOMO, PRODOM, Prosite, hidden Markov model (HMM)-based protein family databases such as PFAM, INCY, and TIGRFAM; and HMM-based protein domain databases such as SMART. Full length polynucleotide sequences are also analyzed using MACDNASIS PRO software (MiraiBio, Alameda CA) and LASERGENE software (DNASTAR). Polynucleotide and polypeptide sequence alignments are generated using default parameters specified by the CLUSTAL algorithm as incorporated into the MEGALIGN multisequence alignment program (DNASTAR), which also calculates the percent identity between aligned sequences.

Table 7 summarizes tools, programs, and algorithms used for the analysis and assembly of Incyte cDNA and full length sequences and provides applicable descriptions, references, and threshold parameters. The first column of Table 7 shows the tools, programs, and algorithms used, the second column provides brief descriptions thereof, the third column presents appropriate references, all of which are incorporated by reference herein in their entirety, and the fourth column presents, where applicable, the scores, probability values, and other parameters used to evaluate the strength of a match between two sequences (the higher the score or the lower the probability value, the greater the identity between two sequences).

The programs described above for the assembly and analysis of full length polynucleotide and polypeptide sequences are also used to identify polynucleotide sequence fragments from SEQ ID NO : 63-124. Fragments from about 20 to about 4000 nucleotides which are useful in hybridization and amplification technologies are described in Table 4, column 2.

IV. Identification and Editing of Coding Sequences from Genomic DNA Putative protein modification and maintenance molecules are initially identified by running the Genscan gene identification program against public genomic sequence databases (e. g. , gbpri and gbhtg). Genscan is a general-purpose gene identification program which analyzes genomic DNA sequences from a variety of organisms (Burge, C. and S. Karlin (1997) J. Mol. Biol. 268: 78-94; Burge, C. and S. Karlin (1998) Curr. Opin. Struct. Biol. 8: 346-354). The program concatenates predicted exons to form an assembled cDNA sequence extending from a methionine to a stop codon. The output of Genscan is a FASTA database of polynucleotide and polypeptide sequences. The maximum range of sequence for Genscan to analyze at once is set to 30 kb. To determine which of these Genscan predicted cDNA sequences encode protein modification and maintenance molecules, the encoded polypeptides are analyzed by querying against PFAM models for protein modification and maintenance molecules. Potential protein modification and maintenance molecules are also identified by homology to Incyte cDNA sequences that have been annotated as protein modification and maintenance molecules. These selected Genscan-predicted sequences are then compared by BLAST analysis to the genpept and gbpri public databases. Where necessary, the Genscan-predicted sequences are then edited by comparison to the top BLAST hit from genpept to correct errors in the sequence predicted by Genscan, such as extra or omitted exons. BLAST analysis is also used to find any Incyte cDNA or public cDNA coverage of the Genscan-predicted sequences, thus providing evidence for transcription. When Incyte cDNA coverage is available, this information is used to correct or confirm the Genscan predicted sequence. Full length polynucleotide sequences are obtained by assembling Genscan-predicted coding sequences with Incyte cDNA sequences and/or public cDNA sequences using the assembly process described in Example III. Alternatively, full length polynucleotide sequences are derived entirely from edited or unedited Genscan-predicted coding sequences.

V. Assembly of Genomic Sequence Data with cDNA Sequence Data "Stitched"Sequences Partial cDNA sequences are extended with exons predicted by the Genscan gene identification program described in Example IV. Partial cDNAs assembled as described in Example III are mapped to genomic DNA and parsed into clusters containing related cDNAs and Genscan exon predictions from one or more genomic sequences. Each cluster is analyzed using an algorithm based on graph theory and dynamic programming to integrate c : DNA and genomic information, generating possible splice variants that are subsequently confirmed, edited, or extended to create a full length sequence. Sequence intervals in which the entire length of the interval is present on more than

one sequence in the cluster are identified, and intervals thus identified are considered to be equivalent by transitivity. For example, if an interval is present on a cDNA and two genomic sequences, then all three intervals are considered to be equivalent. This process allows unrelated but consecutive genomic sequences to be brought together, bridged by cDNA sequence. Intervals thus identified are then"stitched"together by the stitching algorithm in the order that they appear along their parent sequences to generate the longest possible sequence, as well as sequence variants. Linkages between intervals which proceed along one type of parent sequence (cDNA to cDNA or genomic sequence to genomic sequence) are given preference over linkages which change parent type (cDNA to genomic sequence). The resultant stitched sequences are translated and compared by BLAST analysis to the genpept and gbpri public databases. Incorrect exons predicted by Genscan are corrected by comparison to the top BLAST hit from genpept. Sequences are further extended with additional cDNA sequences, or by inspection of genomic DNA, when necessary.

"Stretched"Sequences Partial DNA sequences are extended to full length with an algorithm based on BLAST analysis. First, partial cDNAs assembled as described in Example III are queried against public databases such as the GenBank primate, rodent, mammalian, vertebrate, and eukaryote databases using the BLAST program. The nearest GenBank protein homolog is then compared by BLAST analysis to either Incyte cDNA sequences or GenScan exon predicted sequences described in Example IV. A chimeric protein is generated by using the resultant high-scoring segment pairs (HSPs) to map the translated sequences onto the GenBank protein homolog. Insertions or deletions may occur in the chimeric protein with respect to the original GenBank protein homolog. The GenBank protein homolog, the chimeric protein, or both are used as probes to search for homologous genomic sequences from the public human genome databases. Partial DNA sequences are therefore "stretched"or extended by the addition of homologous genomic sequences. The resultant stretched sequences are examined to determine whether they contain a complete gene.

VI. Chromosomal Mapping of PMMM Encoding Polynucleotides The sequences used to assemble SEQ ID NO : 63-124 are compared with sequences from the Incyte LIFESEQ database and public domain databases using BLAST and other implementations of the Smith-Waterman algorithm. Sequences from these databases that matched SEQ ID NO : 63-124 are assembled into clusters of contiguous and overlapping sequences using assembly algorithms such as Phrap (Table 7). Radiation hybrid and genetic mapping data available from public resources such as the Stanford Human Genome Center (SHGC), Whitehead Institute for Genome Research (WIGR), and Généthon are used to determine if any of the clustered sequences have been previously mapped.

Inclusion of a mapped sequence in a cluster results in the assignment of all sequences of that cluster, including its particular SEQ ID NO:, to that map location.

Map locations are represented by ranges, or intervals, of human chromosomes. The map position of an interval, in centiMorgans, is measured relative to the terminus of the chromosome's p- arm. (The centiMorgan (cM) is a unit of measurement based on recombination frequencies between chromosomal markers. On average, 1 cM is roughly equivalent to 1 megabase (Mb) of DNA in <BR> <BR> humans, although this can vary widely due to hot and cold spots of recombination. ) The cM distances are based on genetic markers mapped by Généthon which provide boundaries for radiation hybrid markers whose sequences were included in each of the clusters. Human genome maps and other resources available to the public, such as the NCBI"GeneMap'99"World Wide Web site (http ://www. ncbi. nlm. nih. gov/genemap/), can be employed to determine if previously identified disease genes map within or in proximity to the intervals indicated above.

VII. Analysis of Polynucleotide Expression Northern analysis is a laboratory technique used to detect the presence of a transcript of a gene and involves the hybridization of a labeled nucleotide sequence to a membrane on which RNAs from a particular cell type or tissue have been bound (Sambrook and Russell, supra, ch. 7; Ausubel et al. , supra, ch. 4).

Analogous computer techniques applying BLAST are used to search for identical or related molecules in databases such as GenBank or LIFESEQ (Incyte). This analysis is much faster than multiple membrane-based hybridizations. In addition, the sensitivity of the computer search can be modified to determine whether any particular match is categorized as exact or similar. The basis of the search is the product score, which is defined as: BLAST Score x Percent Identity 5 x minimum {length (Seq. 1), length (Seq. 2)} The product score takes into account both the degree of similarity between two sequences and the length of the sequence match. The product score is a normalized value between 0 and 100, and is calculated as follows: the BLAST score is multiplied by the percent nucleotide identity and the product is divided by (5 times the length of the shorter of the two sequences). The BLAST score is calculated by assigning a score of +5 for every base that matches in a high-scoring segment pair (HSP), and-4 for every mismatch. Two sequences may share more than one HSP (separated by gaps). If there is more than one HSP, then the pair with the highest BLAST score is used to calculate

the product score. The product score represents a balance between fractional overlap and quality in a BLAST alignment. For example, a product score of 100 is produced only for 100% identity over the entire length of the shorter of the two sequences being compared. A product score of 70 is produced either by 100% identity and 70% overlap at one end, or by 88% identity and 100% overlap at the other. A product score of 50 is produced either by 100% identity and 50% overlap at one end, or 79% identity and 100% overlap.

Alternatively, polynucleotides encoding PMMM are analyzed with respect to the tissue sources from which they are derived. For example, some full length sequences are assembled, at least in part, with overlapping Incyte cDNA sequences (see Example III). Each cDNA sequence is derived from a cDNA library constructed from a human tissue. Each human tissue is classified into one of the following organ/tissue categories: cardiovascular system; connective tissue; digestive system; embryonic structures; endocrine system; exocrine glands; genitalia, female; genitalia, male; germ cells; hemic and immune system; liver; musculoskeletal system; nervous system; pancreas; respiratory system; sense organs; skin; stomatognathic system; unclassified/mixed; or urinary tract.

The number of libraries in each category is counted and divided by the total number of libraries across all categories. Similarly, each human tissue is classified into one of the following disease/condition categories: cancer, cell line, developmental, inflammation, neurological, trauma, cardiovascular, pooled, and other, and the number of libraries in each category is counted and divided by the total number of libraries across all categories. The resulting percentages reflect the tissue-and disease-specific expression of cDNA encoding PMMM. cDNA sequences and cDNA library/tissue information are found in the LIFESEQ database (Incyte, Palo Alto CA).

VIII. Extension of PMMM Encoding Polynucleotides Full length polynucleotides are produced by extension of an appropriate fragment of the full length molecule using oligonucleotide primers designed from this fragment. One primer is synthesized to initiate 5'extension of the known fragment, and the other primer is synthesized to initiate 3' extension of the known fragment. The initial primers are designed using OLIGO 4.06 software (National Biosciences), or another appropriate program, to be about 22 to 30 nucleotides in length, to have a GC content of about 50% or more, and to anneal to the target sequence at temperatures of about 68°C to about 72°C. Any stretch of nucleotides which would result in hairpin structures and primer-primer dimerizations is avoided.

Selected human cDNA libraries are used to extend the sequence. If more than one extension is necessary or desired, additional or nested sets of primers are designed.

High fidelity amplification is obtained by PCR using methods well known in the art. PCR is <BR> <BR> performed in 96-well plates using the PTC-200 thermal cycler (MJ Research, Inc. ). The reaction mix contains DNA template, 200 nmol of each primer, reaction buffer containing Mg2+, (NH4) 2SO4, and 2- mercaptoethanol, Taq DNA polymerase (Amersham Biosciences), ELONGASE enzyme (Invitrogen), and Pfu DNA polymerase (Stratagene), with the following parameters for primer pair PCI A and PCI B: Step 1: 94°C, 3 min; Step 2: 94°C, 15 sec ; Step 3: 60°C, 1 min ; Step 4: 68°C, 2 min; Step 5: Steps 2,3, and 4 repeated 20 times; Step 6: 68 °C, 5 min; Step 7: storage at 4°C. In the alternative, the parameters for primer pair T7 and SK+ are as follows: Step 1: 94°C, 3 min; Step 2: 94°C, 15 sec ; Step 3: 57°C, 1 min; Step 4: 68°C, 2 min; Step 5: Steps 2,3, and 4 repeated 20 times; Step 6: 68°C, 5 min; Step 7 : storage at 4°C.

The concentration of DNA in each well is determined by dispensing 100, ut PICOGREEN quantitation reagent (0.25% (v/v) PICOGREEN; Molecular Probes, Eugene OR) dissolved in 1X TE and 0. 5 ul of undiluted PCR product into each well of an opaque fluorimeter plate (Corning Costar, Acton MA), allowing the DNA to bind to the reagent. The plate is scanned in a Fluoroskan II (Labsystems Oy, Helsinki, Finland) to measure the fluorescence of the sample and to quantify the concentration of DNA. A 5, MI to 10 MI aliquot of the reaction mixture is analyzed by electrophoresis on a 1 % agarose gel to determine which reactions are successful in extending the sequence.

The extended nucleotides are desalted and concentrated, transferred to 384-well plates, digested with CviJI cholera virus endonuclease (Molecular Biology Research, Madison WI), and sonicated or sheared prior to religation into pUC 18 vector (Amersham Biosciences). For shotgun sequencing, the digested nucleotides are separated on low concentration (0.6 to 0.8%) agarose gels, fragments are excised, and agar digested with Agar ACE (Promega). Extended clones were religated using T4 ligase (New England Biolabs, Beverly MA) into pUC 18 vector (Amersham Biosciences), treated with Pfu DNA polymerase (Stratagene) to fill-in restriction site overhangs, and transfected into competent E. coli cells. Transformed cells are selected on antibiotic-containing media, and individual colonies are picked and cultured overnight at 37°C in 384-well plates in LB/2x carb liquid media.

The cells are lysed, and DNA is amplified by PCR using Taq DNA polymerase (Amersham Biosciences) and Pfu DNA polymerase (Stratagene) with the following parameters: Step 1: 94°C, 3 min; Step 2: 94°C, 15 sec ; Step 3: 60°C, 1 min; Step 4: 72°C, 2 min; Step 5 : steps 2,3, and 4 repeated 29 times; Step 6: 72°C, 5 min; Step 7: storage at 4°C. DNA is quantified by PICOGREEN reagent (Molecular Probes) as described above. Samples with low DNA recoveries are reamplified using the same conditions as described above. Samples are diluted with 20% dimethysulfoxide (1 : 2, v/v), and

sequenced using DYNAMIC energy transfer sequencing primers and the DYNAMIC DIRECT kit (Amersham Biosciences) or the ABI PRISM BIGDYE Terminator cycle sequencing ready reaction kit (Applied Biosystems).

In like manner, full length polynucleotides are verified using the above procedure or are used to obtain 5'regulatory sequences using the above procedure along with oligonucleotides designed for such extension, and an appropriate genomic library.

IX. Identification of Single Nucleotide Polymorphisms in PMMM Encoding Polynucleotides Common DNA sequence variants known as single nucleotide polymorphisms (SNPs) are identified in SEQ ID NO : 63-124 using the LIFESEQ database (Incyte). Sequences from the same gene are clustered together and assembled as described in Example III, allowing the identification of all sequence variants in the gene. An algorithm consisting of a series of filters is used to distinguish SNPs from other sequence variants. Preliminary filters remove the majority of basecall errors by requiring a minimum Phred quality score of 15, and remove sequence alignment errors and errors resulting from improper trimming of vector sequences, chimeras, and splice variants. An automated procedure of advanced chromosome analysis is applied to the original chromatogram files in the vicinity of the putative SNP. Clone error filters use statistically generated algorithms to identify errors introduced during laboratory processing, such as those caused by reverse transcriptase, polymerase, or somatic mutation. Clustering error filters use statistically generated algorithms to identify errors resulting from clustering of close homologs or pseudogenes, or due to contamination by non-human sequences. A final set of filters removes duplicates and SNPs found in immunoglobulins or T-cell receptors.

Certain SNPs are selected for further characterization by mass spectrometry using the high <BR> <BR> throughput MASSARRAY system (Sequenom, Inc. ) to analyze allele frequencies at the SNP sites in four different human populations. The Caucasian population comprises 92 individuals (46 male, 46 female), including 83 from Utah, four French, three Venezualan, and two Amish individuals. The African population comprises 194 individuals (97 male, 97 female), all African Americans. The Hispanic population comprises 324 individuals (162 male, 162 female), all Mexican Hispanic. The Asian population comprises 126 individuals (64 male, 62 female) with a reported parental breakdown of 43% Chinese, 31% Japanese, 13% Korean, 5% Vietnamese, and 8% other Asian. Allele frequencies are first analyzed in the Caucasian population; in some cases those SNPs which show no allelic variance in this population are not further tested in the other three populations.

X. Labeling and Use of Individual Hybridization Probes

Hybridization probes derived from SEQ ID NO : 63-124 are employed to screen cDNAs, genomic DNAs, or mRNAs. Although the labeling of oligonucleotides, consisting of about 20 base pairs, is specifically described, essentially the same procedure is used with larger nucleotide fragments. Oligonucleotides are designed using state-of-the-art software such as OLIGO 4.06 software (National Biosciences) and labeled by combining 50 pmol of each oligomer, 250, uCi of [-I-"Pj adenosine triphosphate (Amersham Biosciences), and T4 polynucleotide kinase (DuPont NEN, Boston MA). The labeled oligonucleotides are substantially purified using a SEPHADEX G-25 superfine size exclusion dextran bead column (Amersham Biosciences). An aliquot containing 101 counts per minute of the labeled probe is used in a typical membrane-based hybridization analysis of human genomic DNA digested with one of the following endonucleases: Ase I, Bgl II, Eco RI, Pst I, Xba I, or Pvu II (DuPont NEN).

The DNA from each digest is fractionated on a 0.7% agarose gel and transferred to nylon membranes (Nytran Plus, Schleicher & Schuell, Durham NH). Hybridization is carried out for 16 hours at 40°C. To remove nonspecific signals, blots are sequentially washed at room temperature under conditions of up to, for example, 0. 1 x saline sodium citrate and 0.5% sodium dodecyl sulfate.

Hybridization patterns are visualized using autoradiography or an alternative imaging means and compared.

XI. Microarrays The linkage or synthesis of array elements upon a microarray can be achieved utilizing photolithography, piezoelectric printing (ink-jet printing; see, e. g. , Baldeschweiler et al., supra), mechanical microspotting technologies, and derivatives thereof. The substrate in each of the aforementioned technologies should be uniform and solid with a non-porous surface (Schena, M., ed.

(1999) DNA Microarrays: A Practical Approach, Oxford University Press, London). Suggested substrates include silicon, silica, glass slides, glass chips, and silicon wafers. Alternatively, a procedure analogous to a dot or slot blot may also be used to arrange and link elements to the surface of a substrate using thermal, UV, chemical, or mechanical bonding procedures. A typical array may be produced using available methods and machines well known to those of ordinary skill in the art and may contain any appropriate number of elements (Schena, M. et al. (1995) Science 270: 467-470; Shalon, D. et al. (1996) Genome Res. 6: 639-645 ; Marshall, A. and J. Hodgson (1998) Nat. Biotechnol.

16 : 27-31).

Full length cDNAs, Expressed Sequence Tags (ESTs), or fragments or oligomers thereof may comprise the elements of the microarray. Fragments or oligomers suitable for hybridization can be selected using software well known in the art such as LASERGENE software (DNASTAR). The

array elements are hybridized with polynucleotides in a biological sample. The polynucleotides in the biological sample are conjugated to a fluorescent label or other molecular tag for ease of detection.

After hybridization, nonhybridized nucleotides from the biological sample are removed, and a fluorescence scanner is used to detect hybridization at each array element. Alternatively, laser desorbtion and mass spectrometry may be used for detection of hybridization. The degree of complementarity and the relative abundance of each polynucleotide which hybridizes to an element on the microarray may be assessed. In one embodiment, microarray preparation and usage is described in detail below.

Tissue or Cell Sample Preparation Total RNA is isolated from tissue samples using the guanidinium thiocyanate method and poly (A) + RNA is purified using the oligo- (dT) cellulose method. Each poly (A) + RNA sample is reverse transcribed using MMLV reverse-transcriptase, 0.05 pglitl oligo- (dT) primer (21mer), 1X first strand buffer, 0.03 units/, 1 RNase inhibitor, 500 yM dATP, 500, uM dGTP, 500, uM dlTP, 40, uM dCTP, 40, uM dCTP-Cy3 (BDS) or dCTP-Cy5 (Amersham Biosciences). The reverse transcription reaction is performed in a 25 ml volume containing 200 ng poly (A) + RNA with GEMBRIGHT kits (Incyte). Specific control poly (A) + RNAs are synthesized by iM vitro transcription from non-coding yeast genomic DNA. After incubation at 37° C for 2 hr, each reaction sample (one with Cy3 and another with Cy5 labeling) is treated with 2.5 ml of 0.5M sodium hydroxide and incubated for 20 minutes at 85° C to the stop the reaction and degrade the RNA. Samples are purified using two successive CHROMA SPIN 30 gel filtration spin columns (BD Clontech, Palo Alto CA) and after combining, both reaction samples are ethanol precipitated using 1 ml of glycogen (1 mg/ml), 60 ml sodium acetate, and 300-ml of 100% ethanol. The sample is then dried to completion using a SpeedVAC (Savant Instruments Inc. , Holbrook NY) and resuspended in 14 ul 5X SSC/0. 2% SDS.

Microarrav Preparation Sequences of the present invention are used to generate array elements. Each array element is amplified from bacterial cells containing vectors with cloned cDNA inserts. PCR amplification uses primers complementary to the vector sequences flanking the cDNA insert. Array elements are amplified in thirty cycles of PCR from an initial quantity of 1-2 ng to a final quantity greater than 5 ttg.

Amplified array elements are then purified using SEPHACRYL-400 (Amersham Biosciences).

Purified array elements are immobilized on polymer-coated glass slides. Glass microscope slides (Corning) are cleaned by ultrasound in 0. 1% SDS and acetone, with extensive distilled water washes between and after treatments. Glass slides are etched in 4% hydrofluoric acid (VWR Scientific Products Corporation (VWR), West Chester PA), washed extensively in distilled water, and

coated with 0.05% aminopropyl silane (Sigma-Aldrich, St. Louis MO) in 95% ethanol. Coated slides are cured in a 110°C oven.

Array elements are applied to the coated glass substrate using a procedure described in U. S.

Patent No. 5,807, 522, incorporated herein by reference. 1 Al of the array element DNA, at an average concentration of 100 ng/, ul, is loaded into the open capillary printing element by a high-speed robotic apparatus. The apparatus then deposits about 5 nl of array element sample per slide.

Microarrays are UV-crosslinked using a STRATALINKER UV-crosslinker (Stratagene).

Microarrays are washed at room temperature once in 0. 2% SDS and three times in distilled water.

Non-specific binding sites are blocked by incubation of microarrays in 0.2% casein in phosphate <BR> <BR> buffered saline (PBS) (Tropix, Inc. , Bedford MA) for 30 minutes at 60° C followed by washes in 0.2% SDS and distilled water as before.

Hybridization Hybridization reactions contain 9, ul of sample mixture consisting of 0. 2, ug each of Cy3 and Cy5 labeled cDNA synthesis products in 5X SSC, 0.2% SDS hybridization buffer. The sample mixture is heated to 65° C for 5 minutes and is aliquoted onto the microarray surface and covered with an 1. 8 cml coverslip. The arrays are transferred to a waterproof chamber having a cavity just slightly larger than a microscope slide. The chamber is kept at 100% humidity internally by the addition of 140 , ul o1F 5X SSC in a corner of the chamber. The chamber containing the arrays is incubated for about 6.5 hours at 60°C. The arrays are washed for 10 min at 45°C in a first wash buffer (1X SSC, 0. 1% ; SDS), three times for 10 minutes each at 45° C in a second wash buffer (0. 1X SSC), and dried.

Detection Reporter-labeled hybridization complexes are detected with a microscope equipped with an <BR> <BR> Innova 70 mixed gas 10 W laser (Coherent, Inc. , Santa Clara CA) capable of generating spectral lines at 488 nm for excitation of Cy3 and at 632 nm for excitation of Cy5. The excitation laser light is focused on the array using a 20X microscope objective (Nikon, Inc. , Melville NY). The slide containing the array is placed on a computer-controlled X-Y stage on the microscope and raster- scanned past the objective. The 1.8 cm x 1.8 cm array used in the present example is scanned with a resolution of 20 micrometers.

In two separate scans, a mixed gas multiline laser excites the two fluorophores sequentially.

Emitted light is split, based on wavelength, into two photomultiplier tube detectors (PMT R1477, Hamamatsu Photonics Systems, Bridgewater NJ) corresponding to the two fluorophores. Appropriate filters positioned between the array and the photomultiplier tubes are used to filter the signals. The emission maxima of the fluorophores used are 565 nm for Cy3 and 650 nm for Cy5. Each array is

typically scanned twice, one scan per fluorophore using the appropriate filters at the laser source, although the apparatus is capable of recording the spectra from both fluorophores simultaneously.

The sensitivity of the scans is typically calibrated using the signal intensity generated by a cDNA control species added to the sample mixture at a known concentration. A specific location on the array contains a complementary DNA sequence, allowing the intensity of the signal at that location to be correlated with a weight ratio of hybridizing species of 1: 100,000. When two samples from different sources (e. g., representing test and control cells), each labeled with a different fluorophore, are hybridized to a single array for the purpose of identifying genes that are differentially expressed, the calibration is done by labeling samples of the calibrating cDNA with the two fluorophores and adding identical amounts of each to the hybridization mixture.

The output of the photomultiplier tube is digitized using a 12-bit RTI-835H analog-to-digital (A/D) conversion board (Analog Devices, Inc. , Norwood MA) installed in an IBM-compatible PC computer. The digitized data are displayed as an image where the signal intensity is mapped using a linear 20-color transformation to a pseudocolor scale ranging from blue (low signal) to red (high signal). The data is also analyzed quantitatively. Where two different fluorophores are excited and measured simultaneously, the data are first corrected for optical crosstalk (due to overlapping emission spectra) between the fluorophores using each fluorophore's emission spectrum.

A grid is superimposed over the fluorescence signal image such that the signal from each spot is centered in each element of the grid. The fluorescence signal within each element is then integrated to obtain a numerical value corresponding to the average intensity of the signal. The software used for signal analysis is the GEMTOOLS gene expression analysis program (Incyte). Array elements that exhibit at least about a two-fold change in expression, a signal-to-background ratio of at least about 2.5, and an element spot size of at least about 40%, are considered to be differentially expressed.

Expression For example, SEQ ID NO : 64-66, SEQ ID NO : 77, and SEQ ID NO : 79 showed tissue-specific expression as determined by microarray analysis. RNA samples isolated from a variety of normal human tissues were compared to a common reference sample. Tissues contributing to the reference sample were selected for their ability to provide a complete distribution of RNA in the human body and include brain (4%), heart (7%), kidney (3%), lung (8%), placenta (46%), small intestine (9%), spleen (3%), stomach (6%), testis (9%), and uterus (5%). The normal tissues assayed were obtained from at least three different donors. RNA from each donor was separately isolated and individually hybridized to the microarray. Since these hybridization experiments were conducted using a common

reference sample, differential expression values are directly comparable from one tissue to another.

The expression of SEQ ID NO : 64 was increased by at least two-fold in spleen and liver tissue as compared to the reference sample. Therefore, SEQ ID NO : 64 can be used as a tissue marker for heart, omentum, spleen, and liver tissue. The expression of SEQ ID NO : 65-66 was increased by at least two-fold in skeletal muscle and liver tissue as compared to the reference sample. Therefore, SEQ ID NO : 65 and/or SEQ ID NO : 66 can be used as a tissue marker for skeletal muscle and liver tissue. The expression of SEQ ID NO : 77 and SEQ ID NO : 79 was increased by at least two-fold in blood leukocytes as compared to the reference sample. Therefore, SEQ ID NO : 77 and/or SEQ ID NO : 79 can be used as a tissue marker for blood leukocytes. The expression of SEQ ID NO : 82 was increased by at least two-fold in blood leukocytes as compared to the reference sample. Therefore, in an embodiment, SEQ ID NO : 82 can be used as a tissue marker for blood leukocytes. The expression of SEQ ID NO : 85 was increased by at least two-fold in liver and pancreas as compared to the reference sample. Therefore, in an embodiment, SEQ ID NO : 85 can be used as a tissue marker for liver and pancreas. The expression of SEQ ID NO : 88 was increased by at least two-fold in brain tissues, including the cerebellum and hippocampus, and in spinal cord tissue, as compared to the reference sample. Therefore, in an embodiment, SEQ ID NO : 88 can be used as a tissue marker for cerebellum, hippocampus, and spinal cord. The expression of SEQ ID NO : 98 was increased by at least two-fold in pancreas, gallbladder, and bladder tissue as compared to the reference sample.

Therefore, SEQ ID NO : 98 can be used as a tissue marker for pancreas, gallbladder, and bladder tissue. The expression of SEQ ID NO : 100 was increased by at least two-fold in thyroid tissue as compared to the reference sample. Therefore, SEQ ID NO : 100 can be used as a tissue marker for thyroid tissue. The expression of SEQ ID NO : 117 was increased by at least two-fold in blood leukocytes as compared to the reference sample. The expression of SEQ ID NO : 123 was increased by at least two-fold in pancreas, gallbladder, and bladder tissues as compared to the reference sample.

Therefore, SEQ ID NO : 117 can be used as a tissue marker for blood leukocytes. SEQ ID NO : 123 can be used as a tissue marker for pancreas, gallbladder, and bladder tissues.

In an alternative example, expression of SEQ ID NO : 63 was downregulated in peripheral blood mononuclear cells (PBMCs) treated with beclomethasone versus untreated PBMCs as determined by microarray analysis. PBMCs from the blood of 6 healthy volunteer donors were incubated for 24 hours in the presence of beclomethasone dissolved in DMSO. One sample was incubated with 25, uM beclomethasone. A second sample was incubated with 5 uM beclomethasone.

In addition, matching PBMCs were treated for the same duration with matching doses of DMSO in order to monitor the possible effects of the vehicle alone. The treated PBMC were compared to

matching untreated PBMC maintained in culture for the same duration. Expression of SEQ ID NO : 63 was decreased in both samples treated with beclomethasone. Therefore, in various embodiments, SEQ ID NO : 63 can be used for monitoring beclomethasone treatment of a variety of disorders.

In an alternative example, the gene expression profile of a nonmalignant mammary epithelial cell line was compared to the gene expression profiles of breast carcinoma lines at different stages of tumor progression. Cell lines compared included : a) BT-20, a breast carcinoma cell line derived iii vitro from the cells emigrating out of thin slices of tumor mass isolated from a 74-year-old female, b) BT-474, a breast ductal carcinoma cell line that was isolated from a solid, invasive ductal carcinoma of the breast obtained from a 60-year-old woman, c) BT-483, a breast ductal carcinoma cell line that was isolated from a papillary invasive ductal tumor obtained from a 23-year-old normal, menstruating, parous female with a family history of breast cancer, d) Hs 578T, a breast ductal carcinoma cell line isolated from a 74-year-old female with breast carcinoma, e) MCF7, a nonmalignant breast adenocarcinoma cell line isolated from the pleural effusion of a 69-year-old female, f) MCF-10A, a breast mammary gland (luminal ductal characteristics) cell line isolated from a 36-year-old woman with fibrocystic breast disease, g) MDA-MB-468, a breast adenocarcinoma cell line isolated from the pleural effusion of a 51-year-old female with metastatic adenocarcinoma of the breast, and h) HMEC, a primary breast epithelial cell line isolated from a normal donor. In one experiment, cells were grown under optimal growth conditions, in the presence of growth factors and nutrients. Expression of SEQ ID NO : 64 was decreased in BT-474, BT-483, MCF-10A, and MCF7 cells. Expression of SEQ ID NO : 69 was increased in BT-20 cells, in both samples tested. Expression of SEQ ID NO : 84 was decreased by at least two-fold in the MCF7, BT-483, BT-20, T-47D, Sk-BR-3, and MDA-mb-435S breast cancer cell lines as compared to the non-malignant HMEC cell line, and was also decreased by at least two-fold in the MCF7, BT-20, T-47D, Sk-BR-3, and MDA-mb-231 breast cancer cell lines as compared to the non-malignant MCF-1OA cell line. Expression of SEQ ID NO : 100 was decreased in the T-47D, Sk-BR-3, and MDA-mb-231 cell lines versus the MCP-1OA line. Expression of SEQ ID NO : 113 was increased at least two-fold in the MCF7 sample. In a second experiment, cells were grown in basal media in the absence of growth factors and hormones for 24 hours prior to comparison.

Expression of SEQ ID NO : 64 was decreased in BT-20, BT-483, MCF7, and MDA-MB-468 cells.

Therefore, in various embodiments, SEQ ID NO : 64, SEQ ID NO : 69, SEQ ID NO : 84, SEQ ID NO : 100, and/or SEQ ID NO : 113 can be used for one or more of the following: i) monitoring treatment of breast cancer, ii) diagnostic assays for breast cancer, and iii) developing therapeutics and/or other treatments for breast cancer.

In an alternative example, expression of SEQ ID NO : 64-66 was upregulated in sigmoid colon tumor tissue versus normal sigmoid colon tissue, as determined by microarray analysis. Gene expression profiles were obtained by comparing normal sigmoid colon tissue from a donor to a sigmoid colon tumor originating from a metastatic gastric sarcoma (stromal tumor) from the same donor (Huntsman Cancer Institute, Salt Lake City, UT). Expression of SEQ ID NO : 64-66 was increased in sigmoid colon tumor tissue. Therefore, in various embodiments, SEQ ID NO : 64, SEQ ID NO : 65, and/or SEQ ID NO : 66 can be used for one or more of the following: i) monitoring treatment of colon cancer, ii) diagnostic assays for colon cancer, and iii) developing therapeutics and/or other treatments for colon cancer.

In an alternative example, expression of SEQ ID NO : 77 was downregulated in prostate carcinoma cells versus normal prostate epithelial cells, as determined by microarray analysis. Gene expression profiles of the prostate carcinoma lines CA-HPV-10, LNCaP, PC-3, and DU 145 were compared to that of nontumorigenic PZ-HPV-7. RNA was harvested when the cells grown in the defined serum-free TCH medium reached 70-80% confluence. PZ-HPV-7 was derived from epithelial cells cultured from normal tissue from the peripheral zone of the prostate. CA-HPV-10 was derived from cells from a 63-year-old male with prostatic adenocarcinoma of Gleason Grade 4/4. DU 145 is a prostate carcinoma cell line isolated from a metastatic site in the brain of 69-year old male with widespread metastatic prostate carcinoma. LNCaP is a prostate carcinoma cell line isolated from a lymph node biopsy of a 50-year-old male with metastatic prostate carcinoma. PC-3 is a prostate adenocarcinoma cell line that was isolated from a metastatic site in the bone of a 62-year-old male with grade IV prostate adenocarcinoma. Expression of SEQ ID NO : 77 was decreased in the CA-HPV-10, DU 145, and PC-3 lines. Therefore, in various embodiments, SEQ ID NO : 77 can be used for one or more of the following: i) monitoring treatment of prostate cancer, ii) diagnostic assays for prostate cancer, and iii) developing therapeutics and/or other treatments for prostate cancer.

In an alternative example, expression of SEQ ID NO : 77 was downregulated in C3A cells treated with steroids versus untreated C3A cells, as determined by microarray analysis. Early confluent C3A cells were treated for 1,3, and 6 hours with graded doses (1,10, and 100 AM) of a variety of steroids including progesterone, beclomethasone, medroxyprogesterone, budesonide, prednisone, dexamethasone, and betamethasone. The treated cells were compared to untreated early confluent C3A cells. Expression of SEQ ID NO : 77 was decreased in C3A cells treated with progesterone, beclomethasone, medroxyprogesterone, budesonide, prednisone, dexamethasone, or betamethasone. Therefore, in various embodiments, SEQ ID NO : 77 can be used for the diagnosis of

and as a therapeutic target for liver toxicity and clearance, inflammatory diseases and humoral immune response.

In an alternative example, expression of SEQ ID NO : 79 was downregulated in ovarian tumor tissue versus normal ovarian tissue as determined by microarray analysis. A normal ovary from a donor was compared to an ovarian tumor from the same donor (Huntsman Cancer Institute, Salt Lake City, UT). Expression of SEQ ID NO : 79 was decreased in ovarian tumor tissue. Therefore, in various embodiments, SEQ ID N0 : 79 can be used for one or more of the following: i) monitoring treatment of ovarian cancer, ii) diagnostic assays for ovarian cancer, and iii) developing therapeutics and/or other treatments for ovarian cancer.

In an alternative example, SEQ ID NO : 81-82, SEQ ID NO : 84-85, and SEQ ID NO : 88-90 showed differential expression, as determined by microarray analysis.

For example, SEQ ID NO : 81 and SEQ ID NO : 85 showed differential expression in lung tumor tissues compared to normal lung tissue from the same donor as determined by microarray analysis. Samples of normal lung were compared to lung tumor from the same donor (Roy Castle International Centre for Lung Cancer Research, Liverpool, UK). The expression was increased by at least two-fold in tumor tissue as compared to the matched normal lung for two donors in the case of SEQ ID NO : 81, while the expression of SEQ ID NO : 85 was decreased by at least two-fold in tumor tissue as compared to the matched normal lung for five donors. Therefore, in various embodiments, SEQ ID NO : 81 and/or SEQ ID NO : 85 can each be used for one or more of the following: i) monitoring treatment of lung cancer, ii) diagnostic assays for lung cancer, and iii) developing therapeutics and/or other treatments for lung cancer.

In a further example, SEQ ID NO : 89-90 showed differential expression in colon tumor tissue as compared to normal colon tissue from the same donor as determined by microarray analysis.

Samples of normal colon were compared to colon tumor from the same donor (Huntsman Cancer Institute, Salt Lake City, UT). The expression of SEQ ID NO : 89 was decreased by at least two-fold in colon tumor tissue as compared to the matched normal colon tissue for two donors, and increased by at least two-fold in two other donors, while the expression of SEQ ID NO : 90 was decreased by at least two-fold in the colon tumor tissue as compared to the matched normal colon tissue for three donors. Therefore, in various embodiments, SEQ ID NO : 89 and/or SEQ ID NO : 90 can each be used for one or more of the following: i) monitoring treatment of colon cancer, ii) diagnostic assays for colon cancer, and iii) developing therapeutics and/or other treatments for colon cancer.

In a further example, SEQ ID NO : 89 showed differential expression in breast tumor tissue as compared to normal breast tissue from the same donor as determined by microarray analysis. A

tumor from the right breast of a 43-year-old female diagnosed with invasive lobular carcinoma was compared to grossly uninvolved breast tissue from the same donor (Huntsman Cancer Institute, Salt Lake City, UT). The tumor is described as well differentiated and metastatic to 2 of 13 lymph nodes.

The expression of SEQ ID NO : 89 was decreased by at least two-fold in the breast tumor tissue as compared to the matched normal breast tissue. Therefore, in various embodiments, SEQ ID NO : 89 can be used for one or more of the following: i) monitoring treatment of breast cancer, ii) diagnostic assays for breast cancer, and iii) developing therapeutics and/or other treatments for breast cancer.

In a further example, SEQ ID N0 : 84 showed differential expression in association with vascular inflammation and immune responses, as determined by microarray analysis. Human umbilical vein endothelial cells (HUVECs) were pretreated with IFN-y at 10 ng/ml and 200 ng/ml for 24 hours, washed, and then stimulated with TNF-a for an additional 1,4, and 24 hours. The effect of IFN-y pretreatment was assessed on HUVECs incubated with this factor for 24 hours at 10 ng/ml and 200 ng/ml. In addition, HUVECs were stimulated with TNF-a for 1,4, and 24 hours, in the absence of any pretreatment. Treated HUVECs were compared to HUVECs maintained in culture in the absence of stimuli for 24 hours. The expression of SEQ ID NO : 84 was increased by at least two-fold in HUVECs treated with IFN-y and TNF-a as compared to untreated HUVECs. Thus, in various embodiments, SEQ ID NO : 84 can be used for one or more of the following : i) monitoring treatment of vascular inflammation and immune responses, ii) diagnostic assays for vascular inflammation and immune responses, and iii) developing therapeutics and/or other treatments for vascular inflammation and immune responses.

In a further example, SEQ ID NO : 82 showed differential expression in association with immune responses, as determined by microarray analysis. Human peripheral blood mononuclear cells (PBMCs) were collected from the blood of 5 healthy volunteer donors using standard gradient separation. PBMCs from each donor were placed in culture for 2 and 4 hours in the presence of anti- inflammatory cytokines such as IL-3, IL-4, IL-5, IL-7, IL-10, G-CSF, GM-CSF, Leptin, LIF, and TGF- , B. Cytokine-treated PBMCs and untreated control PBMCs from the different donors were pooled according to their respective treatments. The expression of SEQ ID NO : 82 was increased by at least two-fold in cytokine-treated PBMCs as compared to untreated control PBMCs.

In a separate experiment, PBMCs were stimulated in vitro with 0.1 ttnuml soluble phorbol myristate acetate (PMA) and 1. 0 yM/ml ionomycin for 1,2, 4,8, and 20 hours. These treated cells were compared to untreated PBMCs kept in culture in the absence of stimuli. In another separate experiment, Jurkat cells were stimulated ifs vitro with soluble PMA and ionomycin for 0.5, 1, 2, and 4 hours. These treated cells were compared to untreated Jurkat cells kept in culture in the absence of

stimuli. The expression of SEQ ID NO : 82 was increased by at least two-fold in both the treated PBMCs and Jurkat cells at timepoints after 1 hour, as compared to untreated cells.

In a further experiment, PHA blasts derived from the PBMCs of 5 healthy volunteer donors were stimulated for 9 days in the presence of PHA and IL-2. These T cell blasts were washed and stimulated for 1 and 6 hours in the presence of anti-CD3 monoclonal antibody, anti-CD28 antibody, or a combination of both. These reactivated T cells were compared to matching untreated PHA blasts.

The expression of SEQ ID NO : 82 was increased by at least two-fold in T cell blasts treated with a combination of anti-CD3 and anti-CD-28 antibodies, or anti-CD3 alone, for 6 hours.

Thus, in various embodiments, SEQ ID NO : 82 can be used for one or more of the following: i) monitoring treatment of immune disorders and related diseases and conditions, ii) diagnostic assays for immune disorders and related diseases and conditions, and iii) developing therapeutics and/or other treatments for immune disorders and related diseases and conditions.

In an alternative example, expression of SEQ ID NO : 98 and SEQ ID NO : 100 was downregulated in lung cancer tissue versus normal lung tissue, as determined by microarray analysis.

Normal lung tissue was. compared to lung tumor from the same donor (Roy Castle International Centre for Lung Cancer Research, Liverpool, UK). Expression of SEQ ID NO : 98 was decreased in the lung cancer sample for 7 of 7 donors tested. Expression of SEQ ID NO : 100 was decreased in the lung cancer sample for 2 of 5 donors tested. Therefore, in various embodiments, SEQ ID NO : 98 and/or SEQ ID NO : 100 can be used for one or more of the following: i) monitoring treatment of lung cancer, ii) diagnostic assays for lung cancer, and iii) developing therapeutics and/or other treatments for lung cancer.

In an alternative example, SEQ ID NO : 111 showed differential expression, as determined by microarray analysis. Expression of SEQ ID NO : 111 was upregulated in treated human peripheral mononuclear blood cells (PBMCs) versus untreated PBMCs under two treatment conditions as determined by microarray analysis. In one example, PBMCs were stimulated in vitro with soluble phorbol myristate acetate (PMA) and ionomycin for 1,2, 4,8, and 20 hours. These treated cells were compared to untreated PBMCs kept in culture in the absence of stimuli. SEQ ID NO : 111 was upregulated in treated PBMCs as compared with untreated PBMCs at 1,2, 4, and 8 hours with expression peaking at 4 hours. In another example, SEQ ID NO : 111 was upregulated in PBMCs from healthy donors in response to Staphylococcal enterotoxin B (SEB). To evaluate the variation in gene expression of PBMCs from healthy donors in response to SEB, PBMCs from 7 healthy volunteer donors were stimulated ion vitro with SEB for 24 and 72 hours. The SEB-treated PBMCs from each donor were compared to PBMCs from the same donor, kept in culture for 24 hours in the

absence of SEB. Expression of SEQ ID N0 : 111 was upregulated in treated PBMCs as compared with untreated PBMCs in cells from six of seven donors. Expression of SEQ ID NO : 111 was higher at 24 hours than at 72 hours. Therefore, in various embodiments, SEQ ID NO : 111 can be used for one or more of the following: i) monitoring treatment of immune disorders and related diseases and conditions, ii) diagnostic assays for immune disorders and related diseases and conditions, and iii) developing therapeutics and/or other treatments for immune disorders and related diseases and conditions.

In an alternative example, expression of SEQ ID NO : 117 and SEQ ID NO : 123 was downregulated in squamous cell lung cancer versus normal lung tissue as determined by microarray analysis. Grossly uninvolved lung tissue was compared to lung squamous cell adenocarcinoma tissue from the same donor (Roy Castle International Centre for Lung Cancer Research, Liverpool, UK).

Expression of SEQ ID NO : 123 was decreased at least two-fold in 5 of 5 squamous cell lung cancer samples versus normal lung tissue from the same donor. Expression of SEQ ID NO : 117 was decreased at least two-fold in 2 of 5 squamous cell cancer samples versus noncancerous lung tissue from the same donor. Therefore, in various embodiments, SEQ ID NO : 117 and/or SEQ ID NO : 123 can be used for one or more of the following: i) monitoring treatment of lung cancer, ii) diagnostic assays for lung cancer, and iii) developing therapeutics and/or other treatments for lung cancer.

In an alternative example, expression of SEQ ID NO : 117 was upregulated in human peripheral blood mononuclear cells (PBMCs) treated with cytokines versus untreated PBMCs, as determined by microarray analysis. PBMCs were collected from the blood of 5 healthy volunteer donors using standard gradient separation. PBMCs from each donor were placed in culture for 2 and 4 hours in the presence of anti-inflammatory cytokines such as IL-3, IL-4, IL-5, IL-7, IL-10, G-CSF, GM-CSF, Leptin, LIF, and TGF-, B. Cytokine-treated PBMCs and untreated control PBMCs from the different donors were pooled according to their respective treatments. Expression of SEQ ID NO : 117 was increased at least two-fold in both samples tested. Therefore, in various embodiments, SEQ ID NO : 117 can be used for one or more of the following: i) monitoring treatment of immune disorders and related diseases and conditions, ii) diagnostic assays for immune disorders and related diseases and conditions, and iii) developing therapeutics and/or other treatments for immune disorders and related diseases and conditions.

XII. Complementary Polynucleotides Sequences complementary to the PMMM-encoding sequences, or any parts thereof, are used to detect, decrease, or inhibit expression of naturally occurring PMMM. Although use of oligonucleotides comprising from about 15 to 30 base pairs is described, essentially the same

procedure is used with smaller or with larger sequence fragments. Appropriate oligonucleotides are designed using OLIGO 4.06 software (National Biosciences) and the coding sequence of PMMM.

To inhibit transcription, a complementary oligonucleotide is designed from the most unique 5'sequence and used to prevent promoter binding to the coding sequence. To inhibit translation, a complementary oligonucleotide is designed to prevent ribosomal binding to the PMMM-encoding transcript.

XIII. Expression of PMMM Expression and purification of PMMM is achieved using bacterial or virus-based expression systems. For expression of PMMM in bacteria, cDNA is subcloned into an appropriate vector containing an antibiotic resistance gene and an inducible promoter that directs high levels of cDNA transcription. Examples of such promoters include, but are not limited to, the trp-lac (tac) hybrid promoter and the T5 or T7 bacteriophage promoter in conjunction with the lac operator regulatory element. Recombinant vectors are transformed into suitable bacterial hosts, e. g. , BL21 (DE3).

Antibiotic resistant bacteria express PMMM upon induction with isopropyl beta-D- thiogalactopyranoside (IPTG). Expression of PMMM in eukaryotic cells is achieved by infecting insect or mammalian cell lines with recombinant Autographica californica nuclear polyhedrosis virus (AcMNPV), commonly known as baculovirus. The nonessential polyhedrin gene of baculovirus is replaced with cDNA encoding PMMM by either homologous recombination or bacterial-mediated transposition involving transfer plasmid intermediates. Viral infectivity is maintained and the strong polyhedrin promoter drives high levels of cDNA transcription. Recombinant baculovirus is used to infect Spodopterafrugiperda (Sf9) insect cells in most cases, or human hepatocytes, in some cases.

Infection of the latter requires additional genetic modifications to baculovirus (Engelhard, E. K. et al.

(1994) Proc. Natl. Acad. Sci. USA 91: 3224-3227; Sandig, V. et al. (1996) Hum. Gene Ther. 7: 1937- 1945).

In most expression systems, PMMM is synthesized as a fusion protein with, eg., glutathione S-transferase (GST) or a peptide epitope tag, such as FLAG or 6-His, permitting rapid, single-step, affinity-based purification of recombinant fusion protein from crude cell lysates. GST, a 26-kilodalton enzyme from Schistosomajaponicum, enables the purification of fusion proteins on immobilized glutathione under conditions that maintain protein activity and antigenicity (Amersham Biosciences).

Following purification, the GST moiety can be proteolytically cleaved from PMMM at specifically engineered sites. FLAG, an 8-amino acid peptide, enables immunoaffinity purification using commercially available monoclonal and polyclonal anti-FLAG antibodies (Eastman Kodak). 6-His, a stretch of six consecutive histidine residues, enables purification on metal-chelate resins (QIAGEN).

Methods for protein expression and purification are discussed in Ausubel et al. (supra, ch. 10 and 16).

Purified PMMM obtained by these methods can be used directly in the assays shown in Examples XVII, XVIII, XIX, and XX, where applicable.

XIV. Functional Assays PMMM function is assessed by expressing the sequences encoding PMMM at physiologically elevated levels in mammalian cell culture systems. cDNA is subcloned into a mammalian expression vector containing a strong promoter that drives high levels of cDNA expression. Vectors of choice include PCMV SPORT plasmid (Invitrogen, Carlsbad CA) and PCR3.1 plasmid (Invitrogen), both of which contain the cytomegalovirus promoter. 5-10 Mg of recombinant vector are transiently transfected into a human cell line, for example, an endothelial or hematopoietic cell line, using either liposome formulations or electroporation. 1-2, ug of an additional plasmid containing sequences encoding a marker protein are co-transfected. Expression of a marker protein provides a means to distinguish transfected cells from nontransfected cells and is a reliable predictor of cDNA expression from the recombinant vector. Marker proteins of choice include, e. g. , Green Fluorescent Protein (GFP; BD Clontech), CD64, or a CD64-GFP fusion protein. Flow cytometry (FCM), an automated, laser optics-based technique, is used to identify transfected cells expressing GFP or CD64-GFP and to evaluate the apoptotic state of the cells and other cellular properties. FCM detects and quantifies the uptake of fluorescent molecules that diagnose events preceding or coincident with cell death. These events include changes in nuclear DNA content as measured by staining of DNA with propidium iodide; changes in cell size and granularity as measured by forward light scatter and 90 degree side light scatter; down-regulation of DNA synthesis as measured by decrease in bromodeoxyuridine uptake; alterations in expression of cell surface and intracellular proteins as measured by reactivity with specific antibodies; and alterations in plasma membrane composition as measured by the binding of fluorescein-conjugated Annexin V protein to the cell surface. Methods in flow cytometry are discussed in Ormerod, M. G. (1994; Flow Cytometry, Oxford, New York NY).

The influence of PMMM on gene expression can be assessed using highly purified populations of cells transfected with sequences encoding PMMM and either CD64 or CD64-GFP. CD64 and CD64-GFP are expressed on the surface of transfected cells and bind to conserved regions of human immunoglobulin G (IgG). Transfected cells are efficiently separated from nontransfected cells using magnetic beads coated with either human IgG or antibody against CD64 (DYNAL, Lake Success NY). mRNA can be purified from the cells using methods well known by those of skill in the art.

Expression of mRNA encoding PMMM and other genes of interest can be analyzed by northern analysis or microarray techniques.

XV. Production of PMMM Specific Antibodies

PMMM substantially purified using polyacrylamide gel electrophoresis (PAGE; see, e. g., Harrington, M. G. (1990) Methods Enzymol. 182: 488-495), or other purification techniques, is used to immunize animals (e. g. , rabbits, mice, etc. ) and to produce antibodies using standard protocols.

Alternatively, the PMMM amino acid sequence is analyzed using LASERGENE software (DNASTAR) to determine regions of high immunogenicity, and a corresponding oligopeptide is synthesized and used to raise antibodies by means known to those of skill in the art. Methods for selection of appropriate epitopes, such as. those near the C-terminus or in hydrophilic regions are well described in the art (Ausubel et al., supra, ch. 11).

Typically, oligopeptides of about 15 residues in length are synthesized using an ABI 431A peptide synthesizer (Applied Biosystems) using PMOC chemistry and coupled to KLH (Sigma- Aldrich, St. Louis MO) by reaction with N-maleimidobenzoyl-N-hydroxysuccinimide ester (MBS) to increase immunogenicity (Ausubel et al., supra). Rabbits are immunized with the oligopeptide-KLH complex in complete Freund's adjuvant. Resulting antisera are tested for antipeptide and anti-PMMM activity by, for example, binding the peptide or PMMM to a substrate, blocking with 1% BSA, reacting with rabbit antisera, washing, and reacting with radio-iodinated goat anti-rabbit IgG.

XVI. Purification of Naturally Occurring PMMM Using Specific Antibodies Naturally occurring or recombinant PMMM is substantially purified by immunoaffinity chromatography using antibodies specific for PMMM. An immunoaffinity column is constructed by covalently coupling anti-PMMM antibody to an activated chromatographic resin, such as CNBr-activated SEPHAROSE (Amersham Biosciences). After the coupling, the resin is blocked and washed according to the manufacturer's instructions.

Media containing PMMM are passed over the immunoaffinity column, and the column is washed under conditions that allow the preferential absorbance of PMMM (e. g. , high ionic strength buffers in the presence of detergent). The column is eluted under conditions that disrupt antibody/PMMM binding (e. g., a buffer of pH 2 to pH 3, or a high concentration of a chaotrope, such as urea or thiocyanate ion), and PMMM is collected.

XVII. Identification of Molecules Which Interact with PMMM PMMM, or biologically active fragments thereof, are labeled with 125I Bolton-Hunter reagent (Bolton, A. E. and W. M. Hunter (1973) Biochem. J. 133 : 529-539). Candidate molecules previously arrayed in the wells of a multi-well plate are incubated with the labeled PMMM, washed, and any wells with labeled PMMM complex are assayed. Data obtained using different concentrations of PMMM are used to calculate values for the number, affinity, and association of PMMM with the candidate molecules.

Alternatively, molecules interacting with PMMM are analyzed using the yeast two-hybrid system as described in Fields, S. and 0. Song (1989; Nature 340: 245-246), or using commercially available kits based on the two-hybrid system, such as the MATCHMAKER system (BD Clontech).

PMMM may also be used in the PATHCALLING process (CuraGen Corp. , New Haven CT) which employs the yeast two-hybrid system in a high-throughput manner to determine all interactions between the proteins encoded by two large libraries of genes (Nandabalan, K. et al. (2000) U. S.

Patent No. 6,057, 101).

XVIII. Demonstration of PMMM Activity PMMM activity can be demonstrated using a generic immunoblotting strategy or through a variety of specific activity assays, some of which are outlined below. As a general approach, cell lines or tissues transformed with a vector containing PMMM coding sequences can be assayed for PMMM activity by immunoblotting. Transformed cells are denatured in SDS in the presence of b- mercaptoethanol, nucleic acids are removed by ethanol precipitation, and proteins are purified by acetone precipitation. Pellets are resuspended in 20 mM Tris buffer at pH 7.5 and incubated with Protein G-Sepharose pre-coated with an antibody specific for PMMM. After washing, the Sepharose beads are boiled in electrophoresis sample buffer, and the eluted proteins subjected to SDS-PAGE.

The SDS-PAGE is transferred to a membrane for immunoblotting, and the PMMM activity is assessed by visualizing and quantifying bands on the blot using the antibody specific for PMMM as the primary antibody and"'I-labeled IgG specific for the primary antibody as the secondary antibody.

PMMM kinase activity is measured by quantifying the phosphorylation of a protein substrate by PMMM in the presence of gamma-labeled 32P-ATP. PMMM is incubated with the protein substrate, 32P-ATP, and an appropriate kinase buffer. The 32p incorporated into the substrate is separated from free 32P-ATP by electrophoresis and the incorporated 32p iS counted using a radioisotope counter. The amount of incorporated 32p is proportional to the activity of PMMM. A determination of the specific amino acid residue phosphorylated is made by phosphoamino acid analysis of the hydrolyzed protein.

PMMM phosphatase activity is measured by the hydrolysis of p-nitrophenyl phosphate (PNPP). PMMM is incubated together with PNPP in HEPES buffer, pH 7.5, in the presence of 0. 1%,-mercaptoethanol at 37°C for 60 min. The reaction is stopped by the addition of 6 ml of 10 N NaOH and the increase in light absorbance at 410 nm resulting from the hydrolysis of PNPP is measured using a spectrophotometer. The increase in light absorbance is proportional to the activity of PMMM in the assay (Diamond, R. H. et al. (1994) Mol. Cell. Biol. 14: 3752-3762).

In the alternative, PMMM phosphatase activity is determined by measuring the amount of phosphate removed from a phosphorylated protein substrate. Reactions are performed with 2 or 4 nM enzyme in a final volume of 30/, tl containing 60 mM Tris, pH 7.6, 1 mM EDTA, 1 mM EGTA, 0. 1% 2-mercaptoethanol and 10 CM substrate, 32P-labeled on serine/threonine or tyrosine, as appropriate.

Reactions are initiated with substrate and incubated at 30° C for 10-15 min. Reactions are quenched with 450 ttl of 4% (w/v) activated charcoal in 0.6 M HC1, 90 mM Na4P207, and 2 mM NaH2PO4, then centrifuged at 12,000 x g for 5 min. Acid-soluble 32Pi is quantified by liquid scintillation counting (Sinclair, C. et al. (1999) J. Biol. Chem. 274: 23666-23672).

PMMM protease activity is measured by the hydrolysis of appropriate synthetic peptide substrates conjugated with various chromogenic molecules in which the degree of hydrolysis is quantified by spectrophotometric (or fluorometric) absorption of the released chromophore (Beynon, R. J. and J. S. Bond (1994) Proteolytic Enzymes : A Practical Approach, Oxford University Press, New York, NY, pp. 25-55). Peptide substrates are designed according to the category of protease activity as endopeptidase (serine, cysteine, aspartic proteases, or metalloproteases), aminopeptidase (leucine aminopeptidase), or carboxypeptidase (carboxypeptidases A and B, procollagen C-proteinase).

Commonly used chromogens are 2-naphthylamine, 4-nitroaniline, and furylacrylic acid. Assays are performed at ambient temperature and contain an aliquot of the enzyme and the appropriate substrate in a suitable buffer. Reactions are carried out in an optical cuvette, and the increase/decrease in absorbance of the chromogen released during hydrolysis of the peptide substrate is measured. The change in absorbance is proportional to the enzyme activity in the assay.

In the alternative, an assay for PMMM protease activity takes advantage of fluorescence resonance energy transfer (FRET) that occurs when one donor and one acceptor fluorophore with an appropriate spectral overlap are in close proximity. A flexible peptide linker containing a cleavage site specific for PMMM is fused between a red-shifted variant (RSGFP4) and a blue variant (BFP5) of Green Fluorescent Protein. This fusion protein has spectral properties that suggest energy transfer is occurring from BFP5 to RSGFP4. When the fusion protein is incubated with PMMM, the substrate is cleaved, and the two fluorescent proteins dissociate. This is accompanied by a marked decrease in energy transfer which is quantified by comparing the emission spectra before and after the addition of PMMM (Mitra, R. D. et al (1996) Gene 173: 13-17). This assay can also be performed in living cells.

In this case the fluorescent substrate protein is expressed constitutively in cells and PMMM is introduced on an inducible vector so that FRET can be monitored in the presence and absence of PMMM (Sagot, I. et al (1999) FEBS Letters 447: 53-57).

An assay for ubiquitin hydrolase activity measures the hydrolysis of a ubiquitin precursor. The assay is performed at ambient temperature and contains an aliquot of PMMM and the appropriate substrate in a suitable buffer. Chemically synthesized human ubiquitin-valine may be used as substrate. Cleavage of the C-terminal valine residue from the substrate is monitored by capillary electrophoresis (Franklin, K. et al. (1997) Anal. Biochem. 247: 305-309).

PMMM protease inhibitor activity for alpha 2-HS-glycoprotein (AHSG) can be measured as a decrease in osteogenic activity in dexamethasone-treated rat bone marrow cell cultures (dex-RBMC).

Assays are carried out in 96-well culture plates containing minimal essential medium supplemented with 15% fetal bovine serum, ascorbic acid (50 mg/ml), antibiotics (100 mg/ml penicillin G, 50 mg/ml gentamicin, 0.3 mg/ml fungizone), 10 mM B-glycerophosphate, dexamethasone (10-8 M) and various concentrations of PMMM for 12-14 days. Mineralized tissue formation in the cultures is quantified by measuring the absorbance at 525 nm using a 96-well plate reader (Binkert, C. et al. (1999) J. Biol.

Chem. 274: 28514-28520).

PMMM protease inhibitor activity for inter-alpha-trypsin inhibitor (ITI) can be measured by a continuous spectrophotometric rate determination of trypsin activity. The assay is performed at ambient temperature in a quartz cuvette in pH 7.6 assay buffer containing 63 mM sodium phosphate, 0.23 mM N a-benzoyle-L-arginine ethyl ester, 0.06 mM hydrochloric acid, 100 units trypsin, and various concentrations of PMMM. Immediately after mixing by inversion, the increase in A253 nm is recorded for approximately 5 minutes and the enzyme activity is calculated (Bergmeyer, H. U. et al.

(1974) Meth. Enzym. Anal. 1: 515-516).

PMMM isomerase activity such as peptidyl prolyl cisltrans isomerase activity can be assayed by an enzyme assay described by Rahfeld, J. U. , et al. (1994; FEBS Lett. 352: 180-184). The assay is performed at 10°C in 35 mM HEPES buffer, pH 7.8, containing chymotrypsin (0.5 mg/ml) and PMMM at a variety of concentrations. Under these assay conditions, the substrate, Suc-Ala-Xaa- Pro-Phe-4-NA, is in equilibrium with respect to the prolyl bond, with 80-95% in trans and 5-20% in cis conformation. An aliquot (2 ml) of the substrate dissolved in dimethyl sulfoxide (10 mg/ml) is added to the reaction mixture described above. Only the cis isomer of the substrate is a substrate for cleavage by chymotrypsin. Thus, as the substrate is isomerized by PMMM, the product is cleaved by chymotrypsin to produce 4-nitroanilide, which is detected by it's absorbance at 390 nm. 4-nitroanilide appears in a time-dependent and a PMMM concentration-dependent manner.

PMMM galactosyltransferase activity can be determined by measuring the transfer of radiolabeled galactose from UDP-galactose to a GlcNAc-terminated oligosaccharide chain (Kolbinger, F. et al. (1998) J. Biol. Chem. 273: 58-65). The sample is incubated with 14 y1 of assay stock solution

(180 mM sodium cacodylate, pH 6.5, 1 mg/ml bovine serum albumin, 0.26 mM UDP-galactose, 2 Al of UDP- [3H] galactose), 1 Al of MnCl, (500 mM), and 2. 5 1 ofGlcNAcpO- (CHJ,-CO, Me (37 mg/ml in dimethyl sulfoxide) for 60 minutes at 37°C. The reaction is quenched by the addition of 1 ml of water and loaded on a C18 Sep-Pak cartridge (Waters), and the column is washed twice with 5 ml of water to remove unreacted UDP-[3H] galactose. The [3H] galactosylated GlcNAcßO-(CH2) 8-CO2Me remains bound to the column during the water washes and is eluted with 5 ml of methanol.

Radioactivity in the eluted material is measured by liquid scintillation counting and is proportional to galactosyltransferase activity in the starting sample.

PMMM induction by heat or toxins may be demonstrated using primary cultures of human fibroblasts or human cell lines such as CCL-13, HEK293, or HEP G2 (ATCC). To heat induce PMMM expression, aliquots of cells are incubated at 42°C for 15,30, or 60 minutes. Control aliquots are incubated at 37°C for the same time periods. To induce PMMM expression by toxins, aliquots of cells are treated with 100, uM arsenite or 20 mM azetidine-2-carboxylic acid for 0,3, 6, or 12 hours.

After exposure to heat, arsenite, or the amino acid analogue, samples of the treated cells are harvested and cell lysates prepared for analysis by western blot. Cells are lysed in lysis buffer containing 1% Nonidet P-40,0. 15 M NaCl, 50 mM Tris-HCI, 5 mM EDTA, 2 mM N-ethylmaleimide, 2 mM phenylmethylsulfonyl fluoride, 1 mg/ml leupeptin, and 1 mg/ml pepstatin. Twenty micrograms of the cell lysate is separated on an 8% SDS-PAGE gel and transferred to a membrane. After blocking with 5% nonfat dry milk/phosphate-buffered saline for 1 h, the membrane is incubated overnight at 4°C or at room temperature for 2-4 hours with an appropriate dilution of anti-PMMM serum in 2% nonfat dry milk/phosphate-buffered saline. The membrane is then washed and incubated with a 1: 1000 dilution of horseradish peroxidase-conjugated goat anti-rabbit IgG in 2% dry milk/phosphate-buffered saline. After washing with 0. 1 % Tween 20 in phosphate-buffered saline, the PMMM protein is detected and compared to controls using chemiluminescence.

PMMM lysyl hydroxylase activity is determined by measuring the production of hydroxy [l4C] lysine from [l4C] lysine. Radiolabeled protocollagen is incubated with PMMM in buffer containing ascorbic acid, iron sulfate, dithiothreitol, bovine serum albumin, and catalase. Following a 30 minute incubation, the reaction is stopped by the addition of acetone, and centrifuged. The sedimented material is dried, and the hydroxy ['4C] lysine is converted to ['4C] formaldehyde by oxidation with periodate, and then extracted into toluene. The amount of'4C extracted into toluene is quantified by scintillation counting, and is proportional to the activity of PMMM in the sample (Kivirikko, K. , and R. Myllyla (1982) Methods Enzymol. 82: 245-304).

XIX. Identification of PMMM Substrates

Phage display libraries can be used to identify optimal substrate sequences for PMMM. A random hexamer followed by a linker and a known antibody epitope is cloned as an N-terminal extension of gene III in a filamentous phage library. Gene III codes for a coat protein, and the epitope will be displayed on the surface of each phage particle. The library is incubated with PMMM under proteolytic conditions so that the epitope will be removed if the hexamer codes for a PMMM cleavage site. An antibody that recognizes the epitope is added along with immobilized protein A. Uncleaved phage, which still bear the epitope, are removed by centrifugation. Phage in the supernatant are then amplified and undergo several more rounds of screening. Individual phage clones are then isolated and sequenced. Reaction kinetics for these peptide substrates can be studied using an assay in Example XVIII, and an optimal cleavage sequence can be derived (Ke, S. H. et al. (1997) J. Biol.

Chem. 272: 16603-16609).

To screen for in vivo PMMM substrates, this method can be expanded to screen a cDNA expression library displayed on the surface of phage particles (T7SELECT10-3 Phage display vector, Novagen, Madison, WI) or yeast cells (pYDl yeast display vector kit, Invitrogen, Carlsbad, CA). In this case, entire cDNAs are fused between Gene III and the appropriate epitope.

XX. Identification of PMMM Inhibitors Compounds to be tested are arrayed in the wells of a multi-well plate in varying concentrations along with an appropriate buffer and substrate, as described in the assays in Example XVIII. PMMM activity is measured for each well and the ability of each compound to inhibit PMMM activity can be determined, as well as the dose-response kinetics. This assay could also be used to identify molecules which enhance PMMM activity.

In the alternative, phage display libraries can be used to screen for peptide PMMM inhibitors.

Candidates are found among peptides which bind tightly to a protease. In this case, multi-well plate wells are coated with PMMM and incubated with a random peptide phage display library or a cyclic peptide library (Koivunen, E. et al. (1999) Nature Biotech 17: 768-774). Unbound phage are washed away and selected phage amplified and rescreened for several more rounds. Candidates are tested for PMMM inhibitory activity using an assay described in Example XVIII.

Various modifications and variations of the described compositions, methods, and systems of the invention will be apparent to those skilled in the art without departing from the scope and spirit of the invention. It will be appreciated that the invention provides novel and useful proteins, and their encoding polynucleotides, which can be used in the drug discovery process, as well as methods for using these compositions for the detection, diagnosis, and treatment of diseases and conditions.

Although the invention has been described in connection with certain embodiments, it should be understood that the invention as claimed should not be unduly limited to such specific embodiments.

Nor should the description of such embodiments be considered exhaustive or limit the invention to the precise forms disclosed. Furthermore, elements from one embodiment can be readily recombined with elements from one or more other embodiments. Such combinations can form a number of embodiments within the scope of the invention. It is intended that the scope of the invention be defined by the following claims and their equivalents.

Table 1 Incyte Project ID Polypeptide Incyte Polynucleotide Incyte SEQ ID NO : Polypeptide ID SEQ ID NO : Polynucleotide ID Incyte Full Length Clones 7511804 1 7511804CD1 63 7511804CB1 7512233 2 7512233CD 1 64 7512233CB 1 7512557 3 7512557CD1 65 7512557CB 1 7512559 4 7512559CD 1 66 7512559CB 1 6534745 5 6534745CD 1 67 6534745CB 1 7512625 6 7512625CD 1 68 7512625CB 1 7512761 7 7512761CD1 69 7512761CB1 7512802 8 7512802CD1 70 7512802CB1 7512824 9 7512824CD 1 71 7512824CB 1 2052032CA2 7512760 10 7512760CD1 72 7512760CB 1 7512798 11 7512798CD1 73 7512798CB1 95161728CA2 7512799 12 7512799CD 1 74 7512799CB 1 7512840137512840CD1 757512840CB1 7512889 14 7512889CD1 76 7512889CB 1 7512901 15 7512901CD1 77 7512901CB1 7512949 16 7512949CD1 78 7512949CB 1 7512660 17 7512660CD 1 79 7512660CB 1 7512741 18 7512741CD1 80 7512741CB 1 7513099 19 7513099CD 1 81 7513099CB 1 7511908 20 7511908CD1 82 7511908CB 1 4299961CA2 7513074 21 7513074CD 1 83 7513074CB 1 7513960 22 7513960CD1 84 7513960CB1 95009722CA2 7513984 23 7513984CD1 85 7513984CB 1 7512992 24 7512992CD 1 86 7512992CB 1 7512994 25 7512994CD1 87 7512994CB 1 7513547 26 7513547CD1 88 7513547CB1 90010371CA2 7513357 27 7513357CD1 89 7513357CB1 7513329 28 7513329CD1 90 7513329CB1 7517777 29 7517777CD1 91 7517777CB 1 90136329CA2 Table 1 Incyte Project ID Polypeptide Incyte Polynucleotide Incyte SEQ ID NO : Polypeptide ID SEQ ID NO : Polynucleotide ID Incyte Full Length Clones 7519126 30 7519126CD1 92 7519126CB1 90136381CA2 7519175 31 7519175CD1 93 7519175CB 1 7514648 32 7514648CD1 94 7514648CB1 90212105CA2 7517904 33 7517904CD1 95 7517904CB 1 8004710CA2 7518798 34 7518798CD1 96 7518798CB 1 95068320CA2 7519109. 35 7519109CD 1 97 7519109CB 1 90130192CA2 7519227 36 7519227CD1 98 7519227CB 1 95089362CA2 7519262 37 7519262CD1 99 7519262CB1 90172212CA2 7519371 38 7519371CD1 100 7519371CB1 95091964CA2 7519442 39 7519442CD1 101 7519442CB 1 95065154CA2 7519123 40 7519123CD 1 102 7519123CB 1 90136150CA2, 90136234CA2 7519522 41 7519522CD 1 103 7519522CB 1 95091885CA2 7520023 42 7520023CD 1 104 7520023CB 1 95117413CA2 7519518 43 7519518CD 1 105 7519518CB 1 95092069CA2 95104043CA2, 95104127CA2, 95104135CA2, 95104203CA2, 95104251CA2, 95104283CA2, 95104311CA2, 95104327CA2, 7519955 44 7519955CD1 106 7519955CB1 95104335CA2, 95104343CA2, 95104383CA2 7514925 45 7514925CD1 107 7514925CB 1 7518514 46 7518514CD1 108 7518514CB1 95068419CA2 7519481 47 7519481CD1 109 7519481CB1 95092619CA2 7519529 48 7519529CD 1 110 7519529CB 1 7519549 49 7519549CD1 111 7519549CB1 95092053CA2 7520124 50 7520124CD 1 112 7520124CB 1 95117616CA2, 95117708CA2, 95117929CA2 7515245 51 7515245CD 1 113 7515245CB 1 7519933 52 7519933CD1 114 7519933CB1 95113610CA2 7520101 53 7520101CD1 115 7520101CB1 95113718CA2 7520145 54 7520145CD1 116 7520145CB 1 95109808CA2, 95109948CA2, 95109956CA2 7520174 55 7520174CD1 117 7520174CB1 95109916CA2 7520191 56 7520191CD1 118 7520191CB1 95107938CA2 Table 1 Incyte Project ID Polypeptide Incyte Polynucleotide Incyte SEQ ID NO : Polypeptide ID SEQ ID NO : Polynucleotide ID Incyte Full Length Clones 7520243 57 7520243CD1 119 7520243CB 1 95117450CA2, 95117550CA2 7521695 58 7521695CD 1 120 7521695CB 1 7520801 59 7520801CD1 121 7520801CB1 95122779CA2 7520817 60 7520817CD1 122 7520817CB1 95127803CA2, 95128166CA2 7520937 61 7520937CD1 123 7520937CB1 95131020CA2 7521694 62 7521694CD 1 124 7521694CB 1 Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 1 7511804CD1 g6561816 1. 6E-143 [Homo sapiens] aspartyl protease 3 Yan, R. et al. Membrane-anchored aspartyl protease with Alzheimer's disease beta- secretase activity, Nature 402, 533-537 (1999) 1 7511804CD1 3409061NAPl 5. 0E-127 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Pronapsin A, aspartic-type endopeptidase that may play a role in lung surfactant precursor proteolytic processing and as a marker for primary lung adenocarcinoma ; lack of NAP1 in the urine is associated with kidney dysfunction Suzuki, T. et al. Molecular cloning of a novel apoptosis-related gene, human Napl (NCKAP1), and its possible relation to Alzheimer disease. Genomics 63, 246-54 (2000). 1 7511804CD1 711592|Kdap 5. 7E-103 [Rattus norvegicus] Kidney-derived aspartic protease-like protein (napsin), aspartic-type endopeptidase ; human NAP1 may act as a marker for primary lung adenocarcinoma and lack of human NAP1 in the urine is associated with kidney dysfunction Schauer-Vukasinovic, V. et al. Cloning, expression and functional characterization of rat napsin. Biochim Biophys Acta 1492, 207-10. (2000). 2 7512233CD1 g473615 5. 5E-175 [Homo sapiens] haptoglobin-related protein Maeda, N. Nucleotide sequence of the haptoglobin and haptoglobin-related gene pair. The haptoglobin-related gene contains a retrovirus-like element, J. Biol. Chem. 260, 6698-6709 (1985) 2 7512233CD1 613425|HPR 7. 0E-176 [Homo sapiens] [Structural protein] Haptoglobin-related protein, a plasma protein with similarity to haptoglobin, functions as a component of the Trypanosome lytic factor complex in host defense against Trypanosoma brucei brucei ; upregulated during tumor progression Smith, A. B. et al. Killing of trypanosomes by the human haptoglobin-related protein, Science 268, 284-6 (1995). Arcoleo, J. P. et al. Hemoglobin binding site and its relationship to the serine protease-like active site of haptoglobin. J Biol Chem 257, 10063-8 (1982).

Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 2 7512233CD1 341638lHP 1. 2E-158 [Homo sapiens] [Structural protein] Haptoglobin, a hemoglobin-binding plasma glycoprotein with putative antioxidant and angiogenic properties, may function in infection and inflammation ; genetic mutations are associated with anhaptoglobinemia, a transfusion- related anaphylaxis response Dumoutier, L. et al. Human interleukin-10-related T cell-derived inducible factor : molecular cloning and functional characterization as an hepatocyte-stimulating factor, Proc Natl Acad Sci U S A 97, 10144-9 (2000). 3 7512557CD1 gl483187 0. 0 [Homo sapiens] inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP) Saguchi, K. et al. Cloning and characterization of cDNA for inter-alpha-trypsin inhibitor family heavy chain-related protein (IHRP), a novel human plasma glycoprotein, J. Biochem. 117, 14-18 (1995) 3 7512557CD1 336080|ITIH4 0. 0 [Homo sapiens] [Regulatory subunit ; Structural protein ; Inhibitor or repressor] [Extracellular matrix (cuticle and basement membrane)] Inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein), non-catalytic subunit of protease inhibitor complex which stabilizes the extracellular matrix, sensitive to plasma kallikrein ; increases in serum during acute phase response Pineiro, M. et al. ITIH4 serum concentration increases during acute-phase processes in human patients and is up-regulated by interleukin-6 in hepatocarcinoma HepG2 cells. Biochem Biophys Res Commun 263, 224-9. (1999). 3 7512557CD1 608150|Itih4 2. 9E-250 [Mus musculus] [Regulatory subunit ; Structural protein ; Inhibitor or repressor] [Extracellular matrix (cuticle and basement membrane)] Inter alpha-trypsin inhibitor (heavy chain 4), inter alpha-trypsin inhibitor proteoglycan family member, noncatalytic subunits of a protease inhibitor complex that stabilizes the extracellular matrix, may play a role in liver development Cai, T. et al. Identification of mouse itih-4 encoding a glycoprotein with two EF-hand motifs from early embryonic liver. Biochim Biophys Acta 1398, 32-7 (1998).

Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 4 7512559CD1 gl483187 0. 0 [Homo sapiens] inter-alpha-trypsin inhibitor family heavy chain-related protein (BHRP) Saguchi, K. et al. (supra) 4 7512559CD1 3360801ITIH4 0. 0 [Homo sapiens] [Regulatory subunit ; Structural protein ; Inhibitor or repressor] [Extracellular matrix (cuticle and basement membrane)] Inter-alpha (globulin) inhibitor H4 (plasma Kallikrein-sensitive glycoprotein), non-catalytic subunit of protease inhibitor complex which stabilizes the extracellular matrix, sensitive to plasma kallikrein ; increases in serum during acute phase response Pineiro, M. et al. ITIH4 serum concentration increases during acute-phase processes in human patients and is up-regulated by interleukin-6 in hepatocarcinoma HepG2 cells. Biochem Biophys Res Commun 263, 224-9. (1999). (supra) 4 7512559CD1 6081501Itih4 0. 0 [Mus musculus] [Regulatory subunit ; Structural protein ; Inhibitor or repressor] [Extracellular matrix (cuticle and basement membrane)] Inter alpha-trypsin inhibitor (heavy chain 4), inter alpha-trypsin inhibitor proteoglycan family member, noncatalytic subunits of a protease inhibitor complex that stabilizes the extracellular matrix, may play a role in liver development Cai, T. et al. Identification of mouse itih-4 encoding a glycoprotein with two EF-hand motifs from early embryonic liver. Biochim Biophys Acta 1398, 32-7 (1998). (supra) 5 6534745CD1 g6850321 1. 2E-146 [Arabidopsis thaliana] Contains similarity to YTA7 ATPase gene 5 6534745CD1 716281lMGC525 3. 0E-216 [Homo sapiens] Member of the ATPase family associated with various cellular activities, 4 has a region of moderate similarity to a region of valosin containing protein (mouse Vcp), which is a clathrin-binding ATPase involved in cell cycle control and protein degradation 6 7512625CD1 g219681 1. 3E-70 [Homo sapiens] HGF activator precursor Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Miyazawa, K. et al. Molecular cloning and sequence analysis of the cDNA for a human serine protease reponsible for activation of hepatocyte growth factor. Structural similarity of the protease precursor to blood coagulation factor XII, J. Biol. Chem. 268, 10024-10028 (1993) 6 7512625CD1 335774|HGFAC 1. OE-71 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Hepatocyte growth factor activator, a factor XIIa (F12)-like serine protease that processes and activates the hepatocyte growth factor precursor (HGF), altered expression and HGF activation may contribute to the progression of colorectal carcinomas Kataoka, H. et al. Activation of hepatocyte growth factor/scatter factor in colorectal carcinoma, Cancer Res 60, 6148-59 (2000). 6 7512625CD1 608438lHgfac 7. 9E-37 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] Hepatocyte growth factor activator, a serine protease that processes and activates the hepatocyte growth factor precursor (Hgf), plays a key role in glomerulogenesis and nephrogenesis, and may function in maintenance of the gastrointestinal tract van Adelsberg, J. et al. Activation of hepatocyte growth factor (hgf) by endogenous hgf activator is required for metanephric kidney morphogenesis in vitro. J Biol Chem 276, 15099-106. (2001). 7 7512761CD1 g3746882 5. 2E-12 [Homo sapiens] 26S proteasome subunit 11 7 7512761CD1 475423lPSMDl3 l. 9E-12 [Homo sapiens] [Proteasome subunit] [Cytoplasmic] Proteasome (prosome, macropain) 26S subunit (non-ATPase, 13), a subunit of the PA700 regulatory comples of the 26S proteasome Coux, O. et al. Structure and functions of the 20S and 26S proteasomes. Annu Rev Biochem 65, 801-47 (1996). 7512761CD1 4301881Psmdl3 1. 4E-11 [Mus musculus] [Proteasome subunit] [Cytoplasmic] Proteasome (prosome, macropain) 26S subunit (non-ATPase, 13), the putative homolog of human PSMD13, which is a non- ATPase subunit of the 26S proteasome Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Hori, T. et al. cDNA cloning and functional analysis of p28 (Nas6p) and p40. 5 (Nas7p), two novel regulatory subunits of the 26S proteasome. Gene 216, 113-122 (1998). (supra) 8 7512802CD1 g4322263 4. 6E-68 [Mus musculus] metallocarboxypeptidase CPX-1 Lei, Y. et al. Identification of mouse CPX-1, a novel member of the metallocarboxypeptidase gene family with highest similarity to CPX-2, DNA Cell Biol. 18, 175-185 (1999) 8 7512802CD1 611008lCPXM 7. 9E-106 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Metallocarboxypeptidase CPX-1, member of the carboxypeptidase A (M14) family of zinc carboxypeptidases, has strong similarity to murine CPX-1, contains a F5/8 type C (discoidin) domain which is found in some extracellular and membrane proteins 8 7512802CD1 6086701Cpxl 3. 6E-69 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] Carboxypeptidase XI, member of carboxypeptidase E family that does not cleave typical carboxypeptidase substrates and thus is unlikely to function in processing of neuroendocrine peptides, may have a role in development Lei, Y. et al. Identification of mouse CPX-1, a novel member of the metallocarboxypeptidase gene family with highest similarity to CPX-2. DNA Cell Biol 18, 175-85 (1999). 9 7512824CD1 g951198 0. 0 [Homo sapiens] erythrocyte membrane protein Korsgren, C. et al. Organization of the gene for human erythrocyte membrane protein 4. 2 : structural similarities with the gene for the a subunit of factor XIII, Proc. Natl. Acad. Sci. U. S. A. 88, 4840-4844 (1991) 9 7512824CD1 339322EPB42 0. 0 [Homo sapiens] [Structural protein] [Cytoplasmic ; Cytoskeletal ; Plasma membrane] Erythrocyte membrane protein 4. 2, an ATP-binding protein involved in strenghtening cytoskeletal-membrane interactions ; deficiency causes spheocytosis and hemolytic anemia Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : I Azim, A. C. et al. Human erythrocyte dematin and protein 4. 2 (pallidin) are ATP binding proteins. Biochemistry 35, 3001-6 (1996). 9 7512824CD1 586971lEpb4. 2 5. 8E-260 [Mus musculus] [Structural protein] [Unspecified membrane ; Plasma membrane] Erythrocyte membrane protein 4. 2 ; deficiency of human EPB42 causes spheocytosis and hemolytic anemia Huang, S. et al. P/CAF-mediated acetylation regulates the function of the basic helix-loop- helix transcription factor TALl/SCL. Embo Journal 19, 6792-6803 (2000). 10 7512760CD1 g10933784 6. 8E-276 [Homo sapiens] aminopeptidase B 10 7512760CD1 703771|RNPEP 1. 4E-267 [Homo sapiens] Aminopeptidase B (arginyl aminopeptidase), zinc metallopeptidase in the Ml family of metallopeptidases, has a substrate preference for basic N-terminal residues, may regulate concentrations of mediators of T cell activation Fukasawa, K. M. et al. Aminopeptidase B is structurally related to leukotriene-A4 hydrolase but is not a bifunctional enzyme with epoxide hydrolase activity. Biochem J 339, 497-502 (1999). 10 7512760CD1 704992|Rnpep 8. 2E-241 [Rattus norvegicus] [Hydrolase ; Protease (other than proteasomal)] Aminopeptidase B, zinc metallopeptidase in the M1 family of metallopeptidases, has a substrate preference for N- terminal arginine and lysine residues, may function in secretory pathways and in spermatid development Cadel, S. et al. Aminopeptidase B from the rat testis is a bifunctional enzyme structurally related to leukotriene-A4 hydrolase. Proc Natl Acad Sci U S A 94, 2963-8 (1997). 11 7512798CD1 g6581112 7. 4e-22 [Rattus norvegicus] tubulin tyrosine ligase 12 7512799CD1 g2200 4. 1E-168 [Sus scrofa] tubulin-tyrosine ligase Ersfeld, K. et al. Characterization of the tubulin-tyrosine ligase, J. Cell Biol. 120, 725-732 (1993) Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 12 7512799CD1 5696041DKFZP4 2. 2E-12 [Homo sapiens] Member of the tubulin-tyrosine ligase family 34B 103 12 7512799CD1 709719lNYD-6. 7E-12 [Homo sapiens] Member of the tubulin-tyrosine ligase family TSPG 13 7512840CD1 gl850823 6. 0E-59 [Homo sapiens] sialidase Milner, C. M. et al. Identification of a sialidase encoded in the human major histocompatibility complex, J. Biol. Chem. 272, 4549-4558 (1997) 13 7512840CD1 339542lNEUl 4. 7E-60 [Homo sapiens] [Hydrolase] [Lysosome/vacuole ; Cytoplasmic] Neuraminidase 1 (lysosomal neuraminidase, sialidase 1), acts in catabolism of sialoglycoconjugates, forms a complex with beta galactosidase (GLB 1) and protective protein cathepsin A (PPGB) ; deficiency is associated with sialidosis and galactosialidosis Bonten, E. J. et al. Novel mutations in lysosomal neuraminidase identify functional domains and determine clinical severity in sialidosis, Hum Mol Genet 9, 2715-25 (2000). 13 7512840CD1 586483|Neul 1. 4E-35 [Mus musculus] [Hydrolase] [Lysosome/vacuole ; Cytoplasmic] Neuraminidase 1 (lysosomal sialidase), catalyzes the hydrolysis of terminal sialic acid residues, may form a complex with beta galactosidase (Bgl) and cathepsin A (Ppgb) ; lack of human NEU1 is associated with sialidosis and galactosialidosis Carrillo, M. B. et al. Cloning and characterization of a sialidase from the murine histocompatibility-2 complex : low levels of mRNA and a single amino acid mutation are responsible for reduced sialidase activity in mice carrying the Neula allele. Glycobiology 7, 975-86 (1997). 14 7512889CD1 gll36406 0. 0 [Homo sapiens] similar to pig tubulin-tyrosine ligase. 14 7512889CD1 7732451ZK1128. 2. 1E-105 [Caenorhabditis elegans] Possible tubulin tyrosine ligase, putative ortholog of H. sapiens Hs. 1699 10 protein 14 7512889CD1 6257771TTLL1 4. 1E-36 [Homo sapiens] Member of the tubulin-tyrosine ligase family Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Trichet, V. et al. Characterization of the human tubulin tyrosine ligase-like 1 gene (TTLL1) mapping to 22ql3. 1, Gene 257, 109-17 (2000). 15 7512901CD1 gl332508 4. 1E-53 [Homo sapiens] geranylgeranyl transferase II Johannes, L. et al. Characterization of the interaction of the monomeric GTP-binding protein Rab3a with geranylgeranyl transferase II, Eur. J. Biochem. 239, 362-368 (1996) 15 7512901CD1 341152lRABGG 3. 2E-54 [Homo sapiens] [Transferase] Beta subunit of geranylgeranyl transferase, may transfer TB geranylgeranyl groups to cysteines at the C-terminus of Rab proteins, may play a role in vision Seabra, M. C. et al. Retinal degeneration in choroideremia : deficiency of rab geranylgeranyl transferase. Science 259, 377-81 (1993). 15 7512901CD1 772638lRabggtb 4. 2E-52 [Rattus norvegicus] [Transferase] Beta subunit of geranylgeranyl transferase, transfers geranylgeranyl groups to cysteines at the C-terminus of Rab proteins, plays a role in prenyl- mediated Rab protein interaction with the cellular membrane Bruscalupi, G. et al. Enhanced prenyltransferase activity and Rab content in rat liver regeneration. Biochem Biophys Res Commun 269, 226-31 (2000). 16 7512949CD1 g340070 1. 8E-20 [Homo sapiens] ubiquitin-like protein Toniolo, D. et al. A'housekeeping'gene on the X chromosome encodes a protein similar to ubiquitin, Proc. Natl. Acad. Sci. U. S. A. 85, 851-855 (1988) 16 7512949CD1 569526lUBL4 1. 4E-21 [Homo sapiens] [Protein conjugation factor] Ubiquitin-like 4, protein with similarity to ubiquitin, may have a role in protein-protein interactions, may act as a housekeeping protein 16 7512949CD1 3214281Mm. 3979 6. 9E-20 [Mus musculus] [Protein conjugation factor] Member of the ubiquitin family 17 7512660CD1 g243888 1. 7E-29 [Homo sapiens] ubiquitin carboxyl extension protein ; HUBCEP80 Adams, S. M. et al. Differential expression of translation-associated genes in benign and malignant human breast tumours, Br. J. Cancer 65, 65-71 (1992) 18 7512741CD1 gl4279329 0. 0 [Homo sapiens] (AF266283) ubiquitin specific protease Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Valero, R. et al. Characterization of alternatively spliced products and tissue-specific isoforms of USP28 and USP25, Genome Biol. 2001 ; 2 (10) : RESEARCH0043 18 7512741CD1 438259lUsp25 1. 2E-259 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] Ubiquitin specific protease 25, putative C-terminal ubiquitin hydrolase, may be involved in the development and differentiation of highly proliferative tissues ; human USP25 shows loss of heterozygosity in non small cell lung carcinomas Valero, R. et al. USP25, a novel gene encoding a deubiquitinating enzyme, is located in the gene-poor region 21ql 1. 2. Genomics 62, 395-405 (1999). 18 7512741CD1 432832lUSP25 2. 0E-259 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Ubiquitin specific protease 25, a C-terminal ubiquitin hydrolase ; loss of heterozygosity is seen in non small cell lung carcinomas, candidate for involvement in chromosome 21 Trisomy (Down syndrome) and its associated defective spermiogenesis Groet, J. et al. Narrowing of the region of allelic loss in 21ql 1-21 in squamous non-small cell lung carcinoma and cloning of a novel ubiquitin-specific protease gene from the deleted segment. Genes Chromosomes Cancer 27, 153-61 (2000). 19 7513099CD1 g3954938 2. 6E-145 [Homo sapiens] acetylglucosaminyltransferase-like protein Peyrard, M. et al., The human LARGE gene from 22ql2. 3-ql3. 1 is a new, distinct member of the glycosyltransferase gene family, Proc. Natl. Acad. Sci. U. S. A. 96, 598-603 (1999) 19 7513099CD1 3408221LARGE 2. 0E-146 [Homo sapiens] [Transferase] [Golgi ; Cytoplasmic] Acetylglucosaminyltransferase-like protein, an N-acetylglucosaminyltransferase, abnormal function may lead to the development of meningioma ; altered posttranslational modification of mouse Large may contribute to myodystrophy Peyrard, M. et al., (supra) Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 19 7513099CD1 585179Large 2. 6E-146 [Mus musculus] [Transferase] [Golgi ; Cytoplasmic] Acetylglucosaminyltransferase-like protein, an N-acetylglucosaminyltransferase that functions in protein glycosylation, abnormal posttranslational modification may contribute to myodystrophy ; abnormal function of human LARGE may contribute to meningioma Grewal, P. K. et al., Mutant glycosyltransferase and altered glycosylation of alpha- dystroglycan in the myodystrophy mouse., Nat Genet 28, 151-4. (2001). 20 7511908CD1 g338430 3. 9E-32 [Homo sapiens] serine protease Meier, M. et al., Cloning of a gene that encodes a new member of the human cytotoxic cell protease family, Biochemistry 29, 4042-4049 (1990) 20 7511908CD1 7491381CTLAl 3. 0E-33 [Homo sapiens] Granzyme H (cytotoxic serine protease-C), serine protease that functions in cell-mediated cytotoxicity MacIvor, D. M. et al., The 5'flanking region of the human granzyme H gene directs expression to T/natural killer cell progenitors and lymphokine-activated killer cells in transgenic mice., Blood 93, 963-73 (1999). Edwards, K. M. et al., The human cytotoxic T cell granule serine protease granzyme H has chymotrypsin-like (chymase) activity and is taken up into cytoplasmic vesicles reminiscent of granzyme B-containing endosomes., J Biol Chem 274, 30468-73. (1999). 20 7511908CD1 3406681GZMB 9. 4E-23 [Homo sapiens] [Ligand ; Activator ; Hydrolase ; Protease (other than proteasomal)] [Cytoplasmic] Granzyme B (cytotoxic T-lymphocyte-associated serine esterase 1), a serine protease that is released by cytotoxic T-cells and induces apoptosis in target cells, plays a role in the immune response and in the host response to bacteria Rogge, L. et al., Transcript imaging of the development of human T helper cells using oligonucleotide arrays., Nat Genet 25, 96-101 (2000).

Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : a Barry, M. et al., Granzyme B short-circuits the need for caspase 8 activity during granule- mediated cytotoxic T-lymphocyte killing by directly cleaving Bid., MoI Cell Biol 20, 3781- 94 (2000). 21 7513074CD1 g6966967 0. 0 [Homo sapiens] dipeptidyl-peptidase III 21 7513074CD1 6239101DPP3 0. 0 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Dipeptidylpeptidase III, a zinc metalloexopeptidase that catalyzes removal of dipeptides, preferably Arg-Arg, from the N terminus of oligopeptides, degrades enkephalins (PENK), upregulated in endometrial and ovarian cancers Fukasawa, K. et al., The HELLGH motif of rat liver dipeptidyl peptidase m is involved in zinc coordination and the catalytic activity of the enzyme., Biochemistry 38, 8299-303 (1999). Simaga, S. et al., Dipeptidyl peptidase III in malignant and non-malignant gynaecological tissue., Eur J Cancer 34, 399-405. (1998). 21 7513074CD1 757284|Dpp3 0. 0 [Rattus norvegicus] [Hydrolase ; Protease (other than proteasomal)] Dipeptidyl peptidase III, a cytosolic zinc metalloexopeptidase that catalyzes removal of dipeptides from N-terminus of oligopeptides, degrades enkephalins (Penk) and angiotensins (Agt) ; human DPP3 is upregulated in endometrial and ovarian cancers Fukasawa, K. et al., (supra) Ohkubo, I. et al., Dipeptidyl peptidase III from rat liver cytosol : purification, molecular cloning and immunohistochemical localization., Biol Chem 380, 1421-30. (1999). 22 7513960CD1 g33793 5. 4E-177 [Homo sapiens] interleukin-lB converting enzyme Thornberry et, al., Interleukin-lB converting enzyme : a novel cysteine protease required for IL-1 beta production and implicated in progammed cell death, Protein Sci 4, 3-12. (1995).

Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 22 7513960CD1 748972lCASPl 4. 2E-178 [Homo sapiens] [Activator ; Hydrolase ; Protease (other than proteasomal)] Caspase 1 (interleukin-1 beta converting enzyme), a cysteine (thiol) protease that activates interleukin- 1 beta (IL1B) and stimulates apoptosis, as well as having roles in inflammation Ona, V. O. et al., Inhibition of caspase-1 slows disease progression in a mouse model of Huntington's disease, Nature 399, 263-7 (1999). Alnemri, E. S. et al., Cloning and expression of four novel isoforms of human interleukin-1 beta converting enzyme with different apoptotic activities., J Biol Chem 270, 4312-7 (1995). 22 7513960CD1 589903lCaspl 3. 3E-105 [Rattus norvegicus] [Activator ; Hydrolase ; Protease (other than proteasomal)] Caspase 1 (interleukin-1 beta converting enzyme), a cysteine (thiol) protease that activates interleukin- 1 beta (Illb) and stimulates apoptosis, as well as having roles in inflammation Keane, K. M. et al., Cloning, tissue expression and regulation of rat interleukin 1 beta converting enzyme., Cytokine 7, 105-10 (1995). Irahara, M. et al., Expression and hormonal regulation of rat ovarian interleukin-lbeta converting enzyme, a putative apoptotic marker : endocrine-and paracrine-dependence., J Reprod Immunol 45, 67-79 (1999). 23 7513984CD1 gl82833 3. lE-103 [Homo sapiens] preprofactor XI Fujikawa, K. et al., Amino acid sequence of human factor XI, a blood coagulation factor with four tandem repeats that are highly homologous with plasma prekallikrein, Biochemistry 25, 2417-2424 (1986) 23 7513984CD1 3361661KLKBl 6. 0E-60 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Extracellular (excluding cell wall)] Plasma kallikrein B 1 (Fletcher factor, prekallikrein), a serine protease that activates plasma prorenin to renin and functions early in blood coagulation, functions in adipogensis ; some alleles may be associated with end stage renal disease Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Yu, H. et al., Genomic structure of the human plasma prekallikrein gene, identification of allelic variants, and analysis in end-stage renal disease, Genomics 69, 225-34 (2000). Selvarajan, S. et al., A plasma kallikrein-dependent plasminogen cascade required for adipocyte differentiation., Nat Cell Biol 3, 267-75. (2001). 23 7513984CD1 6108281Ell 2. 6E-59 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Plasma membrane] Coagulation factor XI, a serine protease that promotes platelet-mediated blood coagulation, activates coagulation factor IX (F9), and may regulate cell adhesion ; alterations of the corresponding gene cause deficiency and altered blood coagulation Sun, M. F. et al., Identification of amino acids in the factor XI apple 3 domain required for activation of factor IX., J Biol Chem 274, 36373-8. (1999). Martincic, D. et al., Factor XI messenger RNA in human platelets., Blood 94, 3397-404. (1999). 24 7512992CD1 g6425040 2. 2E-148 [Homo sapiens] N-acetylglucosamine-l-phosphodiester alpha-N-acetylglucosaminidase Kornfeld, R. et al., Molecular cloning and functional expression of two splice forms of human N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase, J. Biol. Chem. 274, 32778-32785 (1999) 24 7512992CD1 475837LOC5117 1. 7E-149 [Homo sapiens] [Hydrolase] [Unspecified membrane] N-acetylglucosamine-1- 2 phosphodiester alpha-N-acetylglucosaminidase (mannose 6-phosphate uncovering enzyme), catalyzes the second step in the synthesis of the mannose 6-phosphate recognition signal on lysosomal enzymes Komfeld, R. et al., (supra) 24 7512992CD1 419869lApaa 2. 6E-107 [Mus musculus] [Hydrolase] [Plasma membrane] N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase, putative enzyme that functions in the synthesis of the mannose 6-phosphate recognition signal on lysosomal enzymes Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Kornfeld, R. et al., (supra) 25 7512994CD1 g6425040 2. 1E-255 [Homo sapiens] N-acetylglucosamine-l-phosphodiesteralpha-N-acetylglucosamin idase Kornfeld, R. et al. (supra) 25 7512994CD1 4758371LOC5117 1. 6E-256 [Homo sapiens] [Hydrolase] [Unspecified membrane] N-acetylglucosamine-1- 2 phosphodiester alpha-N-acetylglucosaminidase (mannose 6-phosphate uncovering enzyme), catalyzes the second step in the synthesis of the mannose 6-phosphate recognition signal on lysosomal enzymes Kornfeld, R. et al., (supra) 25 7512994CD 1 419869|Apaa 9. 2E-199 [Mus musculus] [Hydrolase] [Plasma membrane] N-acetylglucosamine-1-phosphodiester alpha-N-acetylglucosaminidase, putative enzyme that functions in the synthesis of the mannose 6-phosphate recognition signal on lysosomal enzymes Komfeld, R. et al., (supra) 26 7513547CD1 gl6756125 0. 0 [Homo sapiens] UDP-N-acetyl-alpha-D-galactosamine : polypeptide N- acetylgalactosaminyltransferase 7 Kumar, S. et al., Identification and initial characterization of 5000 expressed sequenced tags (ESTs) each from adult human normal and osteoarthritic cartilage cDNA libraries, Osteoarthr. Cartil. 9, 641-653 (2001) 26 7513547CD1 7558261LL_O-. G 0. 0 [Homo sapiens] Member of the glycosyl transferase family 2, contains a QXW (ricin B) ALNT7 lectin repeat domain, which may bind simple sugars, has moderate similarity to UDP-N- acetyl-alpha-D-galactosamine : polypeptide N-acetylgalactosaminyltransfer 4 (human GALNT4) 26 7513547CD 1 587925lGalnt4 1. 4E-79 [Mus musculus] [Transferase] [Golgi ; Cytoplasmic] DP-N-acetyl-alpha-D- galactosamine : polypeptide N-acetylgalactosaminyltransfer 4, transfers N- acetylgalactosamine to acceptor polypeptides at serine and threonine residues Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Hagen, F. K. et al., cDNA cloning and expression of a novel UDP-N-acetyl-D- galactosamine : polypeptide N-acetylgalactosaminyltransferase., J Biol Chem 272, 13843-8 (1997). 27 7513357CD1 gl 89778 3. 0E-208 [Homo sapiens] pigment epithelial-differentiating factor Steele, F. R. et al., Pigment epithelium-derived factor : neurotrophic activity and identification as a member of the serine protease inhibitor gene family, Proc. Natl. Acad. Sci. U. S. A. 90, 1526-1530 (1993) 27 7513357CD1 585783Serpinfl 1. 3E-185 [Mus musculus] [Inhibitor or repressor] [Extracellular matrix (cuticle and basement membrane)] Pigment epithelium-derived factor (caspin), a secreted protein that binds collagens, may be involved in embryogenesis and metastasis of tumors, a member of the serpin family of serine protease inhibitors Kozaki, K. et al., Isolation, purification, and characterization of a collagen-associated serpin, caspin, produced by murine colon adenocarcinoma cells., J Biol Chem 273, 15125- 30 (1998). 27 7513357CD1 3368661SERPINF 8. 3E-182 [Homo sapiens] [Inhibitor or repressor] Pigment epithelium-derived factor, inhibits 1 angiogenesis in the eye, has an NF-kappa B-mediated protective effect on cerebellar granule neurons, member of the serpin family of serine protease inhibitors but may have no protease inhibitor activity Dawson, D. W. et al., Pigment epithelium-derived factor : a potent inhibitor of angiogenesis., Science 285, 245-8 (1999). Steele, F. R. et al., Pigment epithelium-derived factor : neurotrophic activity and identification as a member of the serine protease inhibitor gene family., Proc Natl Acad Sci U S A 90, 1526-30 (1993). Stellmach, V. V et al., Prevention of ischemia-induced retinopathy by the natural ocular antiangiogenic agent pigment epithelium-derived factor., Proc Natl Acad Sci U S A 98, 2593-2597. (2001). 28 7513329CD1 g25815116 10. 0 Homo sapiens] UDP-GalNAc-transferase 12 Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 28 7513329CD1 587925|Galnt4 2. 2E-155 [Mus musculus] [Transferase] [Golgi ; Cytoplasmic] DP-N-acetyl-alpha-D- galactosamine : polypeptide N-acetylgalactosaminyltransfer 4, transfers N- acetylgalactosamine to acceptor polypeptides at serine and threonine residues Hagen, F. K. et al., (supra) 28 7513329CD1 3442181GALNT4 1. 8E-151 [Homo sapiens] [Transferase] [Golgi ; Cytoplasmic] UDP-N-acetyl-alpha-D- galactosamine : polypeptide N-acetylgalactosaminyltransfer 4 (GalNAc-T4), transfers N- acetylgalactosamine to acceptor polypeptides at serine and threonine residues Bennett, E. P. et al., Cloning of a human UDP-N-acetyl-alpha-D- Galactosamine : polypeptide N-acetylgalactosaminyltransferase that complements other GaINAc-transferases in complete 0-glycosylation of the MUC1 tandem repeat., J Biol Chem 273, 30472-81 (1998). Hassan, H. et al., The lectin domain of UDP-N-acetyl-D-galactosamine : Polypeptide N- acetylgalactosaminyltransferase-T4 directs its glycopeptide specificities, J Biol Chem 275, 38197-205 (2000). 29 7517777CD1 g7673618 3. 7E-118 [Mus musculus] ubiquitin specific protease Means, G. D. et al., A transcript map of a 2-Mb BAC contig in the proximal portion of the mouse X chromosome and regional mapping of the scurfy mutation, Genomics 65, 213-223 (2000) 29 7517777CD1 425064JUSP22 6. 0E-149 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Member of the ubiquitin carboxyl-terminal hydrolase family 2, contains a ubiquitin carboxyl-terminal hydrolases family 2 domain and a Zn-finger in ubiquitin-hydrolases and other proteins domain, has low similarity to S. cerevisiae Ubp8p 297517777CD1 573701) Usp27x 2. 8E-119 [Mus musculus] Ubiquitin specific protease 27 (X chromosome) 30 7519126CD1 g6683668 2. 7E-12 [Carassius auratus] alpha 4 subunit of 20S proteasome Tokumoto, M. et al., Two proteins, a goldfish 20S proteasome subunit and the protein interacting with 26S proteasome, change in the meiotic cell cycle, Eur. J. Biochem. 267, 97- 103 (2000) Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 30 7519126CD1 3373061PSMA7 9. 3E-12 [Homo sapiens] [Proteasome subunit ; Activator ; Hydrolase ; DNA-binding protein ; Transcription factor ; Protease (other than proteasomal)] [Cytoplasmic] Proteasome (prosome, macropain) subunit (alpha type) 7, a subunit of the 20S core proteasome, a target of hepatitis B virus X protein ; may be involved in pathogenesis of pancreatic cancer Huang, J. et al., Proteasome complex as a potential cellular target of hepatitis B virus X protein., J Virol 70, 5582-91 (1996). 30 7519126CD1 586619lPsma7 9. 3E-12 [Mus musculus] [Proteasome subunit ; Hydrolase ; Protease (other than proteasomal)] [Nuclear ; Cytoplasmic] Proteasome (prosome, macropain) subunit (alpha type) 7, a subunit of the 20S core proteasome, may play a role in sperm physiology Elenich, L. A. et al., The complete primary structure of mouse 20S proteasomes., Immunogenetics 49, 835-42 (1999). 31 7519175CD1 g7673618 1. 2E-208 [Mus musculus] ubiquitin specific protease Means, G. D. et al., A transcript map of a 2-Mb BAC contig in the proximal portion of the mouse X chromosome and regional mapping of the scurfy mutation, Genomics 65, 213-223 (2000) (supra) 31 7519175CD1 5737011Usp27x 9. 0E-210 [Mus musculus] Ubiquitin specific protease 27 (X chromosome) Means, G. D. et al. (supra) 31 7519175CD1 425064lUSP22 2. 8E-209 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Member of the ubiquitin carboxyl-terminal hydrolase family 2, contains a ubiquitin carboxyl-terminal hydrolases family 2 domain and a Zn-finger in ubiquitin-hydrolases and other proteins domain, has low similarity to S. cerevisiae Ubp8p 32 7514648CD1 gl90418 8. 7E-114 [Homo sapiens] preprocathepsin L precursor Joseph, L. J. et al., Complete nucleotide and deduced amino acid sequences of human and murine preprocathepsin L. An abundant transcript induced by transformation of fibroblasts, J. Clin. Invest. 81, 1621-1629 (1988) Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 32 7514648CD1 334900|CTSL 6. 6E-115 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Lysosome/vacuole ; Cytoplasmic] Cathepsin L, a lysosomal cysteine (thiol) proteinase of papain superfamily that cleaves collagen and elastin ; overexpression is associated with highly invasive tumors, may serve as a marker of tumor progression Shuja, S. et al., Marked increases in cathepsin B and L activities distinguish papillary carcinoma of the thyroid from normal thyroid or thyroid with non-neoplastic disease., Int J Cancer 66, 420-6 (1996). 32 7514648CD1 334898lCTSL2 5. 4E-88 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Cathepsin L2 (cathepsin V), cysteine-type protease expressed predominantly in the thymus and testis, expression in corneal epithelium suggests a role in corneal function ; CTSL2 gene expression in various cancers suggests involvement with tumorigenesis Santamaria, 1. et al., Cathepsin L2, a novel human cysteine proteinase produced by breast and colorectal carcinomas., Cancer Res 58, 1624-30 (1998). 33 7517904CD1 g2459395 l. lE-38 [Homo sapiens] ubiquitin protease Gray, D. A. et al., Elevated expression of Unph, a proto-oncogene at 3p21. 3, in human lung tumors, Oncogene 10, 2179-2183 (1995) 33 7517904CD1 338842|USP4 8. 4E-40 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Nuclear ; Cytoplasmic] Ubiquitin specific protease 4 (ubiquitous nuclear protein human), efficiently cleaves ubiquitin-proline bonds, expression is elevated in small cell lung carcinomas ; corresponding gene maps to a chromosomal region frequently rearranged in tumor cells Gilchrist, C. A. et al., A ubiquitin-specific protease that efficiently cleaves the ubiquitin- proline bond., J Biol Chem 272, 32280-5. (1997).

Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 33 7517904CD1 5861131Usp4 1. 7E-35 [Mus musculus] [Hydrolase ; Protease (other than proteasomal) ; Small molecule-binding protein] [Nuclear] Ubiquitin specific protease 4 (ubiquitous nuclear protein), efficiently cleaves ubiquitin-proline bonds, transforms cells when overexpressed, may bind to the retinoblastoma gene product ; expression of human USP4 is elevated in small cell lung carcinomas Layfield, R. et al., Chemically synthesized ubiquitin extension proteins detect distinct catalytic capacities of deubiquitinating enzymes., Anal Biochem 274, 40-9. (1999). 34 7518798CD1 g3184184 3. 2E-48 [Homo sapiens] airway trypsin-like protease Yamaoka, K. et al., Cloning and characterization of the cDNA for human airway trypsin- like protease, J. Biol. Chem. 273, 11895-11901 (1998) 34 7518798CD1 340682|HAT 2. 5E-49 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Plasma membrane] Airway trypsin-like protease, a trypsin-like serine protease that cleaves fibrinogen and may play a role in the anticoagulation process in the airway, may play a role in host defense in airway mucous and bronchial secretions Takahashi, M. et al., Localization of human airway trypsin-like protease in the airway : an immunohistochemical study., Histochem Cell Biol 115, 181-7. (2001). 34 7518798CD1 657563AF19808 5. 4E-29 [Rattus norvegicus] Member of the trypsin family of serine proteases, has moderate 7 similarity to proprostasin (human PRSS8), which is a precursor of an active, membrane- bound serine protease that may act as a potential suppressor of invasive prostate cancer Bicknell, A. B. et al., Characterization of a serine protease that cleaves pro-gamma- melanotropin at the adrenal to stimulate growth., Cell 105, 903-12. (2001). 35 7519109CD1 gl2698338 6. 4E-200 [Homo sapiens] matrix metalloproteinase-28 precursor Lohi, J. et al., Epilysin, a novel human matrix metalloproteinase (MMP-28) expressed in testis and keratinocytes and in response to injury, J. Biol. Chem. 276, 10134-10144 (2001) Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 35 7519109CD1 690642MMP28 4. 9E-201 [Homo sapiens] Matrix metalloproteinase 28 (epilysin), a metalloprotease of the MMP19 subfamily that may have a role in tissue repair, expressed in keratinocytes and upregulated upon injury, widely expressed in carcinomas Marchenko, G. N. et al., MMP-28, a new human matrix metalloproteinase with an unusual cysteine-switch sequence is widely expressed in tumors., Gene 265, 87-93. (2001). 35 7519109CD1 585309lMmp24 l. lE-30 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] [Extracellular (excluding cell wall) ; Plasma membrane] Matrix metalloproteinase 24 (membrane type 5 matrix metalloproteinase), proteolytically activates Mmp2, shed by a furin-type convertase, has a role in axonal growth ; human MMP24 colocalizes with plaques in Alzheimer brain and may be associated with aging Hayashita-Kinoh, H. et al., Membrane-type 5 matrix metalloproteinase is expressed in differentiated neurons and regulates axonal growth., Cell Growth Differ 12, 573-80. (2001). 36 7519227CD1 g4261576 5. 6E-19 [Homo sapiens] beta-tryptase Blom, T. et al., Characterization of a tryptase mRNA expressed in the human basophil cell line KU812, Scand. J. Immunol. 37, 203-208 (1993) 36 7519227CD1 7039611TPSB2 4. 3E-20 [Homo sapiens] Protein with very strong similarity to tryptase beta 1 (human TPSB1), which is a mast cell serine protease that activates mast cells and may play a role in asthma pathogenesis, member of the trypsin family of serine proteases Huang, C. et al., Human tryptases alpha and beta/II are functionally distinct due, in part, to a single amino acid difference in one of the surface loops that forms the substrate-binding cleft., J Biol Chem 274, 19670-6. (1999). 36 7519227CD 1 703959|TPSB 1 4. 3E-20 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Tryptase beta 1, a mast cell serine protease involved in angiogenesis, cell proliferation, chemotaxis, and possibly the inflammatory response, may play a role in asthma pathogenesis Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score NID NO : He, S. et al., The activation of synovial mast cells : modulation of histamine release by tryptase and chymase and their inhibitors., Eur J Pharmacol 412, 223-9. (2001). 37 7519262CD1 gl2698338 3. 7E-171 [Homo sapiens] matrix metalloproteinase-28 precursor Lohi, J. et al., (supra) 37 7519262CD1 6906421MMP28 2. 8E-172 [Homo sapiens] Matrix metalloproteinase 28 (epilysin), a metalloprotease of the MMP19 subfamily that may have a role in tissue repair, expressed in keratinocytes and upregulated upon injury, widely expressed in carcinomas Marchenko, G. N. et al. (supra) 37 7519262CD1 663680MMP16 7. 2E-35 [Homo sapiens] [Hydrolase ; Activator ; Protease (other than proteasomal)] [Plasma membrane] Matrix metalloproteinase 16, a transmembrane protease that activates progelatinase A (MMP2), and contributes to tumorigenesis by increasing cell invasiveness, proprotein form is converted to active form by furin (PACE) Ellenrieder, V. et al., Role of MT-MMPs and MMP-2 in pancreatic cancer progression., Int J Cancer 85, 14-20. (2000). 38 7519371CD1 gl4603232 6. 7E-158 [Homo sapiens] serine carboxypeptidase 1 precursor protein 38 7519371CD1 622005|RISC 1. 5E-223 [Homo sapiens] Protein with weak similarity to S. cerevisiae Prclp, which is a carboxypeptidase Y (CPY/yscY) and a serine-type protease Chen, J. et al., Cloning of a novel retinoid-inducible serine carboxypeptidase from vascular smooth muscle cells., J Biol Chem 276, 34175-81. (2001). 38 7519371CD1 783860jRisc 8. 3E-186 [Rattus norvegicus] Member of the serine carboxypeptidase family, has low similarity to carboxypeptidase Y (S. cerevisiae Prclp), which is a vacuolar serine protease 39 7519442CD1 g5734367 1. 5E-41 [Homo sapiens] ubiquitin-specific protease ISG43 Li, X. L. et al., RNase-L-dependent destabilization of interferon-induced mRNAs. A role for the 2-5A system in attenuation of the interferon response, J. Biol. Chem. 275, 8880- 8888 (2000) Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 39 7519442CD1 571286USP18 1. 2E-42 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Nuclear] Ubiquitin specific protease 18, member of a family of proteases that catalyze the cleavage of ubiquitin from ubiquitinated protein substrates ; the corresponding gene maps within the critical region commonly deleted in DiGeorge syndrome Schwer, H. et al., Cloning and characterization of a novel human ubiquitin-specific protease, a homologue of murine UBP43 (Uspl8)., Genomics 65, 44-52 (2000). 39 7519442CD1 430466lUspl8 9. 7E-23 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] Ubiquitin specific protease 18, catalyzes the cleavage of ubiquitin from ubiquitinated protein substrates, may play a role in hematopoesis ; the human USP18 gene maps within the critical region commonly deleted in DiGeorge syndrome Liu, L. Q. et al., A novel ubiquitin-specific protease, UBP43, cloned from leukemia fusion protein AMLl-ETO-expressing mice, functions in hematopoietic cell differentiation., Mol Cell Biol 19, 3029-38 (1999). 40 9519123CD1 g6683668 2. 7E-12 [Carassius auratus] alpha 4 subunit of 20S proteasome Tokumoto, M. et al., Two proteins, a goldfish 20S proteasome subunit and the protein interacting with 26S proteasome, change in the meiotic cell cycle, Eur. J. Biochem. 267, 97- 103 (2000) 40 7519123CD1 3373061 6. 9E-12 [Homo sapiens] [Proteasome subunit ; Activator ; Hydrolase ; DNA-binding PSMA7 protein ; Transcription factor] [Cytoplasmic] Proteasome (prosome, macropain) subunit (alpha type) 7, a subunit of the 20S core proteasome, a target of hepatitis B virus X protein ; may be involved in pathogenesis of pancreatic cancer Coux, O. et al., Structure and functions of the 20S and 26S proteasomes, Annu Rev Biochem 65, 801-47 (1996). Tipler, C. P. et al., Purification and characterization of 26S proteasomes from human and mouse spermatozoa, Mol Hum Reprod 3, 1053-60 (1997).

Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 40 7519123CD1 5866191 6. 9E-12 [Mus musculus] [Proteasome subunit ; Hydrolase ; Protease (other than Psma7 proteasomal)] [Nuclear ; Cytoplasmic] Proteasome (prosome, macropain) subunit (alpha type) 7, a subunit of the 20S core proteasome, may play a role in sperm physiology Elenich, L. A. et al., The complete primary structure of mouse 20S proteasomes, Immunogenetics 49, 835-42 (1999). 41 7519522CD1 g537292 1. 5E-192 [Homo sapiens] ICH-1L Wang, L. et al., Ich-1, an Ice/ced-3-related gene, encodes both positive and negative regulators of programmed cell death, Cell 78, 739-750 (1994) 41 7519522CD1 743470J 2. 4E-193 [Homo sapiens] [Activator ; Hydrolase ; Protease (other than proteasomal)] [Golgi ; Nuclear ; CASP2 Cytoplasmic] Caspase 2, a cysteine aspartate protease, has a long alternative splice form that promotes apoptosis, and a short form that inhibits apoptosis Wang, L. et al., supra 41 7519522CD1 7903711 7. 3E-176 [Rattus norvegicus] [Hydrolase ; Protease (other than proteasomal)] Caspase 2, a cysteine Casp2 aspartate protease, has a long alternative splice form that promotes apoptosis, and a short form that inhibits apoptosis Leloup, C. et al., M1 muscarinic receptors block caspase activation by phosphoinositide 3- kinase-and MAPK/ERK-independent pathways, Cell Death Differ 7, 825-33 (2000). 42 7520023CD1 g3510663 2. 2E-199 [Homo sapiens] thymus specific serine peptidase Bowlus, C. L. et al., Cloning of a novel MHC-encoded serine peptidase highly expressed by cortical epithelial cells of the thymus, Cell. Immunol. 196, 80-86 (1999) 42 7520023CD1 6084981 6. 8E-156 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] Thymic-specific serine Prssl6 peptidase, a putative serine protease potentially involved in thymocyte development and function Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Carrier, A. et al., Differential gene expression in CD3epsilon-and RAGl-deficient thymuses : definition of a set of genes potentially involved in thymocyte maturation., Immunogenetics 50, 255-70 (1999). 42 7520023CD1 2411041 2. 1E-28 [Caenorhabditis elegans] Member of the alpha or beta hydrolase fold family, has a region of C46C2. 4 low similarity to dipeptidyl peptidase II (quiescent cell proline dipeptidase, rat Dpp7), which is a serine protease that may be involved in the response to wounding 43 7519518CD 1 gl702930 l. lE-26 [Homo sapiens] matrix metalloproteinase Cossins, J. et al., Identification of MMP-18, a putative novel human matrix metalloproteinase, Biochem. Biophys. Res. Commun. 228, 494-498 (1996) 43 7519518CD1 618748 5. 2E-17 [Mus musculus] Martix metalloproteinase 19, putative metalloendopeptidase of the matrixin Mmpl9 family of extracellular matrix metalloproteases, induced during ovulation and may play a role in tissue degradation during ovarian follicle rupture Stracke, J. O. et al., Biochemical characterization of the catalytic domain of human matrix metalloproteinase 19. Evidence for a role as a potent basement membrane degrading enzyme., J Biol Chem 275, 14809-16 (2000). 44 751995SCD1 g5809682 8. 9E-24 [Homo sapiens] carboxypeptidase M precursor Tan, F. et al., Molecular cloning and sequencing of the cDNA for human membrane-bound carboxypeptidase M. Comparison with carboxypeptidases A, B, H, and N, J. Biol. Chem. 264, 13165-13170 (1989) 44 7519955CD1 568458|CPM 6. 7E-25 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Unspecified membrane ; Plasma membrane] Carboxypeptidase M, a membrane-associated lysine (arginine) metalloprotease that removes basic carboxy-terminal residues from peptide hormones, may be a marker of differentiated macrophages, and may play a role in ovulation and corpora luteal formation Tan, F. et al., supra Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Skidgel, R. A. et al., Human carboxypeptidase M. Purification and characterization of a membrane-bound carboxypeptidase that cleaves peptide hormones., J Biol Chem 264, 2236- 41. (1989). 45 7514925CD1 g6572164 9. 6E-120 [Homo sapiens] dJ1057D18. 1 (novel protein similar to yeast and bacterial PEPP (aminopeptidase P, aminoacylproline aminopeptidase)) 45 7514925CD1 6262431 3. 4E-202 [Homo sapiens] Member of the metallopeptidase family M24, has low similarity to LOC63929 peptidase D (prolidase, human PEPD), which catalyzes hydrolysis of dipeptides having a C- terminal proline and is associated with iminodipeptiduria, mental retardation and tissue defects 45 7514925CD1 33951 1. 4E-52 [Saccharomyces cerevisiae] [Hydrolase ; Protease (other than proteasomal)] Protein with YER078C similarity to X-prolyl aminopeptidases Smith, V. et al., Functional analysis of the genes of yeast chromosome V by genetic footprinting., Science 274, 2069-74 (1996). 46 7518514CD1 g3184184 4. 9E-16 [Homo sapiens] airway trypsin-like protease Yamaoka, K. et al., Cloning and characterization of the cDNA for human airway trypsin- like protease, J. Biol. Chem. 273, 11895-11901 (1998) 46 7518514CD1 340682|HAT 3. 7E-17 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Plasma membrane] Airway trypsin-like protease, a trypsin-like serine protease that cleaves fibrinogen and may play a role in the anticoagulation process in the airway, may play a role in host defense in airway mucous and bronchial secretions Yamaoka, K. et al., Cloning and characterization of the cDNA for human airway trypsin- like protease., J Biol Chem 273, 11895-901 (1998). 46 7518514CD1 5695981 2. 1E-14 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Member of the trypsin DESC1 family of serine proteases, has moderate similarity to airway trypsin-like protease (human HAT), which is a serine protease that cleaves fibrinogen and may function in anticoagulation and host defense processes in airway secretions 47 7519481CD1 g339977 6. 0E-40 [Homo sapiens] tryptase-I Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Vanderslice, P. et al., Human mast cell tryptase : multiple cDNAs and genes reveal a multigene serine protease family, Proc. Natl. Acad. Sci. U. S. A. 87, 3811-3815 (1990) 47 7519481CD1 703961) 4. 5E-41 [Homo sapiens] Protein with very strong similarity to tryptase beta 1 (human TPSB 1), TPSB2 which is a mast cell serine protease that activates mast cells and may play a role in asthma pathogenesis, member of the trypsin family of serine proteases Pallaoro, M. et al., Characterization of genes encoding known and novel human mast cell tryptases on chromosome 16pl3. 3., J Biol Chem 274, 3355-62 (1999). 47 7519481CD1 7042771 1. lE-28 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] Mast cell protease 7, a serine Mcpt7 protease that exhibits anticoagulant activity, and may regulate clot formation and fibrinogen and integrin-dependent cellular responses during mast cell-mediated inflammatory reactions Huang, C. et al., The tryptase, mouse mast cell protease 7, exhibits anticoagulant activity in vivo and in vitro due to its ability to degrade fibrinogen in the presence of the diverse array of protease inhibitors in plasma., J Biol Chem 272, 31885-93. (1997). 48 7519529CD1 g6002714 8. 2E-124 [Homo sapiens] membrane-type serine protease 1 Takeuchi, T. et al., Reverse biochemistry : use of macromolecular protease inhibitors to dissect complex biological processes and identify a membrane-type serine protease in epithelial cancer and normal tissue, Proc. Natl. Acad. Sci. U. S. A. 96, 11054-11061 (1999) i 48 7519529CD1 625929|ST14 6. 2E-125 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Extracellular matrix (cuticle and basement membrane) ; Plasma membrane] Matriptase, a type 2 integral membrane serine protease, degrades extracellular matrix, activates hepatocyte growth factor (HGF) and urokinase plasminogen activator (PLAU), and may play a role in progression and metastasis of epithelial-derived cancers Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Lin, C. Y. et al., Molecular cloning of cDNA for matriptase, a matrix-degrading serine protease with trypsin-like activity., J Biol Chem 274, 18231-6 (1999). Oberst, M. D. et al., Expression of the Serine Protease Matriptase and Its Inhibitor HAI-1 in Epithelial Ovarian Cancer : Correlation with Clinical Outcome and Tumor Clinicopathological Parameters., Clin Cancer Res 8, 1101-7. (2002). 48 7519529CD 1 587557|Stl4 2. 4E-106 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] [Unspecified membrane] Epithin (matriptase), a type 2 membrane serine protease that contains two tandem CUB domains, four low density lipoprotein receptor (LDLR) modules, and a carboxy-terminal serine protease domain List, K. et al., Matriptase/MT-SPl is required for postnatal survival, epidermal barrier function, hair follicle development, and thymic homeostasis., Oncogene 21, 3765-79. (2002). 49 7519549CD1 g2253587 6. 3E-237 [Homo sapiens] matrix metalloproteinase RASI-1 Sedlacek, R. et al., RASI-l, a novel autoantigen in Rheumatoid Arthritis, Immunbiol. 194, 153-153 (1995) 49 7519549CD1 6187481 2. 3E-179 [Mus musculus] Martix metalloproteinase 19, putative metalloendopeptidase of the matrixin Mmpl9 family of extracellular matrix metalloproteases, induced during ovulation and may play a role in tissue degradation during ovarian follicle rupture Stracke, J. O. et al., Biochemical characterization of the catalytic domain of human matrix metalloproteinase 19. Evidence for a role as a potent basement membrane degrading enzyme., J Biol Chem 275, 14809-16 (2000). 49 7519549CD1 7603591 6. 5E-73 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Extracellular matrix (cuticle MMP19 and basement membrane) ; Extracellular (excluding cell wall)] Matrix metalloproteinase 19, a secreted metalloendopeptidase that hydrolyzes extracellular matrix components, may play a role in inflammation and angiogenesis, and may be associated with rheumatoid arthritis and other autoimmune diseases Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Pendas, A. M. et al., Identification and characterization of a novel human matrix metalloproteinase with unique structural characteristics, chromosomal location, and tissue distribution., J Biol Chem 272, 4281-6 (1997). 50 7520124CD 1 345060|CLN2 4. 0E-11 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] [Lysosome/vacuole ; Cytoplasmic] Tripeptidyl peptidase I (ceroid-lipofuscinosis neuronal 2), a lysosomal serine- type peptidase required for degradation of ATP synthase subunit c (ATP5G1 and ATP5G2) ; mutations in the corresponding gene cause late infantile neuronal ceroid lipofuscinosis Ezaki, J. et al. A lysosomal proteinase, the late infantile neuronal ceroid lipofuscinosis gene (CLN2) product, is essential for degradation of a hydrophobic protein, the subunit c of ATP synthase. J Neurochem 72, 2573-82. (1999). 51 7515245CD1 gl276912 3. 2E-98 [Homo sapiens] UHX1 protein Swanson, D. A. et al. A ubiquitin C-terminal hydrolase gene on the proximal short arm of the X chromosome : implications for X-linked retinal disorders, Hum. Mol. Genet. 5, 533- 538 (1996) 51 7515245CD1 341412USP11 2. 4E-99 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Ubiquitin specific protease 11, a member of the ubiquitin-specific cysteine (thiol) protease family which removes ubiquitin from ubiquitin-conjugated protein substrates ; may play a role in oncogenesis D'Andrea, A. et al. Deubiquitinating enzymes : a new class of biological regulators. Crit Rev Biochem Mol Biol 33, 337-52 (1998). 51 7515245CD1 742564lUSPl5 7. 6E-77 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Ubiquitin-specific protease 15, a member of the ubiquitin-specific cysteine (thiol) protease family, cleaves ubiquitin from ubiquitin-conjugated protein substrates, may play a role in growth regulation Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Baker, R. T. et al. Identification, functional characterization, and chromosomal localization of USP15, a novel human ubiquitin-specific protease related to the UNP oncoprotein, and a systematic nomenclature for human ubiquitin-specific proteases, Genomics 59, 264-74 (1999). 52 7519933CD1 g963048 7. 0E-62 [Homo sapiens] CLPP Bross, P. et al. Human CIpP protease : cDNA sequence, tissue-specific expression and chromosomal assignment of the gene, FEBS Lett. 377, 249-252 (1995) 52 7519933CD1 342966lCLPP 5. 2E-63 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] ATP-dependent caseinolytic protease proteolytic subunit (CLPP), putative protease proteolytic subunit that is localized in the mitochondrial matrix and near the inner mitochondrial membrane, mitochondria- specific function is unknown de Sagarra, M. R. et al. Mitochondrial localization and oligomeric structure of HClpP, the human homologue of E. coli CIpP. J Mol Biol 292, 819-25 (1999). 52 7519933CD1 5876651CIpp 3. 9E-42 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] ATP-dependent caseinolytic protease proteolytic subunit (ClpP), putative protease proteolytic subunit that is synthesized in the cytosol and imported into mitochondria, interaction with ClpX suggests function in a chaperone-protease system Andresen, B. S. et al. Characterization of mouse Clpp protease cDNA, gene, and protein. Mamm Genome 11, 275-80 (2000). 53 7520101CD1 g963048 1. 6E-96 [Homo sapiens] CLPP Bross, P. et al. (supra) 53 7520101CD1 342966lCLPP 1. 2E-97 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] ATP-dependent caseinolytic protease proteolytic subunit (CLPP), putative protease proteolytic subunit that is localized in the mitochondrial matrix and near the inner mitochondrial membrane, mitochondria- specific function is unknown de Sagarra, M. R. et al. (supra) Table 2 -| Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 53 7520101CD1 587665lClpp 2. 3E-76 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] ATP-dependent caseinolytic protease proteolytic subunit (CIpP), putative protease proteolytic subunit that is synthesized in the cytosol and imported into mitochondria, interaction with ClpX suggests function in a chaperone-protease system Andresen, B. S. et al. (supra) 54 7520145CD1 1 gl 81164 1. 5E-82 [Homo sapiens] cytotoxin serine protease-C precursor Klein, J. L. et al. Characterization of a novel, human cytotoxic lymphocyte-specific serine protease cDNA clone (CSP-C), Tissue Antigens 35, 220-228 (1990) 54 7520145CD1 749138CTLA1 l. lE-83 [Homo sapiens] Cytotoxic T-lymphocyte-associated serine esterase l, a member of the granzyme serine protease family, which functions in cell-mediated cytotoxicity and displays granzyme activity Edwards, K. M. et al. The human cytotoxic T cell granule serine protease granzyme H has chymotrypsin-like (chymase) activity and is taken up into cytoplasmic vesicles reminiscent of granzyme B-containing endosomes. J Biol Chem 274, 30468-73. (1999). 54 7520145CD1 340668|GZMB 6. 6E-63 [Homo sapiens] [Ligand ; Activator ; Hydrolase ; Protease (other than proteasomal)] [Cytoplasmic] Granzyme B (cytotoxic T-lymphocyte-associated serine esterase 1), a serine protease that is released by cytotoxic T-cells and induces apoptosis in target cells, plays a role in the immune response and in the host response to bacteria Wargnier, A. et al. Down-regulation of human granzyme B expression by glucocorticoids. Dexamethasone inhibits binding to the Ikaros and AP-1 regulatory elements of the granzyme B promoter. J Biol Chem 273, 35326-31 (1998). 55 7520174CD1 gl83155 1. 6E-69 [Homo sapiens] cytotoxic T-lymphocyte-associated serine esterase 1 Haddad, P. et al. Structure and evolutionary origin of the human granzyme H gene, Int. Immunol. 3, 57-66 (1991) Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : 55 7520174CD1 749138CTLA1 1. 2E-70 [Homo sapiens] Cytotoxic T-lymphocyte-associated serine esterase 1, a member of the granzyme serine protease family, which functions in cell-mediated cytotoxicity and displays granzyme activity Edwards, K. M. et al. (supra) 55 7520174CD1 3406681GZMB 7. 4E-72 [Homo sapiens] [Ligand ; Activator ; Hydrolase ; Protease (other than proteasomal)] [Cytoplasmic] Granzyme B (cytotoxic T-lymphocyte-associated serine esterase 1), a serine protease that is released by cytotoxic T-cells and induces apoptosis in target cells, plays a role in the immune response and in the host response to bacteria Wargnier, A. et al. (supra) 56 7520191CD1 g9963808 7. 2E-21 [Homo sapiens] sentrin/SUMO-specific protease 56 7520191CD1 789871|SENP7 8. 3E-13 [Homo sapiens] Protein containing a ubiquitin-like protein-specific protease (Ulpl) family C-terminal catalytic domain, which may bind other protein domains 57 7520243CD1 g903982 1. 4E-40 [Homo sapiens] methionine aminopeptidase Arfin, S. M. et al. Eukaryotic methionyl aminopeptidases : two classes of cobalt-dependent enzymes, Proc. Natl. Acad. Sci. U. S. A. 92, 7714-7718 (1995) 57 7520243CD1 428196lMETAP2 1. 0E-41 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Methionine aminopeptidase 2, positive regulator of translation that binds eIF2alpha (EIF2S 1) and prevents its phosphorylation by eIF2alpha kinases, inhibits apoptosis ; targeting by angiogenesis inhibitors serves as a basis for anticancer therapies Catalano, A. et al. Methionine aminopeptidase-2 regulates human mesothelioma cell survival : role of Bcl-2 expression and telomerase activity. Am J Pathol 159, 721-31. (2001). 57 7520243CD1 6295261Amp2 3. 6E-32 [Rattus norvegicus] Methionine aminopeptidase 2, positive regulator of translation that binds eIF2alpha (Eif2sl) and prevents its phosphorylation by eIF2alpha kinases, inhibits apoptosis ; human MNPEP is targeted by anticancer angiogenesis inhibitors Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Datta, B. et al. Induction of apoptosis due to lowering the level of eukaryotic initiation factor 2-associated protein, p67, from mammalian cells by antisense approach. Exp Cell Res 246, 376-83. (1999). 58 7521695CD1 g6492122 6. 8E-68 [Rattus norvegicus] deubiquitinating enzyme Ubpl09 Park, K. C. et al. Tissue-specificity, functional characterization and subcellular localization of a rat ubiquitin-specific processing protease, UBP109, whose mRNA expression is developmentally regulated, Biochem. J. 349 (Pt 2), 443-453 (2000) 58 7521695CD1 742564USP15 1. OE-68 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Ubiquitin-specific protease 15, a member of the ubiquitin-specific cysteine (thiol) protease family, cleaves ubiquitin from ubiquitin-conjugated protein substrates, may play a role in growth regulation Baker, R. T. et al. (supra) 58 7521695CD1 586113Usp4 8. 3E-70 [Mus musculus] [Hydrolase ; Protease (other than proteasomal) ; Small molecule-binding protein] [Nuclear] Ubiquitin specific protease 4 (ubiquitous nuclear protein), efficiently cleaves ubiquitin-proline bonds, transforms cells when overexpressed, may bind to the retinoblastoma gene product ; expression of human USP4 is elevated in small cell lung carcinomas Blanchette, P. et al. Association of UNP, a ubiquitin-specific protease, with the pocket proteins pRb, D107 and pal30. Oncogene 20, 5533-7. (2001). 59 7520801CI ? 1 g1136438 1. 9E-92 [Homo sapiens] similar to ubiquitin-specific proteinase of S. cerevisiae. 59 7520801CD1 620325lUSPl0 1. 4E-93 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Ubiquitin specific protease 10, a member of the ubiquitin-specific cysteine (thiol) protease family, cleaves ubiquitin from ubiquitin-conjugated protein substrates, activity is inhibited upon association with Ras GAP SH3 domain binding protein Soncini, C. et al. Ras-GAP SH3 domain binding protein (G3BP) is a modulator of USP10, a novel human ubiquitin specific protease. Oncogene 20, 3869-79. (2001).

Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : I 59 7520801CD1 581785lUchrp 5. 0E-81 [Mus musculus] [Hydrolase ; Protease (other than proteasomal)] Protein with strong similarity to ubiquitin specific protease 10 (human USP10), which cleaves ubiquitin from ubiquitin-conjugated substrates, member of ubiquitin carboxyl-terminal hydrolase family 2 with a ubiquitin carboxyl-terminal hydrolases 2 domain 60 7520817CD1 gl 1071729 1. 1E-42 [Homo sapiens] putative dipeptidase 60 7520817CD1 6576771LOC6417 7. 9E-44 [Homo sapiens] Protein with high similarity to membrane dipeptidase 1 (renal dipeptidase, 4 human DPEP1), which is a zinc-dependent cell surface metalloprotease that is frequently lost in Wilms tumor, member of the renal dipeptidase family, which hydrolyze dipeptides 60 7520817CD1 657681lLOC6418 2. 3E-17 [Homo sapiens] Protein with high similarity to membrane dipeptidase 1 (renal dipeptidase, 0 human DPEP1), which is a zinc-dependent cell surface metalloprotease that is frequently lost in Wilms tumor, member of the renal dipeptidase family 61 7520937CD1 gl79584 9. 3E-153 [Homo sapiens] beta-tryptase Miller, J. S. et al. Cloning and characterization of a second complementary DNA for human tryptase, J. Clin. Invest. 86, 864-870 (1990) 61 7520937CD1 703961lTPSB2 6. 9E-154 [Homo sapiens] Protein with very strong similarity to tryptase beta 1 (human TPSB1), which is a mast cell serine protease that activates mast cells and may play a role in asthma pathogenesis, member of the trypsin family of serine proteases Hermes, B. et al. Altered expression of mast cell chymase and tryptase and of c-Kit in human cutaneous scar tissue. J Invest Dermatol 114, 51-5. (2000). 61 7520937CD1 703959|TPSB 1 2. 3E-153 [Homo sapiens] [Hydrolase ; Protease (other than proteasomal)] Tryptase beta 1, a mast cell serine protease involved in angiogenesis, cell proliferation, chemotaxis, and possibly the inflammatory response, may play a role in asthma pathogenesis Steinhoff, M. et al. Agonists of proteinase-activated receptor 2 induce inflammation by a neurogenic mechanism. Nat Med 6, 151-8 (2000). 62 7521694CD1 gl5963593 0. 0 [Homo sapiens] ADAMTS13 Table 2 Polypeptide SEQ Incyte GenBank ID NO : Probability Annotation ID NO : Polypeptide ID or PROTEOME Score ID NO : Levy, G. G. et al. Mutations in a member of the ADAMTS gene family cause thrombotic thrombocytopenic purpura, Nature 413, 488-494 (2001) 62 7521694CD1 7557901ADAMT 8. 0E-186 [Homo sapiens] A disintegrin-like and metalloprotease (reprolysin type) with S13 thrombospondin type 1 motif 13 (von Willebrand factor cleaving protease), a metalloprotease that cleaves von Willebrand factor ; mutations in the gene cause thrombotic thrombocytopenic purpura Zheng, X. et al. Structure of von Willebrand factor-cleaving protease (ADAMTS 13), a metalloprotease involved in thrombotic thrombocytopenic purpura. J Biol Chem 276, 41059 63 (2001). 62 7521694CD1 689048|Adamtsl 2. 4E-92 [Rattus norvegicus] A disintegrin and metalloproteinase with thrombospondin motifs 1, may be play a role in ovarian follicle rupture, bone remodeling, and response to injury ; expression in liver endothelial cells is decreased after induction of cirrhosis Miles, R. R. et al. ADAMTS-1 : A cellular disintegrin and metalloprotease with thrombospondin motifs is a target for parathyroid hormone in bone, Endocrinology 141, 4533-42 (2000). Sasaki, M. et al. A disintegrin and metalloprotease with thrombospondin typel motifs (ADAMTS-1) and IL-1 receptor type 1 mRNAs are simultaneously induced in nerve injured motor neurons. Brain Res Mol Brain Res 89, 158-63. (2001).

Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites 1 7511804CD1 277 S60 S106 S129 N90 N125 signal cleavage : Ml-V19 SPSCAN S181 T143 Y78 Signal Peptide : Ml-Vl9 HMMER Signal Peptide : M1-P21 HMMER Signal Peptide : M1-G23 HMMER Signal Peptide : M1-A24MER Signal Peptide : M1-N18HMMER Eukaryotic aspartyl protease : L26-S277 HMMER_PFAM Eukaryotic and viral aspartyl proteases active site BLIMPS BLOCKS IPB001969 : F91-S106, D184-L189, Y220-G236 Pepsin (Al) aspartic protease family signature PR00792 : BLIMPS PRINTS L84-V104, G231-I244 PROTEASE ASPARTYL HYDROLASE PRECURSOR BLAST PRODOM SIGNAL ZYMOGEN GLYCOPROTEIN ASPARTIC PROTEINASE MULTIGENE PD000182 : P69-E263 EUKARYOTIC AND VIRAL ASPARTYL PROTEASES BLAST DOMO DM00126|P24268|20-403 : L26-R264 EUKARYOTIC AND VIRAL ASPARTYL PROTEASES BLAST DOMO DM00126lQ05744l20-396 : L26-E263 EUKARYOTIC AND VIRAL ASPARTYL PROTEASES BLAST DOMO DM00126 P18242 20-406 : L26-R264 EUKARYOTIC AND VIRAL ASPARTYL PROTEASES BLAST DOMO PM001261Q03168119-385 : P65-E263 Eukaryotic and viral aspartyl proteases active site : V93-MOTIFS V104 2 7512233CD1 323 S22 S311 T61 T117 N101 N124 N128 Signal-cleavage : Ml-Al9 SPSCAN T130 T228 T319 Y215 Y269 Trypsin-like serine protease : R78-V316 HMMER_SMART Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Trypsin : I79-V316 HMMER_PFAM Kringle domain IPB000001 : G81-M96, T104-L121, Y159-BLIMPSBLOCKS V173, F276-Q317 Serine proteases, trypsin family IPB001254 : T104-N120, BLIMPS BLOCKS D266-T289, Y303-V316 Chymotrypsin serine protease family (S1) signature BLIMPS PRINTS PR00722 : G105-N120, Y159-V173, E265-A277 Sushi domain proteins (SCR repeat proteins) PF00084 : E46-BLIMPSJPFAM Y57 HAPTOGLOBIN2 PRECURSOR GLYCOPROTEIN BLAST PRODOM SERINE PROTEASE HOMOLOG PLASMA HEMOGLOBIN BINDING LIVER SIGNAL PD 171455 : M1-D64 PROTEASE SERINE PRECURSOR SIGNAL BLAST PRODOM HYDROLASE ZYMOGEN GLYCOPROTEIN FAMILY MULTIGENE FACTOR PD000046 : G105-V316 SIGNAL HAPTOGLOBIN PRECURSOR SERINE BLAST PRODOM PROTEASE HOMOLOG PLASMA HEMOGLOBIN BINDING GLYCOPROTEIN LIVER PD005246 : S22-L84 TRYPSIN DM00018 P00737196-343 : P72-I320BLASTDOMO TRYPSIN DM000181A48918196-343 : P72-I320 BLAST DOMO l l _ TRYPSIN DM00018 P06866 96-343 : P72-I320 BLAST DOMO . TRYPSIN DM00018|P00736|457-700 : P72-K318 BLAST DOMO Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites 3 7512557CD1 748 S45 S185 S286 N81 N207 N517 Signal-cleavage : Ml-A28 SPSCAN S305 S366 S407 N577 S510 S525 S535 S562 S564 S642 S666 S702 T26 T54 T63 T121 T231 T384 T389 T594 Y146 Signal Peptide : M1-H23MER Signal Peptide : M1-Q24MER Signal Peptide : M1-A28 HMMER Signal Peptide : M1-T27HMMER von Willebrand factor (vWF) type A domain : P272-E456 HMMERSMART von Willebrand factor type A domain : N274-V457HMMERPFAM von Willebrand factor type A domain proteins. PF00092 : BLIMPS PFAM L297-L304, G257-G267 INHIBITOR HEAVY CHAIN CHANNEL PD01101 : Q65-BLIMPSPRODOM K98, N256-D308, G348-N367, R439-V493, W548-L557 HEAVY CHAIN PRECURSOR INTERALPHA-TRYPSIN BLAST PRODOM INHIBITOR m SERINE PROTEASE REPEAT SIGNAL PD004379 : Q24-K273 HEAVY CHAIN PRECURSOR INTERALPHA-TRYPSIN BLAST PRODOM INHIBITOR ITI SERINE PROTEASE REPEAT SIGNAL PD004369 : A430-R645 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites l INTERALPHA-TRYPSIN INHIBITOR HEAVY CHAIN BLAST PRODOM H4 PRECURSOR ITI FAMILY CHAINRELATED PROTEIN IHRP PLASMA KALLIKREIN SENSITIVE GLYCOPROTEIN 120 PK GP120 CONTAINS : GP57 SERINE PROTEASE RE PD120343 : W647-P698 INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLAST DOMO COMPONENT II DM03009|JX0368|372-855 : L372-P726 INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLAST_DOMO COMPONENT II DM03690|JX0368|96-278 : K96-I279 INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLASE-DOM _ COMPONENT II DM03009|S30350|378-841 : L372-E610 INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLAST DOMO COMPONENT II DM036901S303501102-284 : K96-I279 ATP/GTP-bindin site motif A (P-loop) : A107-S114 MOTIFS 4 7512559CD1 891 S45 5185 S286 N81 N207 N517 Signal_cleavage : M1-A28 SPSCAN S305 S366 S407 N577 S510 S525 S535 S562 S564 S642 $666 S702 S742 S771 S799 T26 T54 T63 T121 T231 T384 T389 T594 T747 T825 T857 Y146 Signal Peptide : M1-H23 HMER Signal Peptide : M1-Q24MER Signal Peptide : M1-A28 HMMER Signal Peptide : Ml-T27 IHMMER Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites von Willebrand factor (vWF) type A domain : P272-E456 HMMER_SMART von Willebrand factor type A domain : N274-V457 HMMER PFAM INHIBITOR HEAVY CHAIN CHANNEL PD01101 : Q65-BLIMPSPRODOM K98, N256-D308, G348-N367, R439-V493, W548-L557 PROTEIN LIPOPROTEIN MEMBRANE TRA. PD01632 : BLIMPSPRODOM Y538-N577, M125-Y146 SUBUNIT E V-ATPASE VACUOLAR ATP SYNTHASE BLIMPSPRODOM HYDROL. PD02102 : F277-A319, A135-E180 HEAVY CHAIN PRECURSOR INTERALPHA-TRYPSIN BLAST PRODOM INHIBITOR ITI SERINE PROTEASE REPEAT SIGNAL PD004379 : Q24-K273 HEAVY CHAIN H4 PRECURSOR INTERALPHA-BLASTPRODOM TRYPSIN INHIBITOR ITI FAMILY CHAINRELATED PROTEIN PD017446 : P675-L891 HEAVY CHAIN PRECURSOR INTERALPHA-TRYPSIN BLAST PRODOM INHIBITOR ITI SERINE PROTEASE REPEAT SIGNAL PD004369 : A430-R645 INTERALPHA-TRYPSIN INHIBITOR HEAVY CHAIN BLAST PRODOM H4 PRECURSOR ITI FAMILY CHAINRELATED PROTEIN IHRP PLASMA KALLIKREIN SENSITIVE GLYCOPROTEIN 120 PK Gap120 CONTAINS : GP57 SERINE PROTEASE RE PD 120343 : W647-P698 INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLAST_DOMO COMPONENT II DM03009JX0368372-855 : L372-P726 G727-G817 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO ID Sites INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLAST_DOMO COMPONENT II DM036901JX0368196-278 : K96-I279 INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLAST_DOMO COMPONENT II DM03009|S30350|378-841 : L372-E610 G727-Q841 INTER-ALPHA-TRYPSIN INHIBITOR COMPLEX BLAST_DOMO _ COMPONENT II DM03690|S30350|102-284 : K96-I279 ATP/GTP-binding site motif A (P-loop) : A107-S114 MOTIFS 5 6534745CD1 995 S8 S40 S45 S79 N116 N180 N190 ATPases associated with a variety of cellular activities HMMER_SMART S140 S168 S171 (AAA) : P433-D574 S191 S240 S245 S263 S339 S340 S350 S384 S396 S459 S483 S515 S516 S636 S649 S664 S704 S706 S720 S727 S737 S742 S764 S808 S868 S945 S947 S950 T4 T67 T92 T221 T223 T256 T311 T338 T445 T548 T811 T846 T959 T971 T976 Y495 Y894 ATPase family associated with various cellular activities HMMER PFAM (AAA) : G436-R626 26Sp45 : 26S proteasome subunit P45 family : S318-V647 HMMERTIGRFAM Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : Sites AAA-protein (ATPases associated with various cellular BLIMPSBLOCKS activities) IPB001939 : F399-P419, P434-A455, G481-R514, T528-D574 ATP-dependent Clp protease ATP-binding subunit signature BLIMPSPRINTS PR00300 : C437-A455 Endopeptidase La (Lon) serine protease (S 16) signature BLIMPS PRINTS PR00830 : G441-Q460 PROTEIN TAT BINDING HOMOLOG ATP BINDING BLAST PRODOM BROMODOMAIN C31G5. 19 CHROMOSOME I F11A10. 1 PD151474 : Y629-R921 PROTEIN ATP BINDING PROTEASE SUBUNIT BLAST PRODOM HOMOLOG REPEAT CELL DIVISION ATP DEPENDENT NUCLEAR PD000092 : G436-E482 I501- R626 AAA-PROTEIN FAMILY DM00024|P40340|408-571 : S396 BLAST DOMO R559 AAA-PROTEIN FAMILY DM00024|P46464|184-342 : BLAST DOMO V397-R559 AAA-PROTEIN FAMILY DM00024|P54609|201-360 : BLAST DOMO V397-R559 AAA-PROTEIN FAMILY DM00024|P23787 | 198-357 : BLAST_DOMO V397-R559 AAA-protein family signature : I542-R560 MOTIFS ATP/GTP-binding site motif A (P-loop) : G441-T448 MOTIFS 6 7512625CD1 176 S71 N40 N48 Signal cleavage : M1-P35 SPSCAN Signal Peptide : M1-G32 HMMER Signal Peptide : Ml-G38MER Signal Peptide : M1-P35 HMMER Fibronectin type 2 domain : L101-C133 HMMER_SMART Table 3 SEQ'Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Fibronectin type II domain : C108-C138 HMMER PFAM Cytosolic domain : Q34-L176 ; TMHMMER Transmembrane domain : G15-F33 ; Non-cytosolic domain : Ml-P14 Type II fibronectin collagen-binding domain IPB000562 : BLIMPS BLOCKS L101-L137 Fibronectin type II repeat signature PR00013 : G105-Y114, BLIMPSJPRINTS G116-A128 HEPATOCYTE GROWTH FACTOR ACTIVATOR BLAST PRODOM PRECURSOR EC 3. 4. 21. HGF HYDROLASE GLYCOPROTEIN PLASMA SERINE PROTEASE KRINGLE SIGNAL EGF-LIKE DOMAIN REPEAT ZYMOGENPD062554 : R31-P107 FIBRONECTIN TYPE II REPEAT DM004831Q04756l92-BLAST_DOMO 153 : S92-C133 7 17512761CD1 144 Glycosaminoglycan attachment site S14-G17 IMOTIFS 8 7512802CD1 209 S122 S128 S151 N57 Signal_cleavage : M1-G20 SPSCAN T34 T83 T204 Signal Peptide : Ml-G16 BAUMIER Signal Peptide : Ml-A18 HMMER Signal Peptide : M1-G20 HMMER Signal Peptide : Ml-P17 HMMER F5/8 type C domain : P117-Q208 FEVIMER PFAM Coagulation factor 5/8 type C domain (FA58C) IPB000421 : BLIMPS BLOCKS T189-S 194 DISCOIDIN I N-TERMINAL DM00516lS51739l1-128 : BLASE-DOM I149-S194 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites 9 7512824CD1 656 S27 S28 S83 S124 N73 N355 N382 Transglutaminase/protease-like homologues : G225-A318 HMMERSMART S213 S384 S390 N464 N539 N640 S406 S466 S515 S601 T108 T222 T293 T534 Y273 Transglutaminase-like superfamily : V228-S317HMMERPFAM Transglutaminase family, C-terminal ig like domain : P553-HMMER_PFAM A651, L440-Q545 Transglutaminase family : G2-R126 HMMER_PFAM Anaphylatoxin domain IPB000020 : V360-L369, V573-R600 BLIMPSBLOCKS Transglutaminase IPB001102 : N17-L43, F134-H185, V228-BLIMPS_BLOCKS L267, G286-C328, D329-W361, V379-V416, L575-L595 Transglutaminases active site : R210-L268 PROFILESCAN Anaphylatoxin domain signature PR00004 : V359-T368 BLIMPS PRINTS TRANSGLUTAMINASE TRANSFERASE ACYL-BLASTPRODOM TRANSFERASE PROTEIN GLUTAMIN GAMMAGLUTAMYL-TRANSFERASE CALCIUM- BINDING TGASE TISSUE C MEMBRANE PD002491 : E20-Q183 E203-S406 TRANSGLUTAMINASE TRANSFERASE ACYL-BLAST_PRODOM TRANSFERASE PROTEIN GLUTAMINE GAMMAGLUTAMYL-TRANSFERASE TGASE CALCIUM-BINDING TISSUE C MEMBRANE PD002568 : K425-P652 TRANSGLUTAMINASES DM00983P164521-684 : G2-BLAST_DOMO Q183 L184-A651 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites TRANSGLUTAMINASES DM009831I489012-685 : G2-BLAST_DOMO Q183 L184-A651 TRANSGLUTAMINASES DM009831QO1841110-693 : Q3-BLAST DOMO Q183 G212-P652 TRANSGLUTAMINASES DM00983|P51176|2-685 : Q3-BLAST_DOMO Q183 G212-P652 Cell attachment sequence : R453-D455 MOTIFS Transglutaminases active site : G231-G248 MOTIFS 10 7512760CD1 01 S208 S318 S359 Peptidase family M1 : R32-D409HMMERJPFAM T141 T368 T374 T386 Neutral zinc metallopeptidases, zinc-binding region BLIMPS_BLOCKS IPB000130 : V322-F332 Membrane alanyl dipeptidase (Ml) family signature BLIMPS PRINTS PR00756 : R176-Yl91, F220-I235, F295-L305, V322-T337, W341-Y353 AMINOPEPTIDASE B EC 3. 4. 11. 6 ARGINYL ARGININ BLAST PRODOM CYTOSOL IV APB HYDROLASE ZINC METALLOPROTEASE PD143187 : A2-F165 HYDROLASE ZINC METALLOPROTEASE BLAST PRODOM LEUKOTRIENE A4 LTA4 A4 MULTIFUNCTIONAL ENZYME BIOSYNTHESIS PD008823 : G402-Q494 AMINOPEPTIDASE HYDROLASE BLAST PRODOM METALLOPROTEASE ZINC N GLYCOPROTEIN PROTEIN TRANSMEMBRANE SIGNALANCHOR MEMBRANE PDQ01134 : R248-Q355 HYDROLASE ; LEUKOTRIENE ; A-4 ; ZINC ; BLAST_DOMO DM087071P1960217-609 : H38-I399 R396-H485 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites HYDROLASE ; LEUKOTRIENE ; A-4 ; ZINC ; BLASE-DOM DM08707lQl0740l58-670 : A26-S82 W152-D384 K405- _ H485 ZINC ; AMINOPEPTIDASE ; METALLOPEPTIDASE ; BLAST_DOMO NEUTRAL ; DM00700I5544163-916 : A159-Q355 L335- A377 ZINC ; AMINOPEPTIDASE ; METALLOPEPTIDASE ; BLAST DOMO NEUTRAL ; DM00700 P16406 80-887 : G160-Y353 Neutral zinc metallopeptidases, zinc-binding region MOTIFS signature : V322-W331 11 7512798CD1 53 N10 Signal cleavage : Ml-R32 SPSCAN Aminotransferases class-III pyridoxal-phosphate attachment PROFILESCAN site : T3-L52 PROTEIN CHROMOSOME TUBULIN-TYROSINE BLAST PRODOM LIGASE TTL C55A6. 2 ZK1128. 6 III KIAA0173 D2013. 9 PD008766 : M1-G53 12 7512799CD1 329 S76 S123 T83 T223 N10 N276 Signal_cleavage : Ml-R32 SPSCAN Tubulin-tyrosine ligase family : I81-P319 HMMER_PFAM PROTEIN CHROMOSOME TUBULIN-TYROSINE BLAST PRODOM LIGASE TTL C55A6. 2 ZK1128. 6 III KIAA0173 D2013. 9 PD008766 : M1-P314 Q300-L329 13 7512840CD1 146 S45 S67 S100 S101 Signal_cleavage : M1-A47 SPSCAN T76 T85 Signal Peptide : M1-A47 HMMER Cytosolic domain : Ml-119 ; TMHMMER Transmembrane domain : L20-A42 ; Non-cytosolic domain : S43-R146 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites SIALIDASE PRECURSOR SIGNAL G9 LYSOSOMAL BLAST PRODOM PD024919 : P11-D75 14 7512889CD1 1138 S18 S107 S122 N113 N219 N374 Tubulin-tyrosine ligase family : R651-I946 HMMER_PFAM S139 S141 S177 N677 N810 S193 S202 S212 S291 S376 S395 S420 S439 S477 S491 S497 S524 S544 S555 S565 S631 S649 S652 S713 S725 S761 S791 S797 S844 S885 S917 S922 S962 S997 S1018 S 1032 S 1097 S 1107 T31 T344 T416 T511 T591 T772 T986 T1003 T1050 Tllll T1122 Y995 Y1044 KIAA0173 PROTEIN PD143868 : M1-E513 BLAST PRODOM PROTEIN ZK1128. 6 CHROMOSOME III KIAA0173 BLAST PRODOM PD041973 : E514-F685 PROTEIN CHROMOSOME TUBULINTYROSINE BLAST PRODOM LIGASE TTL C55A6. 2 ZK1128. 6 III KIAA0173 D2013. 9 PD008766 : P741-P949 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites PROTEIN CHROMOSOME TUBULINTYROSINE BLAST PRODOM LIGASE TTL C55A6. 2 ZK1128. 6 III KIAA0173 D2013. 9 PD008766 : P694-L896 PROTEIN ZK1128. 6 CHROMOSOME III KIAA0173 BLAST PRODOM PD041972 : L1002-C1071 ATP/GTP-binding site motif A (P-loop) : G189-S196 MOTIFS 15 7512901CD1 139 S32 S133 T55 Y39 Prenyltransferase and squalene oxidase repeat : M66-D109 HMMER PFAM BETA SUBUNIT TRANSFERASE PRENYL-BLAST_PRODOM TRANSFERASE REPEAT ZINC TYPE II GERANYL- GERANYL-TRANSFERASE GERANYLGERANYL PD150761 : M1-M66 GERANYLGERANYL TRANSFERASE TYPE II BETA BLAST PRODOM SUBUNIT EC 2. 5. 1. RAB GERANYLGERANYL- TRANSFERASE GERANYL GERANYLTRANSFERASE GG GGTASE PRENYLTRANSFERASE REPEAT ZINC PD168843 : N67-V113 BETA ; FARNESYLTRANSFERASE ; DPR1 ; CDC43 ; BLASE-DOM DM012661P53611l31-324 : G31-V113 BETA ; FARNESYLTRANSFERASE ; DPR1 ; CDC43 ; BLAST DOMO DM01266|P41992|37-324 : K34-L111 BETA ; FARNESYLTRANSFERASE ; DPR1 ; CDC43 ; BLASE-DOM _ DM01266|P20133|20-320 : S32-V113 BETA ; RIBT ; 21. 0 ; GERANYLGERANYL ; BLAST DOMO DM02620 P5361111-29 : M1-Y30 16 7512949CD1 75 S31 T4 T25 Ubiquitin homologues : M1-G69 HMMERSMART Ubiquitin family : M1-R66HMMERPFAM Ubiquitin domain IPB000626 : V5-S59 BLIMPS_BLOCKS Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Ubiquitin signature PR00348 : R1 1-S3 1, E32-G52 BLIMPS_PRINTS Leucine zipper pattern : L8-L29 MOTIFS 17 7512660CD1 120 S93 S99 S114T9 Ubiquitinhomologues : M1-S74HMMERJ3MART T55 Ubiquitin family : M1-A76HMMERPFAM Ubiquitin domain IPB000626 : V5-Y59 BLIMPS_BLOCKS Myb DNA binding domain IPB001005 : M1-G53 BLIMPS_BLOCKS Ubiquitin signature PR00348 : Kll-Q31, D32-D52, G53-S74 BLIMPS PRINTS . PROTEIN NUCLEAR POLYUBIQUITIN UBIQUITIN BLAST PRODOM POLYPROTEIN UBIQUITINLIKE REPAIR DNA FUSION REPEAT PD000119 : M1-P89 UBIQUITIN DM00160 A26437 1-73 : M1-L73 BLAST_DOMO UBIQUITIN DM00 1601A26437l75-149 : M1-L73 BLAST_DOMO UBIQUITIN DM00160 A26437151-227 : M1-L73 BLAST DOMO UBIQUITIN DM00 160lS462 14|1-75 : M1-L73 BLAST_DOMO Ubiquitin domain signature : K27-D52 MOTIFS Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites 18 7512741CD1 986 S47 S76 S109 S113 N283 N311 N374 Ubiquitin carboxyl-terminal hydrolases familY 2 : V162-HMMERPFAM S137 S205 S228 N580 N652 N763 Y193 S248 S280 S348 S369 S435 S444 S445 S458 S461 S491 S561 S565 S566 S609 S641 S654 S701 S728 S765 S808 S871 S880 S905 S962 T130 T134 T207 T260 T430 T473 T475 T603 T660 T694 T754 T813 T875 T957 T984 Y829 Ubiquitin carboxyl-terminal hydrolase family 2 : R521-N590 HMMERPFAM Ubiquitin carboxyl-terminal hydrolase family 2 IPB001394 : BLIMPSBLOCKS G163-L180 PROBABLE UBIQUITIN CARBOXYL-TERMINAL BLAST-PRODOM HYDROLASE K02C4. 3 EC 3. 1. 2. 15 THIOLESTERASE UBIQUITIN-SPECIFIC PROCESSING PROTEASE DEUBIQUITINATING ENZYME HYPOTHETICAL PROTEIN CONJUGATION THIOL PD138085 : Y317-S445 F481-S661 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites PROTEASE UBIQUITIN HYDROLASE ENZYME BLAST PRODOM UBIQUITIN-SPECIFIC CARBOXYL-TERMINAL DEUBIQUITINATING THIOLESTERASE PROCESSING CONJUGATION PD000590 : P161-N287 Carbamoyl-phosphate synthase subdomain signature 2 : L862-MOTIFS A869 Ubiquitin carboxyl-terminal hydrolases family 2 signature 2 : MOTIFS Y525-Y542 19 7513099CD1 471 S108 S290 S342 N80 N107 N231 signal-cleavage : Ml-G28 SPSCAN S445 S446 T278 T323 T362 Signal Peptide : M1-G23, M1-L25, M1-G28, R8-G32, A13-HMMER G32, L15-G32 Glycosyl transferase family 8 : R110-G368 HMMER_PFAM Cytosolic domain : M1-R6 TMHMMER Transmembrane domain : P7-G29 Non-cytosolic domain : D30-P471 20 7511908CD1 90 S45 S68 signal_cleavage : Ml-G17 SPSCAN Signal Peptide : M1-A16, Ml-T18, M1-E20, M1-G23 HMMER Serine proteases, trypsin family IPB001254 : C49-C65 BLIMPS BLOCKS Serine proteases, trypsin family, active sites : L41-P89 PROFILESCAN Serine proteases, V8 family, active sites : K28-R90 PROFILESCAN Chymotrypsin serine protease family (S 1) signature BLIMPS PRINTS PR00722 : G50-C65 TRYPSIN BLAST_DOMO DM000181P20718l21-242 : I21-S68 DM00018Q0660520-244 : E20-S68 DM000181P80219l1-221 : I21-S68 DM00018 P0831121-241 : I21-S68 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Serine proteases, trypsin family, histidine active site : L60-MOTIFS C65 21 513074CD1 707 S15 S2-7 S267 S287 N145 N162 N376 Peptidase family M49 : Rlll-P675 HMMER_PFAM S294 S310 S427 S474 S475 S600 S638 S669 S671 T29 T52 T85 T116 T147 T201 T217 T344 T389 T395 T563 T616 T627 T647 DIPEPTIDYL III F02E9. 6 PROTEIN PEPTIDASE BLAST PRODOM AMINOPEPTIDASE ARYLAMIDASE RED CELL ANGIOTENSINASE PD014459 : N167-R673 DIPEPTIDYL PEPTIDASE EC 3. 4. 14. 4 DIPEPTIDYL BLAST PRODOM PEPTIDASE III DIPEPTIDYL AMINOPEPTIDASE III DIPEPTIDYL ARYLAMIDASE III RED CELL ANGIOTENSINASE ENKEPHALINASE B HYDROLASE PD143979 : Q90-Y166 DIPEPTIDYL III PEPTIDASE AMINOPEPTIDASE BLAST PRODOM ARYLAMIDASE RED CELL ANGIOTENSINASE ENKEPHALINASE B PD043280 : T4-E94 22 7513960CD1 332 S16 S55 S65 S87 N133 N232 N265 signal-cleavage : M1-Q46 SPSCAN S177 S200 S261 S267 T108 T135 T141 T237 T317 Caspase, interleukin-1 beta converting enzyme : I80-P330 HMMER_SMART ICE-like protease (caspase) plO domain : A245-P330 HMMER_PFAM Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites ICE-like protease (caspase) p20 domain : R89-V220 IIMER_PFAM ICE-like protease (caspase) p20 domain IPB001309 : R91-BLIMPSBLOCKS F101, I104-M139, E151-G173, C198-G215, K248-I282, V294-E306 Interleukin-lB converting enzyme signature PR00376 : R89-BLIMPSJPRINTS D102, R107-G125, G125-L143, T158-G166, C198-D216, S267-I278, V320-F329 INTERLEUKIN1 BETA CONVERTASE PRECURSOR BLAST PRODOM ILIBC EC 3. 4. 22. 36 IL1 CONVERTING ENZYME ICE P45 CASPASE1 CASP1 HYDROLASE THIOL PROTEASE ZYMOGEN 3DSTRUCTURE ALTERNATIVE SPLICING PD169510 : D20-S88 PRECURSOR PROTEASE HYDROLASE THIOL BLAST PRODOM ZYMOGEN APOPTOSIS PROTEIN APOPTOTIC CASPASE1 CYSTEINE PD001408 : R89-D216 PRECURSOR PROTEASE HYDROLASE THIOL BLAST PRODOM ZYMOGEN APOPTOSIS PROTEIN APOPTOTIC CASPASE1 CYSTEINE PD007531 : A245-P330 INTERLEUKIN-1 BETA CONVERTING ENZYME BLAST DOMO FAMILY HISTIDINE DM01067|P29466| 124-307 : P52-P236 DM01067|P29452|123-306 : T53-V227 DM01067P4966297-280 : P52-S226 DM01067 B57511 138-321 : P52-S226 Caspase family cysteine active site : K204-G215 MOTIFS Caspase family histidine active site : H152-G166 MOTIFS 23 7513984CD1 267 S42 S65 S81 S99 N90 N126 signal cleavage : M1-T22 SPSCAN S132 S176 S192 S248 S266 T28 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Signal Peptide : M1-G18HMMER APPLE domain : C20-C103, Cl 10-C193, C201-N267 HMMER_SMART PAN domain : C110-C193, C20-C103, C201-I265 HMMER PFAM Apple domain IPB000177 : D27-S67, E68-S96, G97-Q137, BLIMPS BLOCKS E138-K183, A184-A220, K222-C249 Apple domain : C76-N124, C165-E215 PROFILESCAN Apple domain signature PR00005 : A133-A152, R162-R178, BLIMPS PRINTS K180-H195 COAGULATION FACTOR PRECURSOR PLASMA BLAST PRODOM HYDROLASE SERINE PROTEASE GLYCOPROTEIN BLOOD SIGNAL PD018105 : C20-C103, C110-C193 APPLE BLAST DOMO DM00800P03951 36-123 : T36-N124 DM00800|P03951|215-304 : I35-G122, N126-E215 DM00800P2626237-124 : V38-N124 DM00800lP039511125-213 : Y125-F211 Apple domain : C20-C 103, C 110-C 193 MOTIFS 24 7512992CD1 472 S31 S105 S160 N208 N214 N323 signal cleavage : Ml-G25 SPSCAN S184 S238 S431 T5 N345 N377 N425 T122 T126 T219 T296 T393 Y445 Signal Peptide : M1-G24, M1-S28 HMMER Cytosolic domain : L430-D472 TMHMMER Transmembrane domain : W407-L429 Non-cytosolic domain : M1-A406 EGF DM00003lA45445l178-268 : E283-P351 BLAST DOMO EGF-like domain signature 1 : C335-C346 MOTIFS . EGF-like domain signature 2 : C335-C346 MOTIFS Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites 25 7512994CD1 487 S31 S105 S160 N208 N214 N296 signalcleavage : Ml-G25 SPSCAN S184 S238 T5 T122 N366 N388 N420 T126 T219 T339 T436 T446 Y460 Signal Peptide : M1-E21, M1-A22, M1-G24, M1-G25, Ml-HMMER S28 EGF DM000031A454451178-268 : E326-P394 BLAST_DOMO EGF-like domain signature 1 : C378-C389 MOTIFS EGF-like domain signature 2 : C378-C389 MOTIFS 26 7513547CD1 581 S79 S89 S116 S144 N107 N516 signal cleavage : Ml-M28 SPSCAN S164 S213 S329 S339 S368 S389 S405 S448 S491 S542 T375 T490 Y57 Signal Peptide : M1-M28HMMER Ricin-type beta-trefoil : S448-D573 HMMER_SMART QXW lectin repeat : G535-I575, G449-H489HMMERPPAM Cytosolic domain : MI-PI 1 TMHMMER Transmembrane domain : C12-H34 Non-cytosolic domain : P35-R581 N-ACETYLGALACTOSAMINYLTRANSFERASE BLAST PRODOM TRANSFERASE POLYPEPTIDE ACETYLGALACTOSAMINYLTRANSFERASE UDPGALNAC : POLYPEPTIDE GLYCOSYLTRANSFERASE PROTEIN UDP PROTEIN UDP N PD003162 : W283-S446 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites ACETYLGALACTOSAMINYLTRANSFERASE ; BLASE-DOM POLYPEPTIDE ; DM03891Q0753732-558 : S164-Q235, V249-W570 DM03891|P34678|37-600 : S164-Q235, R248-D573 DM03891I3740521-571 : F87-R113, S164-W343, S247- F572 27 7513357CD1 405 S24 S101 S182 N272 signal cleavage : Ml-G15 SPSCAN S210 S214 S247 S315 S323 T108 T206 T213 T225 T274 T334 T341 Y219 Signal Peptide : M1-G15, Ml-C19, M1-Q20, M1-A23, MU-HUMER P25 SERine Proteinase INhibitors : Y50-P402HMMERJSMART Serpin (serine protease inhibitor) : V38-P402 HMMER_PFAM Serpins IPB000215 : N64-I91, D163-T183, I190-M231, BLIMPS BLOCKS L299-F325, N378-P402 Serpins signature : D354-P405 PROFILESCAN Leuserpin 2 signature PR00780 : P32-R54, E222-L242, C248 « BLIMPS_PRINTS L273 SERPIN INHIBITOR PROTEASE SERINE SIGNAL BLAST PRODOM PRECURSOR GLYCOPROTEIN PLASMA PROTEIN PROTEINASE PD000192 : N39-P402 PIGMENT EPITHELIUMDERIVED FACTOR BLAST_PRODOM PRECURSOR PEDF SERPIN GLYCOPROTEIN SIGNAL CAPSIN STROMALPD012731 : M1-N39 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites SERPINS BLAST DOMO DM00112lP36955l52-413 : N39-D401 DM00112|S47217|80-434 : K40-I399 DM001121P28800l81-435 : K40-I399 DM00112|P05544|33-400 : L41-I399 Serpins sign_ MOTIFS 28 7513329CD1 552 S97 S108 5158 signal cleavage : Ml-G34 SPSCAN S178 S300 S351 S463 S515 S526 T5 T55 T162 T225 T289 T382 T495 T538 Y404 Signal Peptide : M1-A39, R15-V36, R16-A39, E19-A39 HMMER Ricin-type beta-trefoil : R413-K548 HMMER SMART Glycosyl transferase : S139-G322 HMMER_PFAM QXW lectin repeat : G508-R550, G418-Q464HMMERPFAM Cytosolic domain : M1-E19 TMHMMER Transmembrane domain : A20-L37 Non-cytosolic domain : R38-L552 N-ACETYLGALACTOSAMINYLTRANSFERASE BLAST PRODOM TRANSFERASE POLYPEPTIDE ACETYLGALACTOSAMINYLTRANSFERASE UDPGALNAC : POLYPEPTIDE GLYCOSYLTRANSFERASE PROTEIN UDP PROTEIN UDP N PDQ03162 : W287-I317, F315-P414 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites TRANSFERASE N-BLAST PRODOM ACETYLGALACTOSAMINYLTRANSFERASE POLYPEPTIDE ACETYLGALACTOSAMINYLTRANSFERASE UDPGALNAC : POLYPEPTIDE GLYCOSYLTRANSFERASE PROTEIN UDP PROTEIN UDP N PD003677 : L33-T138 ACETYLGALACTOSAMINYLTRANSFERASE ; BLAST_DOMO POLYPEPTIDE ; DM03891Q0753732-558 : P71-I317, F315-K548 DM038911P34678l37-600 : L93-I317 F315-A522 DM03891 I37405 21-571 : G88-I317 F315-F547 29 7517777CD1 299 S129 S189 T29 T69 N153 Signal_cleavage : M1-S22 SPSCAN T134 T151 Signal Peptide : M1-S22HMMER Ubiquitin carboxyl-terminal hydrolases family : R159-D190 HMMER_PFAM Ubiquitin carboxyl-terminal hydrolase family 2 IPB001394 : BLIMPS_BLOCKS G160-L177 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST DOMO FAMILY 2 DM00659|Q09738|149-388 : N163-C297 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST_DOMO FAMILY 2 DM00659lP50102l141-420 : N163-C297 Ubiquitin carboxyl-terminal hydrolases family 2 signature 1 : MOTIFS G160-Q175 30 7519126CD1 41 S3 S32 Proteasome A-type subunits signature IPB000426A : Y5-E42 BLIMPS BLOCKS Proteasome A-type subunits signature : Ml-E41 PROFILESCAN Proteasome A-type and B-type. PF00227 : F12-Y23BLIMPSPFAM Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites PROTEASOME A-TYPE SUBUNITS DM00341IP4800411-BLAST-DOMO 226 : Y5-A34 PROTEASOME A-TYPE SUBUNITS DM00341|S23451|3-BLAST_DOMO 222 : S3-A34 PROTEASOME A-TYPE SUBUNITS DM00341|P22769|3-BLAST_DOMO 222 : S3-A34 PROTEASOME A-TYPE SUBUNITS DM00341|P34120|4-BLAST_DOMO 220 : S3-A34 Proteasome A-type subunits signature : Y5-A27 MOTIFS 31 7519175CD1 711 S26 S48 S49 S77 N71 Ubiquitin carboxyl-terminal hydrolases family : R363-D394 HMMERJPFAM S150 S154 S196 S200 S327 S334 S356 S393 S465 S538 S548 S565 S575 S579 S627 S679 T162 T226 T259 T315 T506 T557 T584 T689 Y695 Ubiquitin carboxyl-terminal hydrolase family : N645-K705 H1\ IMER_PFAM Ubiquitin carboxyl-terminal hydrolase family 2 IPB001394 : BLIMPS BLOCKS G364-L381 PROTEASE UBIQUITIN HYDROLASE UBIQUITIN-BLAST PRODOM SPECIFIC ENZYME DEUBIQUITINATING CARBOXYLTERMINAL THIOLESTERASE PROCESSING CONJUGATION PD017412 : S548-P638 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST DOMO FAMILY 2 DM006591P32571l566-873 : K295-F329, N367- H462, I483-P519, S548-G659, Q323-K355 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST DOMO FAMILY 2 DM006591P40818l782-1103 : L368-N4761483- L518 S548-L701 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST_DOMO FAMILY 2 DM00659|P50102|141-420 : N367-G659 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST_DOMO FAMILY 2 DM006591QO97381149-388 : N367-L518 P547- M621 Ubiquitin carboxyl-terminal hydrolases family 2 signature 1 : MOTIFS G364-Q379 Ubiquitin carboxyl-terminal hydrolases family 2 signature 2 : MOTIFS Y649-Y666 32 7514648CD1 223 S111 S161 T106 N172 Signal_cleavage : Ml-A17 SPSCAN Signal Peptide : Ml-A17 HMMER Signal Peptide : Ml-L19 HMMER Signal Peptide : M1-T20HMMER Signal Peptide : M1-D22 HMMER Papain family cysteine protease : T74-T223HMMERPFAM Eukaryotic thiol (cysteine) proteases active sites IPB000169 : BLIMPS_BLOCKS M83-F92, I110-C120, N126-M134, S149-A157, E205-N217 Eukaryotic thiol (cysteine) proteases active sites : M58-E114 PROFILESCAN Calpain cysteine protease (C2) family signature PR00704 : BLIMPS PRINTS M83-E99 Table 3 l SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Papain cysteine protease (Cl) family signature PR00705 : BLIMPS PRINTS M83-L98 PROTEASE PRECURSOR SIGNAL CYSTEINE BLAST PRODOM PROTEINASE HYDROLASE THIOL ZYMOGEN CATHEPSIN GLYCOPROTEINPD000158 : D119-G218, D82-S169 EUKARYOTIC THIOL (CYSTEINE) PROTEASES BLAST DOMO CYSTEINE DM00081P0771119-332 : L19-M83 D82-E212 EUKARYOTIC THIOL (CYSTEINE) PROTEASES BLAST_DOMO CYSTEINE DM00081|P25975|20-333 : D22-M83 D82- V215 EUKARYOTIC THIOL (CYSTEINE) PROTEASES BLASE-DOM CYSTEINE DM00081p0679719-332 : F21-M83 D82-V215 EUKARYOTIC THIOL (CYSTEINE) PROTEASES BLAST_DOMO CYSTEINE DM000811P15242120-332 : T20-M83 D82-Y210 33 7517904CD1 83 T15 PROTEASE UBIQUITIN HYDROLASE UBIQUITIN-BLAST PRODOM SPECIFIC CARBOXYLTERMINAL THIOLESTERASE PROCESSING DEUBIQUITINATING ENZYME UBIQUITOUS PD009843 : M1-S76 34 7518798CD1 271 S9 S14 S27 S64 Trypsin-like serine protease : S102-I265 HIVI1VVIER_SMART S80 S117 S153 S167 T177 Y151 Trypsin : 178-1265 Cytosolic domain : M1-R29 ; Transmembrane domain : L30-TMHMMER V52 ; Non-cytosolic domain : V53-M271 Kringle domain IPB000001 : G224-I265 BLIMPS BLOCKS Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites _ t BLIMPS BLOCKS Serine proteases, trypsin family IPB001254 : D216-I239, BLIMPSBLOCKS P252-I265 Serine proteases, trypsin family, active sites : I201-A247 PROFILESCAN Chymotrypsin serine protease family (S1) signature BLIMPS PRINTS PR00722 : I215-V227 REPEAT PRECURSOR GLYCOPROTEIN EGF PD00120 : BLIMPSPRODOM D216-G224 PROTEASE SERINE PRECURSOR SIGNAL BLAST PRODOM HYDROLASE ZYMOGEN GLYCOPROTEIN FAMILY MULTIGENE FACTOR PD000046 : N176-I265 AIRWAY TRYPSINLIKE PROTEASE PROTEASE BLAST PRODOM PD103718 : Q23-T171 TRYPSIN DM00018 P03951389-621 : R169-T269 BLAST_DOMO TRYPSIN DM00018 P05981 163-403 : L178-I265 BLAST_DOMO TRYPSINDM000181P03952|392-624 : I174-T269 BLAST DOMO TRYPSIN DM00018 P14272 391-624 : Q175-K268 BLAST_DOMO Serine proteases, trypsin family, serine active site : D216-MOTIFS V227 35 7519109CD1 363 S56 S169 S222 N198 Signal cleavage : Ml-A22 SPSCAN S298 S341 T144 Signal Peptide : M1-A22 HIZMER Signal Peptide : M1-R27 HMIER Hemopexin-like repeats. : F171-P214, V309-C353, I216-HMMER_SMART R259, P261-E307 Hemopexin : I216-R259, F171-P214, V309-C353, P261-HMIER PFAM E307 Hemopexin domain IPB000585 : M86-T96 BLIMPS BLOCKS Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Matrixin (matrix metalloproteinase) IPB001818 : Y229-BLIMPSBLOCKS F239, R33-A81, W209-V221 Hemopexin domain signature : I184-P242 PROFILESCAN Matrixins cysteine switch : V69-P164 PROFILESCAN Matrixin signature PR00138 : M86-Y99 BLIMPS PRINTS 36 7519227CD1 139 S57 Signal cleavage : M1-A25 SPSCAN Signal Peptide : M8-A23 HMMER Signal Peptide : M8-A25 HMMER Signal Peptide : M1-A23MER Signal Peptide : M1-A25 HMMER 37 7519262CD1 343 S56 S152 S197 N280 Signal_cleavage : Ml-A22 SPSCAN S251 S304 T82 T226 Signal Peptide : M1-A22HMMER Signal Peptide : Ml-R27MER Hemopexin-like repeats. : F253-P296HMMERSMART Zinc-dependent metalloprotease : R64-K210HMMERSMART Hemopexin : F253-P296HMMERPFAM Neutral zinc metallopeptidases, zinc-binding region BLIMPS_BLOCKS IPB000130 : V162-G172 Hemopexin domain IPB000585 : R105-R153, G156-Y187, BLIMPS BLOCKS D199-G209, A300-R320 Matrixin IPB001818 : I106-W149, G156-Y187, D199-BLIMPS_BLOCKS G209, Y265-V275 Hemopexin domain signature : I266-G325 PROFILESCAN Neutral zinc metallopeptidases, zinc-binding region PROFILESCAN signature : D144-P185 Matrixins cysteine switch : V69-L130 PROFILESCAN Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Matrixin signature PR00138 : M86-Y99, V162-Y187, L196-BLIMPSPRINTS G209 MATRIXINS CYSTEINE SWITCH DM00558|P22757|100-BLAST_DOMO 337 : E37-D95, F123-G213 MATRIXINS CYSTEINE SWITCH DM00558|P51511|49-BLAST_DOMO 314 : A36-G127, F123-G213 MATRIXINS CYSTEINE SWITCH DM005581P39900128-BLAST_DOMO 273 : E37-Y99, F123-P211 MATRIXINS CYSTEINE SWITCH DM00558|P34960|23-BLAST_DOMO 266 : A36-R105, F123-L212 Neutral zinc metallopeptidases, zinc-binding region MOTIFS signature : V162-L171 38 7519371CD1 414 S61 S204 S220 N64 N126 N324 Signal_cleavage : M1-G26 SPSCAN S280 S284 S313 S379 T44 T104 T188 T411 Signal Peptide : PI 1-A27HMMER Signal Peptide : R6-A27 HMMER Signal Peptide : M1-A25MER Signal Peptide : M1-A27MER Signal Peptide : M1-G26 HMMER Serine carboxypeptidase : P32-Q413 HMMER_PFAM Serine carboxypeptidase (S10) IPB001563 : P69-G92, R101-BLIMPS_BLOCKS Y124, F161-A174, N192-S201, I323-L348, A375-T411 Serine carboxypeptidases, active sites : E372-E414 PROFILESCAN Carboxypeptidase C serine protease (S10) family signature BLIMPS PRINTS PR00724 : R101-F113, V114-Y124, F149-A174, L383-P396 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites CARBOXYPEPTIDASE SERINE HYDROLASE BLAST PRODOM PRECURSOR GLYCOPROTEIN PROTEIN SIGNAL PUTATIVE ZYMOGEN I PD001189 : E34-V241 T297- R408 CARBOXYPEPTIDASE HYDROLASE PRECURSOR BLAST PRODOM GLYCOPROTEIN SIGNAL ZYMOGEN SERINE Y III YSCY PD150036 : D306-M407 SERINE CARBOXYPEPTIDASES, SERINE BLASE-DOM DM00460 P215291-410 : D48-K232 A296-Q412 SERINE CARBOXYPEPTIDASES, SERINE BLAST_DOMO DM00460 P30574126-540 : K37-L293 D306-M407 SERINE CARBOXYPEPTIDASES, SERINE BLAST DOMO DM004601P42660264-470 : D95-Q413, V43-F288 SERINE CARBOXYPEPTIDASES, SERINE BLAST DOMO DM004601P5271211-415 : D48-V233 V299-M407 39 7519442CD1 96 S22 Ubiquitin carboxyl-terminal hydrolases family : V55-W86 HIVBvlER PFAM Ubiquitin carboxyl-terminal hydrolases signature BLIMPS_BLOCKS IPB001394 : G56-F73 40 7519123CD1 63 S3 S32 S57 Proteasome A-type subunit IPB000426 : Y5-M50, I9-V41 BLIMPS_BLOCKS Proteasome A-type subunits signature : M1-A48 PROFILESCAN Proteasome A-type and B-type. PF00227 : F12-Y23 BLIMPS PFAM PROTEASOME A-TYPE SUBUNITS DM00341lP48004l1-BLAST_DOMO 226 : Y5-V37 PROTEASOME A-TYPE SUBUNITS DM00341lS23451i3-BLAST_DOMO 222 : S3-V37 PROTEASOME A-TYPE SUBUNITS DM00341|P22769|3-BLAST_DOMO 222 : S3-V37 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites PROTEASOME A-TYPE SUBUNITS DM00341P341204-BLAST_DOMO 220 : S3-V37 Proteasome A-type subunits signature : Y5-A27 MOTIFS 41 7519522CD1 379 S203 S363 T22 Caspase recruitment domain : M15-T103HMMERSMART T230 T308 T343 Caspase, interleukin-1 beta converting enzyme : A174-P374 HMMERSMART Caspase recruitment domain : H16-T104HMMERPFAM ICE-like protease (caspase) p20 domain : P181-R310HMMERPFAM ICE-like protease (caspase) p20 domain IPB001309 : G183-BLIMPS_BLOCKS F193, L199-M234, A246-G268, C288-G305, R340-P374 Coagulation factor GLA domain signature PR00001 : A88-BLIMPSPRINTS L101 Interleukin-lB converting enzyme signature PR00376 : P181-BLIMPSPRINTS T194, R202-G220, G220-L238, C253-G261, C288-D306 CASPASE2 PRECURSOR CASP2 ICH1 PROTEASE BLAST PRODOM HYDROLASE THIOL APOPTOSIS ZYMOGEN ICH PD008470 : L102-P181 PRECURSOR PROTEASE HYDROLASE THIOL BLAST PRODOM ZYMOGEN APOPTOSIS PROTEIN APOPTOTIC CASPASE1 CYSTEINE PD001408 : R182-D309 PRECURSOR HYDROLASE THIOL PROTEASE BLAST PRODOM ZYMOGEN APOPTOSIS PROTEIN CONVERTING ENZYME CELL PD006849 : H18-L101 CASPASE2 PRECURSOR CASP2 ICH1 PROTEASE BLAST PRODOM HYDROLASE THIOL APOPTOSIS ZYMOGEN ICH PD151745 : M1-Q33 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites INTERLEUKIN-1 BETA CONVERTING ENZYME BLAST DOMO FAMILY HISTIDINE DM010671P29594|149-323 : N150- G325 INTERLEUKIN-1 BETA CONVERTING ENZYME BLAST DOMO FAMILY HISTIDINE DM010671P425761136-311 : N150- G305 INTERLEUKIN-1 BETA CONVERTING ENZYME BLASE-DOM FAMILY HISTIDINE DM07460|P4257611-134 : M15-D149 INTERLEUKIN-1 BETA CONVERTING ENZYME BLAST DOMO FAMILY HISTIDINE DM07460|P29594|1-147 : Ml-D149 Cell attachment sequence : R304-D306 MOTIFS Caspase family cysteine active site : K294-G305 MOTIFS 42 7520023CD1 375 S72 S152 S162 N70 N172 signal_cleavage : Ml-A24 SPSCAN S211 S263 S347 T238 Signal Peptide : M1-G19HMMER Signal Peptide : M1-A22 HMMER Signal Peptide : M1-A24 HMMER Cytosolic domain : M1-W4 TMHMMER Transmembrane domain : L5-L27 Non-cytosolic domain : R28-V375 PROTEIN CARBOXYPEPTIDASE LYSOSOMAL PROX BLAST PRODOM SIMILAR HUMAN CHROMOSOME III F23B2. 12 F23B2. 11 PD149833 : G228-K364 THYMUS SPECIFIC SERINE PEPTIDASE PD173171 : BLAST PRODOM M1-G50 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites PROTEIN CARBOXYPEPTIDASE LYSOSOMAL PROX BLAST PRODOM SIMILAR HUMAN CHROMOSOME III K12H4. 7 F23B2. 12 PD003976 : P51-G103 CARBOXYPEPTIDASE LYSOSOMAL PROX PROTEIN BLAST PRODOM SIMILARHUMANF23B2. 11 THYMUS SPECIFIC SERINEPD150357 : V126-S189 LYSOSOMAL ; PRO-X ; CARBOXYPEPTIDASE ; BLAST DOMO DM03192lP34528l84-584 : Q64-K197 L208-L363 LYSOSOMAL ; PRO-X ; CARBOXYPEPTIDASE ; BLAST_DOMO _ DM03192|P42785|3-487 : L12-K197 L219-K364 LYSOSOMAL ; PRO-X ; CARBOXYPEPTIDASE ; BLASE-DOM DM03192|P34676|1-498 : G60-K197 W234-K364 LYSOSOMAL ; PRO-X ; CARBOXYPEPTIDASE ; BLASE-DOM DM031921P34610131-480 : W61-K197 Y290-L363 43 7519518CD1 66 S17 S63 signal cleavage : Ml-G18 SPSCAN Signal Peptide : Ml-G18 HMMER Signal Peptide : M1-G22 HMMER MATRIX METALLOPROTEINASE19 PRECURSOR EC BLAST PRODOM 3. 4. 24. MMP19 RASH HYDROLASE METALLOPROTEASE ZINC ZYMOGEN CALCIUM SIGNAL PD028998 : M1-D52 44 7519955CD1 64 S51 N38 signal cleavage : Ml-A17 SPSCAN Signal Peptide : M1-A17HMMER Signal Peptide : M1-D19HMMER Signal Peptide : M1-H23 HMMER Signal Peptide : Ml-R24 HMIER Signal Peptide : Ml-G27 HIv11V1ER Zinc carboxypeptidases, carboxypeptidase A metalloprotease BLIMPS BLOCKS (M14) family IPB000834 : Y22-P62 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites 45 7514925CD1 371 S27 S32 S112 T136 N172 Signal Peptide : Ml-A15 HMMER T243 Y164 metallopeptidase family M24 : L109-K358 BNRVMR PFAM Proline dipeptidase IPB001131 : V167-T210, H284-D296, BLIMPS BLOCKS L306-I320, G335-S348 Methionine aminopeptidase, subfamily 1 IPB002467 : I186-BLIMPS BLOCKS N214, M266-S303, L306-S348 Methionine aminopeptidase, subfamily 2 IPB002468 : N182-BLIMPS BLOCKS Y225 Methionine aminopeptidase-1 signature PR00599 : El 90-BLIMPSJPRINTS D206, F275-G287, L304-P316 AMINOPEPTIDASE HYDROLASE METHIONIN BLAST PRODOM PEPTIDASE PROTEIN COBALT M DIPEPTIDASE XPRO MAP PD000555 : L109-L350 AMINOPEPTIDASE P AND PROLINE DIPEPTIDASE BLAST DOMO DM00816|P44881|163-417 : I104-P357 AMINOPEPTIDASE P AND PROLINE DIPEPTIDASE BLASE-DOM DM00816lP40051 l237-484 : I104-S348 AMINOPEPTIDASE P AND PROLINE DIPEPTIDASE BLAST_DOMO DM00816|Q10439|228-475 : L107-P357 AMINOPEPTIDASE P AND PROLINE DIPEPTIDASE BLASE-DOM DM00816 P15034169-423 : I104-Q346 46 7518514CD1 199 S9 S14 S27 S64 Cytosolic domain : M1-R29 TMHMMER S80 S117 S153 Transmembrane domain : L30-V52 S167 S175 T171 Non-cytosolic domain : V53-L199 Y151 AIRWAY TRYPSIN-LIKE PROTEASE PROTEASE BLAST PRODOM PD103718 : 023-N183 47 7519481CD1 85 S54 signal cleavage : Ml-A25 SPSCAN Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Signal Peptide : M8-A23 HMMER Signal Peptide : M8-A25MER Signal Peptide : Ml-A23 BAEVIER Signal Peptide : M1-A25MER Kringle domain IPB000001 : C66-V83 BLIMPS BLOCKS Serine proteases, trypsin family IPB001254 : C66-C82 BLIMPS_BLOCKS Chymotrypsin serine protease family (S1) signature BL1MPS_PRINTS PR00722 : G67-C82 REPEAT PRECURSOR GLYCOPROTEIN EG. PD00120 : BLIMPSPRODOM G67-A79 PROTEASE SERINE PRECURSOR SIGNAL BLAST PRODOM HYDROLASE ZYMOGEN GLYCOPROTEIN FAMILY MULTIGENE FACTOR PD000046 : I38-C82 TRYPSIN DM00018lPl5157l31-270 : I38-P85 BLAST_DOMO TRYPSIN lDM00018 |P 15944131-270 : I38-P85 BLAST DOMO TRYPSIN DM00018 |Q02844|29-268 : I38-P85 BLAST_DOMO TRYPSIN DM000181P21845131-271 : G37-P85 BLAST_DOMO Serine proteases, trypsin family, histidine active site : L77-MOTIFS C82 48 7519529CD1 230 S3 S24 S57 S185 N147 Trypsin-like serine protease : R7-I224 HMMER_SMART S200 T48 T149 T160 Trypsin : K8-I224HMMERJPFAM Apple domain IPB000177 : M164-G204, S57-P95, A96-BLIMPS BLOCKS Y130, V166-S200, G202-V230 Serine proteases, trypsin family IPB001254 : D174-G197, BLIMPS_BLOCKS P211-I224 Serine proteases, trypsin family, active sites : I159-Q207 PROFILESCAN Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Chymotrypsin serine protease family (Sl) signature BLIMPS PRINTS PR00722 : T82-A96, V173-S185 PROTEASE SERINE PRECURSOR SIGNAL BLAST PRODOM HYDROLASE ZYMOGEN GLYCOPROTEIN FAMILY MULTIGENE FACTOR PD000046 : T82-I224 EPITHIN EC 3. 4. 21. SIGNAL ANCHOR BLAST PRODOM GLYCOPROTEIN HYDROLASE SERINE PROTEASE TRANSMEMBRANE REPEAT PD180180 : M1-K46 TRYPSIN DM00018 P98072 800-1033 : K46-K225BLASTDOMO TRYPSIN DM00018lQ05319l543-784 : L51-N227 BLAST DOMO TRYPSIN DM00018jP350412-264 : S57-E226 BLAST_DOMO TRYPSIN DM00018|P35037148-272 : S57-T228 BLAST_DOMO Serine proteases, trypsin family, serine active site : D174-MOTIFS S185 49 7519549CD1 426 S17 S209 S352 N382 signal cleavage : Ml-G18 SPSCAN S418 T95 T110 T124 T143 T232 T422 Y260 Signal Peptide : Ml-G18HMMER Signal Peptide : M1-G22 HMMER Hemopexin-like repeats. : P347-C390, L255-P296, L211-HMMER_SMART R253, L298-N345 Zinc-dependent metalloprotease : L100-W231 HMMER SMART Matrixin : Y31-T188 HMMER_PFAM Hemopexin : P347-C390, L298-N345, L255-P296, L211-HMMERPFAM R253 Hemopexin domain IPB000585 : M80-P90, A152-P200, BLIMPS_BLOCKS S348-R368, Q131-F144 Matrixin IPB001818 : F60-D89, R103-A151, Y359-L369 BLIMPS BLOCKS Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Hemopexin domain signature : K221-N280 PROFILESCAN Matrixins cysteine switch : A63-I113 PROFILESCAN Matrixin signature PR00138 : M80-Q93, L129-F144, D153-BLIMPSJPRINTS R181 MATRIX METALLOPROTEINASEl9 PRECURSOR EC BLAST PRODOM 3. 4. 24. MMP19 RASH HYDROLASE METALLOPROTEASE ZINC ZYMOGEN CALCIUM SIGNAL PD028998 : M1-D52 MATRIX PRECURSOR METALLOPROTEASE BLAST PRODOM HYDROLASE ZINC ZYMOGEN CALCIUM COLLAGEN DEGRADATION SIGNAL PD000673 : Y31-G174 MATRIX METALLOPROTEINASE19 PRECURSOR EC BLAST PRODOM 3. 4. 24. MMP19 RASH HYDROLASE METALLOPROTEASE ZINC ZYMOGEN CALCIUM SIGNAL PD167465 : K175-L216 MATRIX RASH METALLOPROTEINASE BLAST PRODOM METALLOPROTEINASE19 PRECURSOR MMP19 HYDROLASE METALLOPROTEASE ZINC ZYMOGEN PD154027 : G217-L255 MATRIXINS CYSTEINE SWITCH DM005581P08254129-BLAST DOMO 274 : Y31-G174 MATRIXINS CYSTEINE SWITCH DM00558pP0923830-BLASTDOMO 278 : Y31-G174 MATRIXINS CYSTEINE SWITCH DM00558jP2886230-BLASTDOMO 279 : Y31-G174 MATRIXINS CYSTEINE SWITCH DM005581P51511149-BLAST_DOMO 314 : A24-L156 50 7520124CD1 33 S16 T30 Signal cleavage : Ml-C19 |SPSCAN Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Signal Peptide : Ml-Cl9 HMMER Signal Peptide : M1-S20 HIVI1VVIER Signal Peptide : M1-S22 HMMER Signal Peptide : M1-E24 HMMER Signal Peptide : M1-P23 HMMER Lysosome-associated membrane glycoproteins signatures : PROFILESCAN A5-L33 TRIPEPTIDYLPEPTIDASE I PRECURSOR EC 3. 4. 14. 9 BLAST PRODOM TRIPEPTIDYL AMINOPEPTIDASE LYSOSOMAL PEPSTATIN INSENSITIVE PROTEASE LPIC HYDROLASE LYSOSOME GLYCOPROTEIN SIGNAL NEURONAL CEROID LIPOFUSCINOSIS PD183375 : M1- T30 51 7515245CD1 331 S47 S172 S200 N90 N231 Signal_cleavage : Ml-T22 SPSCAN S233 T157 T180 T211 Signal Peptide : Ml-A20 HNI1VIER Signal Peptide : Ml-R25 HMMER Signal Peptide : M1-D24HMMER Ubiquitin carboxyl-terminal hydrolase family : E236-R297 HMMERPFAM PROTEASE UBIQUITIN HYDROLASE UBIQUITIN-BLAST PRODOM SPECIFIC ENZYME DEUBIQUITINATING CARBOXYLTERMINAL THIOLESTERASE PROCESSING CONJUGATION PD017412 : V149-N234 PROTEASE UBIQUITIN HYDROLASE UBIQUITIN-BLAST PRODOM SPECIFIC CARBOXYLTERMINAL THIOLESTERASE PROCESSING DEUBIQUITINATING ENZYME UBIQUITOUS PD009843 : L53-G86 P85-E232 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites UBIQUITIN CARBOXYLTERMINAL HYDROLASE 12 BLAST PRODOM EC 3. 1. 2. 15 THIOLESTERASE UBIQUITIN-SPECIFIC PROCESSING PROTEASE DEUBIQUITINATING ENZYME CONJUGATION THIOL MULTIGENE FAMILY PD163770 : S278-G312 UBIQUITIN ; HYDROLASE ; TERMINAL ; CARBOXYL ; BLAST DOMO DM08763 lP51784l332-608 : K148-G250 UBIQUITIN ; HYDROLASE ; TERMINAL ; CARBOXYL ; BLAST DOMO DM08763 P35123 433-705 : V149-G250 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST_DOMO FAMILY 2 DM00659lP40818|782-1103 : V149-L293 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLASE-DOM FAMILY 2 DM00521|P51784|610-656 : G251-Q298 Ubiquitin carboxyl-terminal hydrolases family 2 signature 2 : MOTIFS Y240-Y257 52 7519933CD1 143 S14 S110 S125 T66 Clp protease IPB001907 : D74-K113 BLIMPS_BLOCKS Clp protease catalytic subunit P signature PR00127 : D74-BLIMPSPRINTS G89, P114-G134 PUTATIVE ATPDEPENDENT CLP PROTEASE BLAST PRODOM PROTEOLYTIC SUBUNIT, MITOCHONDRIAL PRECURSOR EC 3. 4. 21. 92 ENDOPEPTIDASE HYDROLASE SERINE MITOCHONDRION TRANSIT PEPTIDEPD105722 : M1-L58 PROTEASE CLP ENDOPEPTIDASE HYDROLASE BLAST PRODOM SERINE PROTEOLYTIC ATPDEPENDENT SUBUNIT PROBABLE CLPPLIKE PD001650 : 159-S 125 ENDOPEPTIDASE CLP HISTIDINE DM00759|D64088|3-BLAST_DOMO 191 : L58-S125, Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites ENDOPEPTIDASE CLP HISTIDINE DM00759lP36398l2-BLAST_DOMO 191 : I59-S125 ENDOPEPTIDASE CLP HISTIDINE DM007591P19245116-BLAST_DOMO 204 : L58-G123 ENDOPEPTIDASE CLP HISTIDINE DM00759|P54415|1-BLAST_DOMO 189 : L58-S125 Cell attachment sequence : R133-D135 MOTIFS 53 7520101CD1 194 S14 S110 T66 Clp protease : G67-T194 HMMERPFAM clpP : ATP-dependent Clp protease, proteolytic subunit : L56-HMMER_TIGRFAM T194 Clp protease IPB001907 : D74-K113, C144-G183 BLIMPS BLOCKS Endopeptidase Clp active sites : T127-I177 PROFILESCAN Endopeptidase Clp active sites : A151-T194 PROFILESCAN Clp protease catalytic subunit P signature PR00127 : D74-BLIMPSPRINTS G89, P114-D134, T145-G162, M166-R185 PROTEASE CLP ENDOPEPTIDASE HYDROLASE BLAST_PRODOM SERINE PROTEOLYTIC ATPDEPENDENT SUBUNIT PROBABLE CLPPLIKE PD001650 : I59-T194 PUTATIVE ATPDEPENDENT CLP PROTEASE BLAST_PRODOM PROTEOLYTIC SUBUNIT, MITOCHONDRIAL PRECURSOR EC 3. 4. 21. 92 ENDOPEPTIDASE HYDROLASE SERINE MITOCHONDRION TRANSIT PEPTIDEPD105722 : M1-L58 ENDOPEPTIDASE CLP HISTIDINE DM00759|D64088|3-BLAST_DOMO 191 : L58-R185 ENDOPEPTIDASE CLP HISTIDINE DM007591P19245116-BLAST_DOMO 204 : L58-G183 ENDOPEPTIDASE CLP HISTIDINE DM00759|P80244|3-BLAST_DOMO 191 : L58-R185 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites ENDOPEPTIDASE CLP HISTIDINE DM007591P5441611-BLAST_DOMO 189 : L58-R185 Endopeptidase Clp histidine active site : R167-P180 MOTIFS Endopeptidase Cl serine active site : T145-S156 MOTIFS 54 7520145CD1 160 S45 T138 T156 N71 N104 Signal cleavage : Ml-G17 SPSCAN _ Signal Peptide : M1-A16HMMER Signal Peptide : Ml-T18 HMMER Signal Peptide : Ml-E20 HMMER Signal Peptide : Ml-G23MER Trypsin-like serine protease : E20-I153 SMART Trypsin : 121-1153HMMER JPFAM Kringle domain IPB000001 : G23-V38, C49-Q66, Gl 14-BLIMPSBLOCKS R155 Serine proteases, trypsin family IPB001254 : C49-C65, BLIMPS BLOCKS M110-G133, P140-I153 Serine proteases, trypsin family, active sites : L41-T85 PROFILESCAN Serine proteases, trypsin family, active sites : D57-T138 PROFILESCAN Chymotrypsin serine protease family (Sl) signature BLIMPS PRINTS PR00722 : G50-C65, I109-V121 PROTEASE SERINE PRECURSOR SIGNAL BLAST PRODOM HYDROLASE ZYMOGEN GLYCOPROTEIN FAMILY MULTIGENE FACTOR PD000046 : I21-Q113 Q113-I153 TRYPSINDM00018lP20718l21-242 : 121-Q113, Q113-BLASTJDOMO M157 TRYPSIN DM00018Q0660520-244 : E20-Q113, Q113-BLAST_DOMO M157 TRYPSIN DM00018|P8021911-221 : I21-Q113, G114-M157, BLAST_DOMO L8-G24 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites TRYPSINDM00018P2829321-241 : I21-Q113, Q113-BLAST-DOMO M157 Serine proteases, trypsin family, histidine active site : L60-MOTIFS C65 55 7520174CD1 182 S45 S131 T160 N71 N104 Signal-cleavage : Ml-G17 SPSCAN T178 Signal Peptide : M1-A16HMMER Signal Peptide : Ml-T18 HMMER Signal Peptide : M1-E20 HMMER Signal Peptide : Ml-G23 HIVIIVIER Trypsin-like serine protease : E20-I175HMMERSMART Trypsin : 121-1175HMMERPFAM Kringle domain IPB000001 : G23-V38, C49-Q66, N104-BLIMPS JBLOCKS A118, G136-R177 Serine proteases, trypsin family IPB001254 : C49-C65, S 132-BLIMPS BLOCKS G155, P162-I175 Serine proteases, trypsin family, active sites : L41-T85 PROFILESCAN Serine proteases, trypsin family, active sites : D57-T160 PROFILESCAN Chymotrypsin serine protease family (S 1) signature BLIMPS PRINTS PR00722 : G50-C65, N104-A118, S131-V143 Alpha-lytic endopeptidase serine protease (S2A) signature BLIMPS PRINTS PR00861 : F58-V72, A123-D146, V147-P161 PROTEASE SERINE PRECURSOR SIGNAL BLAST_PRODOM HYDROLASE ZYMOGEN GLYCOPROTEIN FAMILY MULTIGENE FACTOR PD000046 : I21-A123 Q135-I175 TRYPSINDM00018|P20718|21-242 : 121-V168, Q135-BLAST_DOMO M179 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO ID Sites TRYPSINDM00018|P28293|21-241 : I21-D137, S132-BLAST_DOMO M179 TRYPSIN DM00018|P43430|21-240 : I21-K133, P130-BLAST_DOMO M179 TRYPSIN DM000181S45113l21-240 : I21-K133, P130-BLASTDOMO M179 Serine proteases, trypsin family, histidine active site : L60-MOTIFS C65 56 7520191CDT63 T13'N44 SignalcIeavage : Ml-S58 SPSCAN 57 7520243CD1 101 S29 S45 S63 S74 METHIONINE AMINOPEPTIDASE METAP PEPTIDASE BLAST PRODOM T30 M INITIATION FACTOR ASSOCIATED GLYCOPROTEIN P67 PD019174 : M1-L76 METHIONINE AMINOPEPTIDASE 2 BLAST-DOMO DM07829 IP50579158-229. K58-K100 58 7521695CD1 1070 S67 S129 S151 Ubiquitin carboxyl-terminal hydrolases famil : Q48-G79HMMERPFAM S157 S237 S284 S324 S405 S419 S455 S463 S582 S630 S634 S659 S668 S676 S691 S743 S785 S812 S928 S933 S1004 S1016 S1024 S1035 T3 T293 T488 T497 T527 T571 T749 T803 T858 T932 T1064 Y629 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Ubiquitin carboxyl-terminal hydrolase family : L595-K656 HMMERPFAM Ubiquitin carboxyl-terminal hydrolase family 2 IPB001394 : BLIMPS BLOCKS G49-L66 PROTEASE UBIQUITIN HYDROLASE ENZYME BLAST PRODOM UBIQUITIN-SPECIFIC CARBOXYLTERMINAL DEUBIQUITINATING THIOLESTERASE PROCESSING CONJUGATION PD000590 : P45-T208 PROTEASE UBIQUITIN HYDROLASE UBIQUITIN-BLAST PRODOM SPECIFIC ENZYME DEUBIQUITINATING CARBOXYLTERMINAL THIOLESTERASE PROCESSING CONJUGATION PD017412 : Q478-Q568 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLASE-DOM FAMILY 2 DM00659|P40818|782-1103 : G54-I219 C487- V566 Y599-L652 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLASE-DOM FAMILY 2 DM00659|P35123|139-432 : G54-T313 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST DOMO FAMILY 2 DM00659IP51784141-33 1 : G54-V305 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLAST DOMO FAMILY 2 DM00659|P35125|220-508 : G54-P325 Ubiquitin carboxyl-terminal hydrolases family 2 signature 1 : MOTIFS G49-Q64 Ubiquitin carboxyl-terminal hydrolases family 2 signature 2 : MOTIFS Y599-Y616 59 7520801CD1 205 S19 S32 S80 S93 N78 N104 Signal cleavage : Ml-G16 SPSCAN S135 S154 S201 T29 T159 T177 T180 T190 Y44 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites UBIQUITIN CARBOXYLTERMINAL HYDROLASE BLAST_PRODOM THIOLESTERASE UBIQUITIN-SPECIFIC PROCESSING PROTEASE DEUBIQUITINATING ENZYME CONJUGATION PD025253 : V81-A163 UBIQUITIN CARBOXYLTERMINAL HYDROLASE BLAST_PRODOM THIOLESTERASE UBIQUITIN-SPECIFIC PROCESSING PROTEASE DEUBIQUITINATING ENZYME CONJUGATION PD042929 : F18-N78 UBIQUITIN CARBOXYLTERMINAL HYDROLASE BLAST_PRODOM THIOLESTERASE UBIQUITIN-SPECIFIC PROCESSING PROTEASE DEUBIQUITINATING ENZYME CONJUGATION PD042929 : M6-E55, T71-S129, S66- D113 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLASE-DOM FAMILY 2 DM006591P52479l414-736 : F18-E183 UBIQUITIN CARBOXYL-TERMINAL HYDROLASES BLASE-DOM FAMILY 2 DM00659|Q01477|464-853 : P20-E85, V81- E165 60 7520817CD1 126 S4 Signal cleavage : M1-C32 SPSCAN Signal Peptide : P9-C32 HMMER Signal Peptide : G13-C32 HMMER Signal Peptide : M1-A33 HMMER Signal Peptide : M1-C32 HMMER Signal Peptide : P9-A33 HMMER Signal Peptide : R14-C32 HMMER Signal Peptide : Tl l-C32 HMMER 61 7520937CD1 333 S105 S277 S301 N291 Signal cleavage : Ml-A25 SPSCAN T256 T273 Signal Peptide : M8-A23 HMMER Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Signal Peptide : M1-A23MER Signal Peptide : M1-A25 HMMER Signal Peptide : M8-A25 BABIER Trypsin-like serine protease : G88-I325 HMMER_SMART Trypsin : 189-1325HMMERJPFAM Kringle domain IPB000001 : G91-L106, C117-V134, Q175-BLIMPS_BLOCKS V189, G284-I325 Apple domain IPB000177 : E150-P188, V189-N223, L268-BLIMPS_BLOCKS W302, G303-K331 Serine proteases, trypsin family IPB001254 : Cl 17-C133, BLIMPSJBLOCKS D276-V299, P312-I325 Serine proteases, trypsin family, active sites : F116-Q158 PROFILESCAN Serine proteases, trypsin family, active sites : V263-Q308 PROFILESCAN Chymotrypsin serine protease family (S1) signature BLIMPS_PRINTS PR00722 : G118-C133, Q175-V189, R275-V287 REPEAT PRECURSOR GLYCOPROTEIN TRANSPORT BLIMPSPRODOM PROTEOME COMPLETE TRANSMEMBRANE PERMEASE SUGAR TRANSPORTER ABC SYSTEM PD00120 : G118-A130, D179-L183, D276-G284 PROTEASE SERINE PRECURSOR SIGNAL BLAST_PRODOM HYDROLASE ZYMOGEN GLYCOPROTEIN FAMILY MULTIGENE FACTOR PD000046 : D157-I325, I89-P208 TRYPSIN DM00018 lP 15157131-270 : I89-V329 BLASE DOM TRYPSIN DM000181P21845131-271 : G88-V329 BLAST DOMO TRYPSIN DM00018 P15944 31-270 : I89-V329 BLAST DOMO Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites TRYPSIN DM00018 Q02844 29-268 : 189-V329 BLAST DOMO Serine proteases, trypsin family, histidine active site : L128-MOTIFS C133 Serine proteases, trypsin family, serine active site : D276-MOTIFS V287 62 7521694CD1 1427 S266 S306 S373 N142 N146 N552 Signal cleavage : M1-F33 SPSCAN S477 S501 S526 N579 N614 N667 S556 S561 S619 N707 N828 N1235 S709 S848 S875 N1354 S886 S941 S1087 S1237 S1263 S1365 S 13 84 S 1400 S 1420 T100 T135 T179 T214 T406 T441 T669 T1032 T1073 T1080 T1098 T1121 T1226 T1249 Signal Peptide : R7-G29 HMMER Signal Peptide : H5-G29 HMMER Signal Peptide : M1-F33 HMMER Signal Peptide : M1-G29 HMMER Thrombospondin type 1 repeats : W387-E439, Y745-P805, HMMERJSMART R1075-V1131, W897-P952, R954-P1013, W1016-T1073, W688-P743 Thrombospondin type 1 domain : S388-C438, W1076-HMMERJPFAM Pull9, G749-C804, W686-C742, A953-C1012 Table 3 SEQ Incyte Amino Acid Potential Potential Signature Sequences, Domains and Motifs Analytical Methods ID Polypeptide Residues Phosphorylation Glycosylation Sites and Databases NO : ID Sites Cytosolic domain : M1-P12 ; Transmembrane domain : L13-TMHMMER H32 ; Non-cytosolic domain : F33-T1427 Neutral zinc metallopeptidases, zinc-binding regio BLIMPS BLOCKS IPB000130 : T221-G231 PROTEIN F25H8. 3 F53B6. 2 KIAA0605 PROCOLLAGEN BLAST_PRODOM C37C3. 6 SERINE PROTEASE INHIBITOR ALTERNATIVE PD007018 : R954-C1067, Y745-P866 THROMBOSPONDIN TYPE 1 REPEAT BLAST_DOMO DM00275 IP354401485-548 : G369-C433 THROMBOSPONDIN TYPE 1 REPEAT BLASE-DOM DM00275 P354421479-542 : V383-C433 Cell attachment sequence : R498-D500 MOTIFS Neutral zinc metallopeptidases, zinc-binding region MOTIFS signature : T221-F230 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 63/7511804CB1 1-271, 17-481, 17-490, 17-1321, 20-249, 20-305, 20-454, 20-467, 22-471, 25-266, 25-527, 25-581, 26-483, 26-521, 27-276, 27-363, 27-527, 1321 27-789, 28-255, 28-266, 29-674, 30-275, 30-325, 30-528, 30-813, 33-441, 33-789, 37-291, 37-545, 37-713, 45-598, 48-258, 48-260, 48-545, 51-288, 51-294, 52-560, 74-212, 74-245, 82-375, 82-605, 92-775, 110-789, 134-684, 143-292, 175-379, 194-750, 222-813, 228-809, 257- 807, 269-718, 276-632, 287-567, 287-912, 292-553, 292-579, 293-767, 305-583, 317-398, 317-603, 393-656, 404-662, 465-743, 484-698, 498-639, 529-792, 535-792, 575-813, 587-806, 815-1320, 836-1318, 841-1321, 846-1321, 850-1321, 851-1316, 853-1320, 857-1319, 858- 1320, 859-1319, 870-1321, 874-1321, 875-1320, 876-1320, 878-1321, 883-1320, 883-1321, 888-1138, 890-1320, 895-1320, 896-1275, 896- 1321, 897-1321, 899-1273, 899-1321, 907-1321, 911-1320, 913-1321, 914-1321, 915-1227, 926-1320, 936-1200, 937-1290, 940-1321, 947- 1153, 947-1321, 948-1273, 949-1320, 962-1259, 968-1280, 973-1320, 974-1321, 975-1273, 976-1321, 977-1281, 977-1320, 987-1321, 993-1321, 1011-1214, 1023-1321, 1026-1321, 1028-1268, 1050-1268, 1054-1273, 1055-1320, 1111-1273, 1117-1320, 1173-1284 64/7512233CB1 1-211, 1-1881, 4-211, 5-211, 7-211, 8-211, 9-211, 10-206, 11-194, 11-211, 12-211, 13-211, 14-140, 14-211, 15-211, 16-211, 17-211, 18- 2939 211, 19-211, 20-211, 21-159, 23-211, 27-211, 28-211, 30-211, 45-174, 62-211, 66-211, 80-209, 80-211, 81-211, 83-211, 94-211, 99-211, 100-211, 107-159, 107-160, 107-173, 107-174, 107-175, 107-179, 107-180, 107-182, 107-183, 107-185, 107-188, 107-189, 107-190, 107- 198, 107-199, 107-203, 107-206, 107-207, 107-208, 107-210, 107-211, 108-211, 109-211, 110-211, 111-362, 112-211, 115-211, 116-208, 116-211, 120-211, 121-211, 122-211, 123-211, 126-211, 128-211, 129-211, 133-211, 134-211, 135-211, 136-211, 143-211, 147-211, 148- 211, 149-211, 151-210, 154-211, 155-211, 164-209, 164-211, 165-211, 167-211, 171-211, 176-211, 178-211, 179-211, 182-211, 187-211, 211-233, 211-235, 211-237, 211-238, 211-239, 211-241, 211-246, 211-247, 211-258, 211-259, 211-261, 211-262, 211-264, 211-265, 211- 268, 211-269, 211-275, 211-278, 211-281, 211-284, 211-289, 211-294, 211-297, 211-301, 211-304, 211-309, 211-314, 211-315, 211-316, 211-318, 211-319, 211-321, 211-323, 211-324, 211-328, 211-330, 211-331, 211-332, 211-336, 211-337, 211- 346, 211-347, 211-351, 211-354, 211-357, 211-362, 211-363, 211-365, 211-367, 211-370, 211-372, 211-376, 211-380, 211-381, 211-382, 211-385, 211-386, 211-391, 211-392, 211-395, 211-399, 211-400, 211-401, 211-405, 211-415, 211-416, 211-419, 211-420, 211-425, 211- 427, 211-430, 211-431, 211-432, 211-433, 211-435, 211-437, 211-440, 211-441, 211-442, 211-444, 211-447, 211-448, 211-449, 211-450, 211-453, 211-456, 211-457, 211-459, 211-460, 211-462, 211-465, 211-469, 211-474, 211-475, 211-476, 211-480, 211-482, 211-483, 211- 505, 211-507, 211-510, 211-512, 211-513, 211-522, 211-523, 211-524, 211-532, 211-533, 211-535, 211-544, 211-552, 211-553, 211-557, 211-559, 211-561, 211-562, 211-566, 211-567, 211-578, 211-590, 211-591, 211-597, 211-599, 211-600, 211-605, 211-606, 211-607, 211- 618, 211-621, 211-623, 211-642, 211-647, 211-654, 211-660, 211-666, 211-673, 211-677, 211-684, 211-685, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 211-686, 212-495, 212-726, 213-343, 213-375, 213-387, 213-456, 213-524, 215-597, 217-245, 219-375, 220-446, 221-439, 222-476, 222- 493, 223-465, 224-495, 225-456, 225-565, 225-569, 227-623, 229-517, 230-482, 233-491, 233-529, 233-623, 234-623, 235-432, 235-507, 235-510, 244-356, 255-460, 256-505, 265-447, 269-529, 269-764, 270-594, 271-455, 272-506, 274-591, 280-554, 285-617, 286-418, 286- 549, 290-553, 290-578, 297-527, 297-570, 297-596, 298-553, 298-568, 300-583, 300-592, 303-428, 315-570, 316-646, 316-683, 325-848, 334-489, 334-596, 334-622, 335-622, 336-536, 338-550, 338-588, 338-595, 339-537, 341-679, 342-601, 343-592, 343-758, 344-653, 349- 620, 350-485, 350-868, 358-513, 360-565, 360-619, 361-684, 362-546, 363-618, 365-584, 365-877, 366-549, 366-720, 367-615, 367-618, 368-566, 373-758, 374-642, 374-652, 385-552, 385-688, 387-506, 400-742, 413-588, 429-544, 446-845, 447-789, 447-842, 449-623, 450- 607, 453-608, 478-567, 484-720, 486-623, 491-1065, 507-653, 508-979, 526-1033, 542-1065, 550-1065, 588-1065, 617-970, 618-908, 618-919, 618-979, 618-1001, 630-1002, 633-860, 633-908, 633-919, 633-962, 633-1065, 638-1065, 644-1065, 648-1065, 650-1042, 651-969, 652-1065, 655-883, 655-906, 655-922, 655-995, 656-1065, 657-929, 658-983, 658-1065, 659-926, 662-1042, 663-1019, 664-947, 668-1050, 670-1055, 673-1065, 680-884, 680-1014, 684-905, 684-939, 694-950, 694-953, 694-1035, 695-1065, 702-898, 703-937, 708-1045, 709-959, 709-1065, 712-1001, 713-957, 713-1038, 716-964, 732-918, 732-936, 732-944, 732-961, 732-972, 732-976, 732-1051, 732-1053, 732-1063, 732-1359, 733-1063, 737-967, 737-1065, 745-1059, 751-1056, 753-1065, 756-1065, 758-956, 763-988, 769-935, 769- 1065, 775-994, 778-1065, 780-1056, 783-1065, 786-1045, 793-946, 793-1028, 793-1059, 798-946, 798-1065, 815-1047, 815-1063, 819- 940, 820-1051, 820-1065, 823-1029, 826-1058, 828-1007, 828-1065, 830-1053, 832-1065, 833-1016, 833-1055, 834-1018, 841-948, 843- 1065, 854-1065, 864-1060, 864-1065, 865-1065, 867-1007, 887-1065, 902-1065, 929-1065, 938-1058, 944-1065, 1058-1460, 1059-1124, 1059-1158, 1059-1178, 1059-1200, 1059-1210, 1059-1221, 1059-1222, 1059-1227, 1059-1228, 1059-1234, 1059- 1240, 1059-1241, 1059-1244, 1059-1249, 1059-1252, 1059-1253, 1059-1259, 1059-1266, 1059-1267, 1059-1269, 1059-1270, 1059-1282, 1059-1284, 1059-1302, 1059-1312, 1059-1330, 1059-1334, 1059-1335, 1059-1336, 1059-1340, 1059-1343, 1059-1364, 1059-1368, 1059- 1369, 1059-1375, 1059-1394, 1059-1395, 1059-1399, 1059-1400, 1059-1424, 1059-1436, 1059-1449, 1059-1456, 1059-1457, 1059-1460, 1059-1483, 1059-1530, 1059-1533, 1059-1537, 1059-1540, 1059-1545, 1059-1554, 1059-1555, 1059-1559, 1059-1560, 1059-1567, 1059- 1571, 1059-1572, 1059-1582, 1059-1603, 1059-1612, 1059-1636, 1059-1641, 1059-1682, 1059-1683, 1059-1686, 1059-1692, 1059-1710, 1059-1712, 1059-1769, 1059-1798, 1060-1566, 1064-1143, 1064-1195, 1064-1235, 1064-1236, 1065-1249, 1065-1320, 1065-1641, 1066- 1245, 1078-1360, 1080-1341, 1082-1324, 1082-1621, 1082-1631, 1084-1350, 1089-1243, 1089-1260, 1089-1269, 1089-1344, 1089-1353, 1089-1716, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 1090-1125, 1090-1129, 1090-1135, 1090-1143, 1090-1147, 1090-1157, 1090-1158, 1090-1159, 1090-1163, 1090-1164, 1090-1166, 1090- 1167, 1090-1169, 1090-1172, 1090-1173, 1090-1174, 1090-1176, 1090-1177, 1090-1182, 1090-1183, 1090-1187, 1090-1190, 1090-1191, 1090-1192, 1090-1198, 1090-1206, 1090-1208, 1090-1211, 1090-1222, 1090-1223, 1090-1234, 1090-1236, 1090-1239, 1090-1247, 1090- 1250, 1090-1251, 1090-1253, 1090-1259, 1090-1265, 1090-1270, 1090-1367, 1092-1270, 1093-1270, 1094-1234, 1094-1236, 1094-1270, 1095-1195, 1095-1270, 1096-1270, 1096-1680, 1099-1270, 1099-1360, 1099-1413, 1100-1270, 1100-1611, 1100-1741, 1101-1349, 1102- 1270, 1104-1270, 1105-1264, 1105-1710, 1106-1270, 1106-1368, 1107-1270, 1110-1270, 1110-1354, 1112-1272, 1113-1671, 1115-1267, 1115-1270, 1116-1270, 1118-1284, 1119-1270, 1120-1247, 1120-1351, 1124-1270, 1124-1711, 1124-1771, 1126-1270, 1127-1270, 1131- 1270, 1131-1520, 1131-1593, 1131-1669, 1132-1270, 1132-1683, 1133-1270, 1135-1270, 1138-1385, 1139-1270, 1142-1270, 1143-1411, 1145-1270, 1147-1270, 1147-1793, 1148-1270, 1155-1270, 1155-1463, 1155-1771, 1160-1270, 1162-1270, 1163-1686, 1166-1416, 1171-1270, 1171- 1428, 1175-1678, 1176-1306, 1179-1270, 1179-1749, 1180-1270, 1182-1270, 1183-1270, 1185-1270, 1186-1270, 1188-1270, 1188-1788, 1188-1881, 1189-1273, 1193-1883, 1194-1270, 1195-1270, 1195-1351, 1195-1427, 1195-1743, 1195-1759, 1200-1477, 1201-1270, 1206- 1270, 1211-1566, 1217-1270, 1220-1803, 1221-1270, 1221-1471, 1221-1617, 1221-1803, 1224-1270, 1225-1270, 1225-1461, 1227-1270, 1227-1482, 1227-1842, 1228-1270, 1229-1270, 1230-1270, 1230-1369, 1230-1463, 1230-1469, 1230-1473, 1230-1495, 1230-1568, 1230- 1802, 1231-1270, 1233-1270, 1236-1346, 1236-1430, 1236-1517, 1236-1797, 1237-1270, 1238-1270, 1238-1593, 1238-1692, 1238-1769, 1238-1795, 1239-1270, 1241-1442, 1242-1270, 1242-1505, 1242-1836, 1243-1270, 1243-1571, 1246-1270, 1248-1270, 1249-1270, 1249- 1501, 1250-1842, 1253-1420, 1253-1494, 1264-1383, 1264-1497, 1267-1301, 1267-1335, 1267-1355, 1267-1376, 1267-1385, 1267-1387, 1267-1398, 1267-1399, 1267-1404, 1267-1405, 1267-1411, 1267-1413, 1267-1417, 1267-1418, 1267-1421, 1267-1426, 1267-1429, 1267-1430, 1267- 1436, 1267-1437, 1267-1443, 1267-1444, 1267-1446, 1267-1447, 1267-1931, 1268-1372, 1268-1412, 1268-1422, 1269-1628, 1269-1835, 1270-1442, 1270-1949, 1271-1411, 1271-1413, 1271-1511, 1272-1372, 1273-1447, 1273-1525, 1273-1827, 1276-1447, 1276-1601, 1277- 1447, 1277-1514, 1277-1520, 1278-1447, 1281-1498, 1282-1441, 1282-1447, 1283-1447, 1283-1789, 1284-1474, 1287-1447, 1287-1500, 1289-1481, 1290-1447, 1292-1444, 1292-1557, 1293-1568, 1295-1447, 1296-1758, 1297-1424, 1297-1447, 1301-1447, 1301-1552, 1301- 1627, 1303-1667, 1304-1857, 1308-1447, 1308-1593, 1308-1692, 1308-1749, 1308-1848, 1308-1868, 1309-1447, 1309-1854, 1310-1554, 1310-1692, 1312-1668, 1315-1447, 1316-1689, 1319-1551, 1320-1447, 1322-1606, 1324-1447, 1324-1583, 1325-1684, 1332-1447, 1332- 1550, 1337-1590, 1337-1598, 1339-1587, 1340-1445, 1343-1447, 1348-1447, 1348-1504, 1348-1537, 1348-1890, 1352-1447, 1353-1447, 1356-1446, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 1356-1928, 1357-1623, 1357-1635, 1359-1701, 1359-1713, 1359-1938, 1360-1622, 1362-1738, 1363-1617, 1365-1447, 1365-1599, 1366- 1735, 1371-1608, 1372-1447, 1372-1618, 1372-1631, 1372-1712, 1375-1656, 1376-1637, 1377-1652, 1378-1447, 1383-1475, 1383-1821, 1386-1606, 1386-1768, 1391-1737, 1397-1447, 1398-1447, 1398-1500, 1398-1652, 1401-1661, 1402-1447, 1402-1651, 1404-1447, 1404- 1567, 1404-1655, 1405-1685, 1405-1881, 1406-1616, 1407-1447, 1407-1996, 1408-1666, 1410-1567, 1410-1673, 1410-1718, 1413-1447, 1414-1890, 1415-1447, 1415-1748, 1415-1749, 1416-1896, 1418-1447, 1419-1447, 1419-1566, 1419-1661, 1419-1668, 1420-1447, 1420- 1663, 1423-1573, 1423-1579, 1423-1676, 1423-1683, 1423-1693, 1423-1696, 1425-1833, 1426-1447, 1426-1713, 1426-1746, 1426-1758, 1427-1447, 1429-1712, 1433-1780, 1433-1826, 1433-1902, 1439-1593, 1439-1695, 1439-1705, 1441-1677, 1441-1698, 1441-1881, 1442- 1905, 1444-1698, 1444-1760, 1445-1651, 1447-1598, 1447-1601, 1447-1944, 1447-2649, 1448-1977, 1449-1760, 1451-1914, 1455-1611, 1457-1675, 1458-1715, 1458-1729, 1459-1701, 1460-1733, 1461-1715, 1461-1801, 1461-1805, 1463-1866, 1465-1753, 1466-1718, 1469-1727, 1469- 1765, 1470-1859, 1471-1743, 1471-1746, 1480-1592, 1491-1696, 1492-1741, 1501-1683, 1505-1765, 1505-2000, 1506-1830, 1507-1691, 1508-1742, 1510-1827, 1516-1790, 1521-1853, 1522-1654, 1522-1785, 1526-1789, 1526-1881, 1533-1763, 1533-1806, 1533-1832, 1534- 1789, 1534-1804, 1536-1819, 1536-1828, 1539-1664, 1551-1806, 1552-1882, 1552-1919, 1561-2084, 1568-1858, 1569-1832, 1570-1725, 1571-1858, 1572-1776, 1574-1786, 1574-1824, 1574-1831, 1575-1774, 1577-1976, 1578-1837, 1579-1828, 1579-1994, 1580-1889, 1585- 1856, 1586-1721, 1586-2104, 1594-1749, 1596-1801, 1596-1855, 1597-1920, 1598-1782, 1599-1854, 1601-1820, 1601-2113, 1602-1785, 1602-1966, 1603-1851, 1603-1854, 1604-1802, 1609-1994, 1610-1880, 1610-1888, 1621-1788, 1621-1923, 1623-1742, 1636-1978, 1649- 1824, 1665-1780, 1680-2215, 1682-2081, 1683-2025, 1683-2078, 1685-1873, 1686-1843, 1689-1848, 1714-1803, 1720-1968, 1722-1881, 1727-2301, 1743-1889, 1762-2269, 1778-2301, 1786-2301, 1824-2301, 1853-2206, 1854-2144, 1854-2155, 1854-2215, 1854-2237, 1858-2096, 1861- 2198, 1863-2301, 1864-2238, 1864-2301, 1866-2301, 1867-2144, 1867-2155, 1879-2301, 1884-2301, 1886-2278, 1887-2205, 1888-2301, 1891-2119, 1891-2142, 1891-2158, 1891-2231, 1892-2301, 1893-2165, 1894-2219, 1894-2301, 1895-2162, 1898-2278, 1899-2255, 1900- 2183, 1904-2286, 1906-2291, 1909-2301, 1916-2120, 1916-2250, 1920-2141, 1920-2175, 1921-2134, 1921-2186, 1921-2271, 1928-2189, 1931-2301, 1939-2173, 1944-2281, 1945-2195, 1945-2301, 1948-2237, 1949-2193, 1949-2274, 1952-2200, 1953-2287, 1953-2299, 1954- 2299, 1957-2154, 1957-2197, 1962-2208, 1964-2180, 1964-2212, 1964-2289, 1965-2172, 1968-2595, 1969-2299, 1970-2301, 1971-2301, 1973-2203, 1981-2295, 1987-2292, 1989-2301, 1992-2301, 1994-2192, 1999-2224, 2005-2171, 2005-2301, 2008-2230, 2014-2301, 2016- 2292, 2019-2301, 2022-2281, 2025-2182, 2027-2264, 2029-2295, 2034-2182, 2034-2301, 2051-2283, 2051-2299, 2055-2176, 2056-2287, 2056-2301, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 2059-2265, 2062-2294, 2064-2243, 2064-2301, 2066-2289, 2068-2301, 2069-2252, 2069-2291, 2070-2254, 2077-2184, 2079-2301, 2090- 2301, 2100-2296, 2100-2301, 2101-2301, 2103-2243, 2123-2301, 2138-2301, 2165-2301, 2174-2294, 2180-2301, 2294-2649, 2295-2360, 2295-2394, 2295-2414, 2295-2436, 2295-2446, 2295-2457, 2295-2458, 2295-2463, 2295-2464, 2295-2470, 2295-2476, 2295-2477, 2295- 2480, 2295-2485, 2295-2488, 2295-2489, 2295-2495, 2295-2502, 2295-2503, 2295-2505, 2295-2506, 2295-2518, 2295-2520, 2295-2538, 2295-2548, 2295-2566, 2295-2570, 2295-2571, 2295-2572, 2295-2576, 2295-2579, 2295-2600, 2295-2604, 2295-2605, 2295-2611, 2295- 2630, 2295-2631, 2295-2635, 2295-2636, 2295-2643, 2295-2648, 2295-2649, 2296-2649, 2300-2379, 2300-2431, 2300-2471, 2300-2472, 2301-2485, 2301-2556, 2301-2649, 2302-2481, 2314-2596, 2316-2577, 2318-2560, 2318-2649, 2320-2586, 2325-2479, 2325-2496, 2325- 2505, 2325-2580, 2325-2589, 2325-2649, 2326-2361, 2326-2365, 2326-2371, 2326-2379, 2326-2383, 2326-2393, 2326-2394, 2326-2395, 2326-2399, 2326-2400, 2326-2402, 2326-2403, 2326-2405, 2326-2408, 2326-2409, 2326-2410, 2326-2412, 2326-2413, 2326-2418, 2326-2419, 2326- 2423, 2326-2426, 2326-2427, 2326-2428, 2326-2434, 2326-2442, 2326-2444, 2326-2447, 2326-2458, 2326-2459, 2326-2470, 2326-2472, 2326-2475, 2326-2483, 2326-2486, 2326-2487, 2326-2489, 2326-2495, 2326-2501, 2326-2506, 2326-2603, 2328-2506, 2329-2506, 2330- 2470, 2330-2472, 2330-2506, 2331-2431, 2331-2506, 2332-2506, 2332-2649, 2335-2506, 2335-2596, 2335-2649, 2336-2506, 2336-2647, 2336-2649, 2337-2585, 2338-2506, 2340-2506, 2341-2500, 2341-2649, 2342-2506, 2342-2604, 2343-2506, 2346-2506, 2346-2590, 2348- 2508, 2349-2649, 2351-2503, 2351-2506, 2352-2506, 2354-2520, 2355-2506, 2356-2483, 2356-2587, 2360-2506, 2360-2649, 2362-2506, 2363-2506, 2367-2506, 2367-2649, 2368-2506, 2368-2649, 2369-2506, 2371-2506, 2374-2621, 2375-2506, 2378-2506, 2379-2647, 2381- 2506, 2383-2506, 2383-2649, 2384-2506, 2391-2506, 2391-2649, 2396-2506, 2398-2506, 2399-2649, 2402-2649, 2407-2506, 2407-2649, 2411-2649, 2412-2542, 2415-2506, 2415-2649, 2416-2506, 2418-2506, 2419-2506, 2421-2506, 2422-2506, 2424-2506, 2424-2649, 2425-2509, 2429- 2649, 2430-2506, 2431-2506, 2431-2587, 2431-2649, 2436-2649, 2437-2506, 2442-2506, 2447-2649, 2453-2506, 2456-2649, 2457-2506, 2457-2649, 2460-2506, 2461-2506, 2461-2649, 2463-2506, 2463-2649, 2464-2506, 2465-2506, 2466-2506, 2466-2605, 2466-2647, 2466- 2649, 2467-2506, 2469-2506, 2472-2582, 2472-2649, 2473-2506, 2474-2506, 2474-2649, 2475-2506, 2477-2649, 2478-2506, 2478-2649, 2479-2506, 2479-2649, 2482-2506, 2484-2506, 2485-2506, 2485-2649, 2486-2649, 2489-2649, 2500-2619, 2500-2649, 2503-2537, 2503- 2571, 2503-2591, 2503-2612, 2503-2621, 2503-2623, 2503-2634, 2503-2635, 2503-2640, 2503-2641, 2503-2644, 2503-2645, 2503-2647, 2503-2648, 2503-2649, 2504-2608, 2504-2648, 2504-2649, 2505-2649, 2506-2649, 2507-2649, 2507-2774, 2507-2929, 2507-2939, 2508- 2608, 2509-2649, 2512-2649, 2513-2649, 2514-2649, 2517-2649, 2518-2649, 2519-2649, 2520-2649, 2523-2649, 2525-2649, 2526-2649, 2528-2649, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 2529-2649, 2531-2649, 2532-2649, 2533-2649, 2537-2649, 2539-2649, 2540-2649, 2544-2649, 2545-2649, 2546-2649, 2548-2649, 2551- 2649, 2552-2649, 2555-2649, 2556-2649, 2558-2649, 2560-2649, 2561-2649, 2568-2649, 2573-2649, 2575-2649, 2576-2649, 2579-2649, 2584-2649, 2588-2649, 2589-2649, 2592-2649, 2593-2649, 2595-2649, 2596-2649, 2598-2649, 2599-2649, 2601-2649, 2602-2649, 2607- 2649, 2608-2649, 2611-2649, 2612-2649, 2613-2649, 2614-2649, 2619-2649, 2622-2649, 2627-2649, 2645-2778, 2646-2665, 2646-2676, 2646-2677, 2646-2678, 2646-2681, 2646-2682, 2646-2683, 2646-2689, 2646-2692, 2646-2693, 2646-2697, 2646-2700, 2646-2702, 2646- 2703, 2646-2708, 2646-2709, 2646-2711, 2646-2713, 2646-2716, 2646-2718, 2646-2721, 2646-2722, 2646-2726, 2646-2727, 2646-2728, 2646-2731, 2646-2733, 2646-2737, 2646-2738, 2646-2741, 2646-2745, 2646-2746, 2646-2747, 2646-2751, 2646-2761, 2646-2762, 2646- 2764, 2646-2765, 2646-2766, 2646-2771, 2646-2773, 2646-2776, 2646-2777, 2646-2778, 2646-2779, 2646-2781, 2646-2783, 2646-2785, 2646-2786, 2646-2788, 2646-2790, 2646-2792, 2646-2793, 2646-2794, 2646-2795, 2646-2796, 2646-2799, 2646-2801, 2646-2802, 2646-2803, 2646- 2805, 2646-2806, 2646-2808, 2646-2811, 2646-2815, 2646-2820, 2646-2821, 2646-2822, 2646-2823, 2646-2825, 2646-2826, 2646-2828, 2646-2837, 2646-2839, 2646-2843, 2646-2848, 2646-2851, 2646-2852, 2646-2853, 2646-2856, 2646-2858, 2646-2859, 2646-2863, 2646- 2868, 2646-2869, 2646-2870, 2646-2873, 2646-2875, 2646-2878, 2646-2879, 2646-2881, 2646-2886, 2646-2890, 2646-2895, 2646-2898, 2646-2899, 2646-2900, 2646-2903, 2646-2905, 2646-2907, 2646-2908, 2646-2911, 2646-2912, 2646-2913, 2646-2914, 2646-2915, 2646- 2916, 2646-2924, 2646-2931, 2646-2932, 2646-2935, 2646-2936, 2646-2937, 2646-2938, 2647-2796, 2647-2899, 2648-2787, 2648-2822, 2648-2934, 2649-2676, 2649-2845, 2650-2793, 2654-2847, 2661-2916, 2662-2938, 2671-2938, 2678-2938, 2679-2936, 2680-2835, 2681- 2938, 2682-2886, 2684-2896, 2684-2934, 2684-2938, 2685-2884, 2687-2938, 2688-2938, 2689-2938, 2690-2938, 2695-2938, 2696-2831, 2696-2938, 2704-2859, 2706-2911, 2706-2938, 2707-2938, 2708-2892, 2709-2938, 2711-2930, 2711-2938, 2712-2895, 2712-2934, 2713-2938, 2714- 2912, 2719-2938, 2720-2938, 2731-2898, 2731-2938, 2733-2852, 2746-2938, 2759-2934, 2775-2890, 2790-2938, 2792-2938, 2793-2938, 2795-2938, 2796-2938, 2799-2938, 2824-2913, 2830-2938, 2832-2938, 2837-2938, 2853-2938, 2888-2937 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 65/7512557CB1 1-799, 1-845, 1-851, 1-870, 1-880, 1-894, 1-907, 1-942, 1-2903, 8-171, 8-193, 11-229, 15-390, 19-619, 199-790, 217-577, 270-1115, 288- 2905 898, 299-804, 339-790, 350-859, 360-629, 391-890, 396-988, 461-739, 545-1115, 587-1301, 595-738, 621-1216, 632-981, 736-1009, 736- 1288, 741-1363, 790-1019, 814-1581, 853-1339, 854-1114, 864-1206, 868-1340, 872-1479, 874-1195, 898-1165, 904-1173, 948-1626, 991- 1220, 1029-1387, 1037-1250, 1047-1803, 1093-1751, 1127-1664, 1160-1409, 1190-1874, 1193-1429, 1235-1576, 1241-1506, 1272-1819, 1297-1463, 1302-1896, 1336-2133, 1370-1491, 1370-1624, 1390-1779, 1401-1574, 1404-1868, 1419-1651, 1437-1886, 1442-1854, 1456- 1756, 1474-1888, 1495-1759, 1542-1901, 1636-2130, 1650-2171, 1706-1973, 1707-1855, 1710-1886, 1796-2035, 1808-1948, 1889-2130, 1914-2091, 1940-2189, 2138-2396, 2196-2733, 2196-2790, 2196-2821, 2204-2738, 2206-2513, 2222-2868, 2234-2905, 2245-2429, 2267- 2844, 2286-2633, 2286-2642, 2306-2529, 2306-2667, 2313-2835, 2322-2582, 2327-2649, 2328-2572, 2353-2891, 2356-2475, 2371-2894, 2386-2637, 2388-2891, 2394-2838, 2395-2628, 2411-2834, 2413-2748, 2420-2678, 2432-2564, 2434-2700, 2434-2712, 2443- 2872, 2474-2692, 2481-2891, 2481-2902, 2481-2903, 2500-2903, 2502-2719, 2513-2856, 2527-2903, 2539-2903, 2543-2799, 2544-2797, 2550-2857, 2571-2903, 2579-2744, 2582-2885, 2588-2838, 2589-2831, 2596-2836, 2596-2859, 2596-2903, 2622-2870, 2654-2903, 2708- 2902, 2715-2903, 2781-2901, 2783-2903 66/7512559CB1 1-799, 1-845, 1-851, 1-870, 1-880, 1-894, 1-907, 1-942, 1-2832, 8-171, 8-193, 11-229, 15-390, 19-619, 199-790, 217-577, 270-1115, 288- 2834 898, 299-804, 339-790, 350-859, 360-629, 391-890, 396-988, 461-739, 545-1115, 587-1301, 595-738, 621-1216, 632-981, 736-1009, 736- 1288, 741-1363, 790-1019, 814-1581, 853-1339, 854-1114, 864-1206, 868-1340, 872-1479, 874-1195, 898-1165, 904-1173, 948-1626, 991- 1220, 1029-1387, 1037-1250, 1047-1803, 1093-1751, 1127-1664, 1127-1774, 1160-1409, 1190-1874, 1193-1429, 1235-1576, 1241-1506, 1272-1819, 1297-1463, 1302-1896, 1336-2133, 1370-1491, 1370-1624, 1390-1779, 1401-1574, 1404-1868, 1419-1651, 1437-1886, 1442- 1854, 1456-1756, 1474-1888, 1542-1901, 1636-2130, 1650-2171, 1706-1973, 1707-1855, 1710-1886, 1796-2035, 1808-1948, 1889-2130, 1914-2091, 1940-2189, 2025-2608, 2029-2832, 2103-2832, 2197-2356, 2197-2771, 2197-2795, 2213-2560, 2213-2569, 2233-2456, 2233- 2594, 2240-2762, 2249-2509, 2254-2576, 2255-2499, 2280-2818, 2283-2402, 2298-2821, 2313-2564, 2315-2818, 2321-2765, 2322-2555, 2338-2761, 2340-2675, 2347-2605, 2359-2491, 2361-2627, 2361-2639, 2370-2799, 2401-2619, 2408-2832, 2408-2834, 2427- 2830, 2429-2646, 2440-2783, 2454-2833, 2466-2831, 2470-2726, 2471-2724, 2477-2784, 2498-2834, 2506-2671, 2509-2812, 2515-2765, 2516-2758, 2523-2763, 2523-2786, 2523-2832, 2549-2797, 2581-2831, 2635-2829, 2642-2832, 2708-2828, 2710-2834 67/6534745CB1 1-605, 133-642, 137-856, 143-922, 145-273, 145-635, 146-646, 153-626, 153-637, 303-558, 364-646, 471-865, 471-866, 471-917, 471- 3702 1069, 534-1072, 553-1252, 619-1069, 693-1273, 718-1035, 778-1273, 890-1310, 975-1343, 1137-1613, 1362-1650, 1362-1699, 1405-2164, 1406-2536, 1733-1909, 1746-1909, 2420-2933, 2420-2935, 2420-2947, 2420-2951, 2420-3007, 2420-3091, 2420-3097, 2420-3099, 2420- 3100, 2420-3102, 2420-3103, 2420-3104, 2629-3103, 2855-3103, 2855-3235, 2855-3410, 2859-3473, 2928-3103, 3001-3618, 3001-3702, 3047-3103 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 68/7512625CB1 1-239, 1-1958, 17-395, 229-881, 939-1204, 939-1246, 939-1332, 939-1495, 939-1496, 939-1675, 939-1689, 939-1809, 980-1123, 1048- 1967 1333, 1162-1967, 1225-1837, 1225-1840, 1257-1923, 1261-1967, 1308-1574, 1381-1966, 1411-1666, 1411-1958, 1427-1964, 1470-1967, 1479-1967, 1547-1808, 1555-1959, 1557-1967, 1574-1967, 1659-1917, 1664-1958, 1664-1959 69/7512761CB1 1-118, 1-163, 2-92, 8-1258, 36-168, 76-334, 76-474, 76-561, 169-789, 175-523, 178-423, 193-676, 195-804, 198-843, 199-503, 199-976, 1283 204-431, 204-459, 204-479, 204-808, 204-809, 205-491, 207-453, 209-465, 209-478, 215-813, 225-466, 225-502, 225-671, 241-456, 251- 531, 252-498, 252-501, 252-574, 255-556, 257-446, 259-469, 260-624, 261-385, 267-634, 269-836, 269-864, 270-496, 274-557, 283-525, 285-474, 285-485, 286-523, 286-538, 290-920, 293-522, 293-548, 296-832, 302-1041, 304-489, 304-530, 304-534, 304-544, 304-596, 308- 1081, 321-426, 323-522, 323-552, 327-581, 338-956, 341-589, 342-635, 354-605, 354-1029, 355-616, 360-838, 362-606, 369-555, 371-600, 372-1081, 379-592, 380-599, 381-898, 384-987, 384-993, 391-788, 397-1043, 399-811, 401-642, 406-685, 407-733, 408-580, 409-708, 410- 677, 411-595, 412-602, 412-612, 412-882, 415-1033, 416-900, 416-918, 425-702, 436-706, 437-1045, 440-650, 447-964, 449-1081, 450- 1078, 452-553, 452-619, 461-731, 461-1014, 462-591, 478-850, 485-757, 486-742, 488-870, 489-774, 492-727, 499-593, 499-701, 499-755, 499-762, 499-781, 499-1116, 499-1130, 500-775, 502-786, 503-727, 504-736, 504-738, 504-1073, 505-1072, 506-1019, 510-810, 510-1025, 511-1066, 516-766, 524-1051, 525-722, 534-786, 536-805, 538-843, 541-805, 544-647, 548-1039, 549-822, 561-827, 564-829, 564-952, 566-780, 570-842, 571-989, 576-856, 576-888, 577-1113, 581-797, 583-1134, 584-1105, 584-1127, 585-830, 585-872, 585-1105, 585-1191, 602-857, 609-1214, 611-831, 625-957, 637-945, 639-1203, 640-748, 640-907, 643-888, 643-895, 643-914, 643-1171, 643-1184, 644-764, 648-1101, 648-1234, 653-889, 654-1203, 655-936, 655-944, 660-927, 663-1203, 669-901, 671-966, 671- 1000, 677-948, 683-934, 689-1282, 692-1005, 696-878, 701-925, 704-1005, 706-925, 711-967, 714-995, 726-989, 733-990, 740-992, 740- 993, 743-1024, 748-1045, 749-1031, 764-1204, 764-1241, 766-1153, 779-1033, 779-1071, 781-1203, 792-1130, 812-1100, 813-1203, 820- 1203, 821-997, 821-1104, 826-884, 826-1126, 830-1094, 836-1000, 836-1040, 836-1109, 836-1229, 846-1026, 849-1138, 850-1018, 856-1077, 856-1108, 857-1119, 867-1076, 867-1126, 870-1083, 874-1149, 875-1283, 877-1041, 877-1065, 877-1140, 880-1172, 883-1112, 883-1114, 887-1017, 903-1152, 904-1150, 904-1152, 908-1090, 915-1142, 917-1175, 918-1221, 919-1194, 922-1112, 930-1182, 933-1189, 951-1206, 953-1205, 967-1241, 978-1228, 978-1248, 978-1258, 1014-1172, 1044-1233, 1046-1258, 1047-1219, 1047-1255, 1051-1273, 1084-1282 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 70/7512802CB1 1-286, 1-296, 1-415, 1-451, 1-487, 1-568, 1-569, 1-609, 1-616, 1-628, 1-641, 1-642, 1-645, 1-2269, 4-624, 9-498, 9-559, 15-639, 17-546, 23- 2269 254, 24-343, 29-605, 35-275, 37-279, 49-580, 230-482, 230-589, 313-577, 395-647, 446-647, 464-975, 644-1116, 644-1159, 644-1300, 653- 1318, 654-946, 657-1347, 658-1224, 664-1348, 683-1232, 693-1367, 694-1175, 705-1412, 708-1221, 708-1335, 717-1284, 719-1001, 729- 1482, 740-1155, 740-1213, 740-1280, 743-1396, 752-894, 769-1260, 776-1047, 787-1531, 799-1083, 809-1239, 812-1047, 812-1205, 813- 1336, 813-1361, 817-1406, 820-1481, 826-1092, 835-1562, 836-1513, 844-1471, 857-1461, 866-1539, 881-1165, 882-1186, 882-1203, 884- 1175, 885-1110, 885-1150, 885-1306, 887-1082, 887-1086, 893-1178, 909-1574, 911-1461, 917-1548, 921-1098, 921-1156, 921-1188, 921- 1272, 921-1539, 921-1555, 921-1565, 921-1601, 922-1412, 923-1177, 931-1176, 932-1555, 934-1554, 935-1182, 939-1611, 942-1236, 943- 1513, 946-1533, 953-1577, 954-1203, 958-1214, 963-1377, 966-1251, 967-1169, 967-1489, 969-1485, 972-1481, 978-1577, 981-1287, 982-1219, 983-1584, 987-1680, 1004-1388, 1007-1891, 1014-1684, 1014-1911, 1024-1688, 1032-1549, 1036-1545, 1043-1598, 1053-1636, 1056-1620, 1058-1770, 1059-1665, 1068-1610, 1073-1649, 1079-1740, 1082-1389, 1084-1759, 1092- 1671, 1092-1684, 1114-1660, 1116-1679, 1133-1750, 1134-1683, 1136-1756, 1152-1769, 1154-1697, 1157-1713, 1171-1414, 1173-1775, 1175-1351, 1175-1848, 1176-1435, 1177-1690, 1179-1888, 1183-1388, 1183-1586, 1183-1614, 1183-1620, 1183-1748, 1185-1502, 1185- 1696, 1186-1580, 1189-1825, 1191-1787, 1192-1819, 1208-1783, 1214-1602, 1217-1490, 1217-1768, 1222-1698, 1227-1586, 1233-1874, 1239-1955, 1240-1526, 1246-1337, 1247-1511, 1252-1919, 1255-1424, 1255-1530, 1255-1754, 1255-1805, 1255-1814, 1255-1834, 1255- 1909, 1255-1939, 1255-1980, 1257-1837, 1260-1901, 1265-1905, 1271-1914, 1282-1552, 1284-1963, 1287-1510, 1287-1770, 1287-1801, 1288-1914, 1292-1960, 1293-1573, 1294-1578, 1295-1795, 1296-1971, 1300-1920, 1302-1900, 1304-1556, 1308-1595, 1320-1790, 1320- 1996, 1320-2054, 1322-1791, 1325-1595, 1338-1570, 1341-1895, 1345-1919, 1352-1868, 1355-2231, 1366-1579, 1366-1657, 1366-1851, 1366- 2017, 1367-1611, 1367-1614, 1372-2236, 1385-1644, 1386-2075, 1389-1602, 1392-1964, 1423-1763, 1424-2115, 1425-2067, 1428-2236, 1436-2059, 1438-1696, 1443-1680, 1447-2015, 1450-2054, 1455-2203, 1467-2122, 1474-1604, 1474-1747, 1475-1973, 1483-1744, 1489- 1720, 1493-2238, 1494-2230, 1498-2102, 1500-1881, 1503-1790, 1509-2071, 1510-1844, 1513-1782, 1513-1830, 1513-2208, 1518-1716, 1522-2187, 1530-2074, 1533-2214, 1536-2154, 1540-2069, 1551-2096, 1556-1805, 1556-1992, 1558-1898, 1564-2108, 1574-1726, 1586- 2269, 1587-1992, 1590-2163, 1591-2164, 1599-1776, 1608-2238, 1621-2144, 1647-2269, 1649-2269, 1653-1886, 1654-1932, 1656-2269, 1659-2083, 1659-2142, 1663-1923, 1666-1936, 1682-2269, 1687-1965, 1690-2215, 1693-1950, 1699-2108, 1703-1991, 1707-1961, 1713- 2269, 1720-2258, 1723-2230, 1730-2010, 1733-1988, 1737-1857, 1742-1989, 1756-2221, 1759-2025, 1769-2050, 1773-1858, 1773-2007, 1792-2059, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 1796-2269, 1801-2241, 1807-2222, 1812-2269, 1814-2022, 1814-2216, 1816-1929, 1845-2269, 1847-2269, 1857-2091, 1859-2269, 1864- 2086, 1876-2269, 1884-2269, 1902-2174, 1906-2016, 1906-2068, 1906-2269, 1909-2221, 1910-2199, 1927-2269, 1931-2166, 1932-2269, 1942-2082, 1942-2219, 1959-2212, 1960-2232, 1973-2227, 1975-2113, 1975-2202, 1975-2269, 1979-2245, 1990-2269, 1991-2234, 1998- 2081, 2007-2154, 2007-2240, 2009-2268, 2009-2269, 2012-2269, 2015-2269, 2020-2269, 2034-2269, 2040-2269, 2055-2269, 2061-2269, 2064-2268, 2064-2269, 2089-2269, 2158-2269, 2191-2269 71/7512824CB1 1-266, 1-336, 1-518, 4-2347, 23-639, 49-589, 128-389, 131-389, 159-671, 160-637, 160-670, 187-643, 192-649, 194-697, 235-897, 239- 2347 554, 239-681, 333-434, 390-594, 506-869, 677-1229, 677-1231, 689-1283, 721-1336, 747-1285, 790-1382, 801-1402, 804-1386, 806-1386, 807-1277, 815-1244, 842-1373, 842-1388, 842-1448, 843-1447, 857-1292, 868-1060, 892-1343, 911-1570, 912-1334, 925-1570, 928-1555, 942-1551, 961-1256, 965-1570, 966-1194, 966-1253, 966-1299, 966-1434, 970-1534, 981-1511, 981-1551, 981-1552, 982-1510, 989-1550, 1008-1551, 1009-1557, 1013-1324, 1023-1543, 1034-1550, 1035-1474, 1036-1475, 1036-1486, 1036-1510, 1036-1544, 1036-1570, 1040- 1229, 1041-1411, 1043-1509, 1043-1510, 1056-1705, 1073-1720, 1089-1239, 1092-1260, 1109-1664, 1113-1575, 1118-1749, 1119-1636, 1121-1624, 1121-1628, 1121-1630, 1127-1664, 1127-1740, 1131-1740, 1136-1832, 1137-1653, 1147-1431, 1147-1754, 1159-1602, 1159- 1616, 1159-1660, 1160-1617, 1162-1616, 1163-1551, 1163-1630, 1171-1758, 1174-1740, 1176-1673, 1176-1675, 1181-1644, 1190-1830, 1192-1830, 1196-1766, 1197-1861, 1213-1829, 1214-1417, 1234-1762, 1237-1765, 1248-1695, 1248-1762, 1272-1770, 1279- 1843, 1286-1955, 1287-1754, 1297-1763, 1308-1809, 1309-1720, 1311-1462, 1311-1934, 1313-1850, 1340-1842, 1361-1885, 1368-1543, 1374-1956, 1377-1929, 1390-1688, 1393-1842, 1394-1962, 1403-1886, 1418-2042, 1427-1920, 1427-1960, 1427-1975, 1435-1826, 1438- 1985, 1443-1955, 1461-1710, 1482-1843, 1508-2074, 1516-2178, 1521-2117, 1543-2081, 1554-1769, 1573-2040, 1579-1966, 1584-2177, 1598-1907, 1608-2178, 1619-2178, 1620-1963, 1630-2104, 1630-2178, 1637-2174, 1647-1798, 1649-2140, 1651-1812, 1652-2116, 1665- 2175, 1669-2118, 1689-2178, 1696-1904, 1699-2174, 1702-2120, 1733-2113, 1746-2178, 1752-2173, 1764-2178, 1766-2158, 1778-2178, 1794-2178, 1831-2062, 1831-2129, 1831-2175, 1838-2025, 1859-2178, 1886-2178, 1908-2117, 1957-2098, 2026-2175, 2058-2347 72/7512760CB1 1-636, 1-671, 1-704, 1-711, 1-728, 1-758, 1-1553, 6-791, 15-901, 26-781, 53-271, 53-378, 53-379, 53-386, 53-434, 53-458, 53-497, 54-118, 1694 54-557, 62-548, 62-568, 63-377, 71-533, 71-536, 71-550, 78-533, 89-505, 90-617, 96-540, 99-546, 179-931, 304-1018, 317-621, 349-501, 365-797, 389-501, 400-501, 401-501, 409-501, 419-501, 450-615, 450-649, 450-934, 457-985, 459-747, 459-821, 459-869, 459-881, 459- 895, 459-1056, 459-1139, 460-1217, 461-1210, 494-1147, 500-761, 503-832, 524-1082, 563-825, 563-1007, 563-1122, 580-1216, 610- 1188, 640-869, 640-1192, 682-1118, 706-992, 744-927, 744-1189, 761-1073, 767-1216, 783-1051, 787-882, 787-1050, 787-1103, 805- 1038, 816-1091, 831-1017, 839-1213, 850-1104, 850-1211, 850-1245, 850-1345, 850-1394, 850-1397, 850-1474, 850-1485, 850-1488, 850- 1497, 858-1105, 861-1073, 870-1099, 880-1504, 884-1118, 941-1216, 983-1479, 1016-1216, 1072-1333, 1110-1354, 1110-1357, 1212- 1359, 1215-1424, 1215-1463, 1215-1471, 1215-1472, 1215-1509, 1215-1690, 1215-1694, 1223-1526, 1238-1495, 1251-1394, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 1253-1660, 1267-1380, 1267-1473, 1267-1491, 1278-1542, 1281-1567, 1291-1434, 1304-1530, 1317-1563, 1319-1595, 1323-1575, 1365- 1512, 1373-1532, 1467-1577 73/7512798CB1 1-1751, 13-612, 158-404, 244-657, 252-899, 257-757, 331-860, 504-1055, 532-753, 582-851, 652-1238, 757-1033, 795-953, 843-1108, 861- 1751 1151, 881-1032, 881-1497, 891-1370, 891-1438, 891-1523, 954-1373, 972-1555, 1004-1497, 1030-1305, 1030-1328, 1078-1579, 1111- 1447, 1160-1751, 1277-1742, 1287-1747, 1437-1718 74/7512799CB11-1686, 64-400, 136-665, 158-425, 170-506, 176-665, 217-483, 323-736, 336-836, 611-832, 664-1543, 889-1308, 907-1490, 939-1432, 965- 1686 1240, 965-1263, 1013-1514, 1046-1382, 1095-1686, 1212-1677, 1222-1682, 1372-1653 75/7512840CB1 1-241, 1-272, 1-438, 1-1736, 10-253, 11-293, 20-438, 24-286, 25-147, 29-161, 32-313, 43-293, 44-280, 45-324, 47-436, 52-182, 55-298, 56- 1736 296, 57-236, 57-281, 57-343, 59-289, 60-326, 61-276, 61-300, 61-348, 62-357, 63-297, 63-306, 63-336, 63-340, 63-406, 63-439, 64-227, 64- 275, 65-318, 68-320, 68-353, 70-345, 71-346, 71-355, 72-345, 73-348, 74-287, 74-302, 74-336, 74-350, 81-442, 82-340, 88-375, 94-320, 94- 322, 95-296, 97-337, 102-314, 111-381, 122-385, 229-442, 240-394, 286-521, 291-434, 442-631, 442-670, 442-686, 442-688, 442-711, 442- 763, 442-857, 442-947, 446-723, 448-610, 448-759, 452-764, 454-711, 454-810, 455-735, 457-778, 458-1095, 460-822, 465-725, 482-1139, 482-1182, 484-711, 484-734, 485-1166, 489-756, 492-737, 493-1010, 496-770, 505-783, 507-964, 509-816, 518-953, 523-808, 537-788, 538-803, 541-1164, 543-783, 556-1247, 558-798, 560-1026, 563-915, 567-1034, 580-1272, 593-1152, 601-1186, 602-1051, 602-1162, 603- 899, 616-894, 621-894, 626-913, 634-1109, 635-873, 635-886, 635-913, 635-924, 635-1221, 637-910, 640-1323, 647-927, 649-887, 651-1332, 664-910, 664-1060, 664-1323, 665-916, 666-942, 666-943, 668-1030, 669-953, 670-752, 672-849, 673-944, 681-1326, 687-1543, 689-872, 691-951, 693-913, 693-944, 697-1265, 704-951, 705-965, 712-1298, 715-1292, 719-964, 719-969, 719-977, 719-1018, 719-1140, 720-1252, 722-1236, 723-1323, 726-990, 727-1138, 728-1331, 731-971, 732-969, 732-1026, 732- 1302, 733-1033, 735-981, 735-989, 735-1105, 736-1327, 740-970, 743-996, 743-1022, 766-1031, 767-968, 767-1344, 767-1407, 770-1247, 773-1094, 777-1198, 778-1034, 781-1593, 783-1046, 786-1476, 790-1035, 791-1084, 792-1192, 815-1109, 815-1353, 815-1396, 816-1111, 818-1074, 825-1285, 830-1591, 832-1084, 833-1070, 833-1104, 833-1289, 838-1309, 839-1086, 840-1168, 840-1251, 842-1102, 844-1121, 847-1306, 849-1577, 858-1265, 865-1080, 873-1160, 874-1482, 877-1498, 878-1170, 879-1222, 893-1031, 894-1359, 894-1426, 896-1182, 900-1247, 903-1121, 903-1297, 908-1528, 913-1189, 922-1415, 930-1164, 934-1321, 946-1384, 952-1194, 953-1265, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 964-1215, 965-1528, 983-1595, 990-1412, 991-1562, 996-1526, 998-1303, 998-1516, 998-1592, 1000-1562, 1002-1544, 1009-1215, 1009- 1604, 1014-1245, 1014-1288, 1014-1554, 1015-1384, 1017-1270, 1017-1308, 1024-1526, 1026-1360, 1027-1319, 1030-1554, 1032-1238, 1034-1546, 1040-1212, 1047-1285, 1049-1327, 1050-1582, 1050-1592, 1051-1311, 1052-1371, 1053-1576, 1059-1591, 1077-1311, 1077- 1321, 1077-1384, 1079-1311, 1084-1592, 1088-1589, 1089-1440, 1089-1589, 1094-1194, 1095-1364, 1097-1589, 1099-1592, 1100-1334, 1108-1491, 1112-1581, 1112-1682, 1115-1248, 1115-1319, 1116-1459, 1118-1588, 1121-1591, 1124-1358, 1125-1589, 1126-1581, 1126- 1589, 1126-1592, 1129-1585, 1132-1591, 1134-1600, 1140-1591, 1141-1592, 1143-1410, 1143-1412, 1143-1591, 1144-1408, 1151-1461, 1151-1589, 1151-1595, 1152-1595, 1156-1591, 1158-1591, 1160-1528, 1160-1592, 1161-1620, 1162-1422, 1162-1592, 1163-1619, 1165- 1458, 1165-1591, 1167-1592, 1168-1588, 1169-1586, 1171-1585, 1173-1585, 1173-1588, 1174-1591, 1174-1592, 1175-1396, 1175-1587, 1176-1552, 1176-1592, 1177-1589, 1178-1592, 1179-1592, 1180-1591, 1182-1600, 1183-1578, 1184-1584, 1184-1631, 1185-1594, 1186- 1585, 1188-1592, 1191-1418, 1191-1543, 1193-1384, 1193-1592, 1195-1600, 1196-1406, 1196-1585, 1196-1587, 1196-1588, 1196-1589, 1196-1592, 1197-1372, 1198-1457, 1199-1585, 1203-1585, 1206-1591, 1208-1545, 1208-1587, 1211-1602, 1212-1603, 1216-1588, 1218- 1578, 1218-1600, 1220-1500, 1221-1486, 1221-1516, 1221-1592, 1222-1589, 1229-1499, 1232-1591, 1236-1588, 1242-1566, 1242-1591, 1243-1591, 1244-1528, 1246-1501, 1246-1592, 1253-1484, 1253-1585, 1258-1600, 1259-1591, 1261-1591, 1262-1589, 1262-1592, 1268- 1588, 1269-1497, 1269-1547, 1276-1541, 1276-1585, 1276-1591, 1287-1578, 1287-1589, 1293-1591, 1294-1591, 1294-1592, 1297-1592, 1298-1589, 1298-1591, 1298-1592, 1312-1587, 1317-1591, 1321-1592, 1321-1604, 1332-1586, 1332-1600, 1335-1589, 1336-1591, 1341- 1592, 1345-1592, 1347-1585, 1348-1592, 1350-1585, 1354-1575, 1354-1589, 1355-1591, 1358-1585, 1358-1591, 1362-1548, 1364-1589, 1364-1591, 1375-1636, 1380-1591, 1390-1592, 1401-1554, 1401-1592, 1404-1585, 1406-1592, 1411-1592, 1417-1589, 1418-1592, 1419-1600, 1445- 1567, 1454-1646, 1454-1704, 1460-1620, 1468-1588, 1480-1645, 1484-1592, 1489-1600 76/7512889CB1 1-256, 1-549, 1-670, 2-280, 2-4129, 102-674, 116-427, 241-803, 408-1033, 531-843, 531-845, 714-1505, 749-1197, 1009-1766, 1347-2033, 4129 1367-2042, 1952-2238, 2075-2339, 2197-2384, 2231-2527, 2281-2903, 2309-2850, 2379-2579, 2385-2884, 2465-2917, 2470-3007, 2525- 2697, 2591-3059, 2604-3135, 2639-3093, 2689-3069, 2788-3069, 2810-3077, 2835-3078, 2835-3155, 2855-3126, 3071-3299, 3071-3581, 3106-3399, 3106-3513, 3106-3582, 3108-3381, 3108-3422, 3109-3371, 3174-3641, 3223-3540, 3230-3589, 3247-3566, 3258-3501, 3293- 3565, 3325-3409, 3507-3675, 3550-3675, 3649-3922, 3660-4124, 3672-3816, 3672-3880, 3672-4061, 3672-4067, 3672-4129, 3673-4129, 3674-3963, 3674-4129, 3675-3909, 3683-4129, 3692-4129, 3693-4129, 3695-4085, 3696-4129, 3697-4129, 3704-3929, 3704-4126, 3707- 3932, 3707-4060, 3707-4128, 3710-4129, 3714-4129, 3726-4128, 3734-3993, 3734-3999, 3735-4129, 3748-4129, 3752-4127, 3765-4128, 3771-4129, 3772-4129, 3776-4047, 3784-4129, 3811-4074, 3865-4093, 3884-4128, 3896-4067, 3919-4128, 3926-4047, 3967-4129 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 77/7512901CB1 1-236, 1-1378, 36-276, 37-245, 37-271, 37-288, 37-307, 37-310, 37-349, 38-236, 38-314, 38-346, 40-267, 40-290, 40-299, 40-305, 40-310, 1378 40-317, 41-288, 41-290, 41-296, 41-311, 41-333, 42-283, 42-288, 42-291, 43-180, 43-246, 43-282, 43-302, 43-316, 43-329, 43-349, 44-270, 44-317, 44-322, 45-311, 48-181, 49-312, 50-291, 50-349, 52-331, 53-346, 55-303, 55-313, 55-314, 62-232, 62-341, 63-260, 63-314, 67-319, 67-336, 68-189, 68-304, 69-321, 72-349, 73-349, 84-346, 94-336, 119-341, 134-270, 185-433, 349-527, 349-564, 349-568, 349-579, 349- 585, 349-772, 352-608, 354-567, 355-576, 360-608, 379-857, 383-666, 384-628, 384-977, 385-583, 388-732, 395-538, 395-630, 395-764, 395-912, 408-689, 408-790, 409-776, 411-689, 411-1010, 417-689, 417-690, 431-691, 431-693, 432-790, 441-690, 444-706, 462-633, 462- 715, 465-931, 466-776, 478-814, 480-1113, 483-815, 491-768, 495-1045, 507-789, 518-760, 521-792, 525-1099, 527-1109, 540-630, 541- 822, 541-1075, 548-770, 549-1052, 550-1084, 559-821, 559-832, 560-968, 571-839, 571-865, 571-869, 580-972, 582-1062, 584-1087, 588-835, 589-843, 594-1099, 598-835, 608-1084, 609-840, 614-1076, 622-1079, 626-761, 626- 1079, 629-878, 632-869, 632-1085, 637-1105, 638-1038, 640-1073, 642-1099, 645-1042, 645-1099, 646-933, 648-1079, 651-1073, 651- 1100, 651-1106, 651-1121, 652-1113, 654-1100, 655-913, 656-1260, 658-1005, 660-1112, 662-1070, 664-1084, 664-1100, 666-1082, 667- 963, 667-1080, 668-1084, 668-1099, 670-1072, 670-1079, 671-1079, 671-1083, 671-1087, 671-1100, 672-1085, 673-1081, 675-1087, 676- 1099, 677-1071, 680-1100, 681-1112, 687-1100, 691-1378, 701-1105, 703-918, 705-1079, 712-1086, 714-912, 714-1014, 715-900, 715- 965, 724-1076, 725-1114, 727-1081, 729-1022, 729-1070, 729-1083, 729-1113, 731-1101, 731-1113, 736-1106, 739-1087, 751-1004, 752- 1114, 754-1086, 761-1105, 761-1113, 768-1079, 769-1072, 774-1355, 777-1021, 789-1079, 789-1083, 796-1069, 796-1073, 799-1045, 801- 1306, 803-1069, 812-1082, 814-1104, 814-1378, 815-1086, 817-1114, 819-1100, 819-1104, 838-1343, 838-1378, 843-1037, 845-1087, 845-1092, 846-1094, 849-994, 855-1114, 857-1084, 859-1114, 873-1378, 879-990, 879-1100, 889-1087, 889-1154, 894-1343, 895-1114, 902-1217, 904-1360, 906-1359, 909-1378, 914-1362, 924-1113, 927-1099, 928-1365, 935-1343, 937-1363, 943-1087, 947-1340, 960-1188, 960-1340, 968-1087, 969-1112, 972-1360, 975-1071, 975-1100, 982-1362, 984-1341, 993-1235, 997-1340, 999-1219, 999-1318, 1005- 1338, 1006-1378, 1010-1378, 1011-1087, 1026-1365, 1065-1330, 1081-1363, 1084-1378, 1107-1360, 1120-1378, 1134-1335, 1194-1343, 1194-1360, 1219-1378, 1280-1370 78/7512949CB11-285, 49-237, 49-406, 69-177, 97-216 406 79/7512660CB11-238, 5-238, 15-223, 15-224, 15-232, 15-250, 15-433, 16-245, 18-230, 19-158, 19-210, 19-217, 19-220, 19-224, 19-230, 19-231, 19-232, 441 19-235, 19-250, 19-251, 20-218, 20-233, 21-127, 21-134, 21-171, 21-199, 21-215, 21-219, 22-148, 22-187, 22-210, 22-214, 22-217, 22-218, 22-229, 22-231, 22-251, 23-147, 23-151, 23-207, 23-222, 23-243, 24-217, 24-230, 25-153, 25-210, 25-223, 25-229, 25-230, 25-234, 27-150, 27-233, 28-158, 28-221, 28-234, 28-240, 29-203, 29-218, 31-202, 31-205, 32-147, 32-235, 32-252, 34-232, 37-213, 38-211, 38-232, 39-177, 40-139, 53-299, 55-212, 56-203, 76-245, 295-441 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 80/7512741CB1 1-240, 1-294, 1-357, 1-392, 1-425, 1-430, 1-467, 1-484, 1-522, 1-545, 1-560, 1-565, 1-567, 1-571, 1-575, 1-577, 1-586, 1-588, 1-594, 1-600, 4339 1-623, 1-627, 1-633, 1-634, 1-635, 1-638, 1-642, 1-644, 1-649, 1-654, 1-657, 1-667, 1-671, 1-673, 1-675, 1-677, 1-730, 1-753, 1-4339, 27- 292, 27-571, 28-275, 28-654, 31-705, 39-788, 71-596, 73-596, 119-788, 163-689, 227-847, 239-778, 239-1110, 256-826, 262-828, 262-844, 285-497, 285-498, 288-497, 295-488, 401-1219, 458-852, 538-1226, 551-1226, 616-1166, 641-1239, 641-1240, 641-1332, 715-1063, 735- 1422, 745-1422, 750-1289, 902-1422, 1301-1675, 1301-2164, 1353-1883, 1417-2125, 1485-1974, 1504-2196, 1521-2346, 1592-2188, 1620- 2251, 1626-2256, 1639-2296, 1641-2384, 1677-2257, 1681-2367, 1718-2279, 1721-1992, 1734-2337, 1744-2359, 1760-2309, 1766-2376, 1774-1993, 1775-2314, 1781-2312, 1782-2425, 1788-2288, 1789-2358, 1799-2330, 1809-2467, 1810-2393, 1810-2575, 1810-2602, 1810- 2672, 1811-2682, 1812-2129, 1813-2476, 1823-2355, 1851-2424, 1857-2227, 1859-2521, 1892-2115, 1892-2141, 1892-2442, 1897-2507, 1900-2371, 1926-2422, 1941-2510, 1958-2563, 1965-2673, 1974-2604, 1978-2501, 2001-2616, 2021- 2450, 2038-2727, 2055-2720, 2071-2625, 2074-2695, 2084-2742, 2093-2289, 2095-2861, 2101-2663, 2122-2351, 2165-2596, 2173-2763, 2174-2756, 2188-2383, 2188-2700, 2190-2723, 2190-2742, 2196-2816, 2199-2688, 2201-2416, 2201-2877, 2214-2870, 2237-2666, 2245- 2810, 2246-2880, 2260-2727, 2274-2472, 2274-2570, 2277-2799, 2286-2763, 2288-2889, 2290-2754, 2315-2977, 2322-2516, 2322-2868, 2334-2835, 2334-2990, 2336-3069, 2345-2918, 2345-3029, 2359-2688, 2377-3130, 2377-3131, 2386-3032, 2388-2915, 2398-3076, 2399- 2614, 2399-2766, 2399-2945, 2399-2963, 2404-2641, 2404-2876, 2404-2889, 2406-3135, 2419-2606, 2419-2987, 2424-3091, 2427-2983, 2438-3124, 2444-3016, 2461-3128, 2462-3114, 2472-2994, 2473-2988, 2475-3067, 2477-2942, 2502-3132, 2503-2708, 2537-3151, 2543- 3127, 2544-3110, 2550-3206, 2551-2856, 2555-2751, 2555-3028, 2555-3122, 2556-3243, 2559-3104, 2566-3197, 2592-3471, 2593-2844, 2599-3163, 2599-3283, 2601-2946, 2603-3167, 2609-3009, 2640-3143, 2644-3293, 2645-3340, 2647-3163, 2648-3214, 2651-3095, 2657-3176, 2657- 3321, 2658-2926, 2660-2921, 2666-3215, 2678-3194, 2679-3000, 2681-3550, 2689-3165, 2691-3297, 2692-3212, 2698-3258, 2701-3157, 2701-3241, 2705-3208, 2705-3300, 2707-3381, 2708-3309, 2709-3218, 2711-3306, 2719-3192, 2720-3345, 2729-3034, 2732-3298, 2737- 3444, 2740-3347, 2745-3043, 2754-3297, 2755-3378, 2760-2934, 2768-3356, 2768-3427, 2773-3508, 2794-3091, 2803-3381, 2806-3376, 2810-3396, 2817-3482, 2818-2996, 2818-3166, 2822-3296, 2822-3680, 2831-3395, 2834-3095, 2834-3430, 2840-3418, 2856-3435, 2857- 3179, 2866-3467, 2867-3072, 2871-3550, 2879-3482, 2883-3468, 2885-3297, 2885-3482, 2891-3567, 2902-3567, 2906-3545, 2926-3436, 2929-3472, 2936-3390, 2938-3386, 2940-3326, 2940-3416, 2942-3509, 2943-3537, 2964-3918, 2979-3190, 2979-3244, 2998-3678, 3002- 3157, 3005-3261, 3007-3142, 3016-3549, 3022-3538, 3042-3439, 3045-3674, 3049-3652, 3061-3683, 3068-3725, 3077-3334, 3077-3441, 3078-3358, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 3079-3345, 3080-3759, 3084-3345, 3091-3919, 3093-3332, 3114-3712, 3138-3641, 3155-3742, 3160-3790, 3198-3799, 3226-3492, 3226- 3787, 3231-3714, 3259-3589, 3268-4117, 3272-3651, 3289-3880, 3295-3704, 3305-3506, 3305-3524, 3306-3566, 3306-3713, 3331-3624, 3336-3594, 3338-4126, 3377-3919, 3390-3944, 3390-4000, 3395-3995, 3404-3679, 3414-3979, 3419-3649, 3420-3975, 3440-3944, 3456- 3695, 3456-4126, 3464-3783, 3467-4077, 3479-3717, 3481-3688, 3481-3783, 3499-3756, 3505-4010, 3516-3793, 3527-3806, 3534-3788, 3554-3783, 3554-3834, 3592-3783, 3595-3783, 3597-3783, 3597-3849, 3598-4143, 3637-3932, 3640-3783, 3640-3863, 3640-3866, 3641- 3868, 3645-4151, 3647-3888, 3650-3864, 3661-3960, 3661-4339, 3677-4148, 3705-3970, 3707-4141, 3716-3989, 3727-3974, 3796-3847, 3815-3847, 3815-4144, 3823-4143, 3865-4146, 3928-4121, 3928-4125, 3929-4137, 3929-4149, 3929-4151, 3936-4151, 3940-4149, 3941- 4149, 3977-4150, 4010-4132, 4047-4120, 4058-4129, 4058-4132 81/7513099CB1 1-763, 40-2448, 98-1034, 297-860, 330-1083, 410-564, 410-983, 432-541, 461-1132, 472-1348, 515-1423, 537-1299, 599-1276, 604-1247, 2450 605-1366, 606-824, 606-1116, 606-1145, 606-1219, 635-1359, 660-1408, 692-1272, 698-1300, 698-1341, 759-1294, 768-1169, 803-1123, 818-1086, 922-1193, 1018-1246, 1047-1270, 1117-1344, 1340-1801, 1438-1763, 1440-2008, 1461-1573, 1591-1740, 1643-1937, 1667- 2447, 1681-1927, 1693-2140, 1717-1965, 1754-2391, 1781-2420, 1793-2447, 1823-2384, 1832-2028, 1832-2031, 1832-2273, 1847-2139, 1867-2125, 1867-2442, 1868-2448, 1868-2450, 1874-2181, 1889-2401, 1912-2364, 1959-2390, 1973-2448, 1984-2449, 1989-2417, 1990- 2449, 1995-2268, 2018-2449, 2021-2449, 2030-2279, 2032-2449, 2059-2449, 2060-2449, 2067-2449, 2070-2449, 2097-2449, 2109-2391, 2112-2449, 2114-2355, 2115-2449, 2117-2449, 2121-2391, 2134-2449, 2159-2449, 2169-2449, 2183-2441, 2183-2443, 2206-2446, 2207- 2449, 2225-2449, 2239-2449, 2296-2449, 2310-2449, 2315-2449, 2317-2449 82/7511908CB1 1-275, 1-573, 1-761, 1-768, 1-797, 1-838, 25-447, 70-855, 82-326, 441-854 855 83/7513074CB1 1-131, 1-263, 1-2588, 2-314, 3-270, 4-265, 11-277, 12-326, 24-186, 34-132, 34-255, 34-281, 34-290, 34-326, 34-435, 38-287, 41-217, 41- 2588 267, 41-284, 41-286, 41-298, 41-318, 41-326, 51-298, 84-326, 324-592, 324-781, 324-848, 365-1119, 365-1131, 365-1143, 449-1098, 467- 1045, 470-853, 506-1033, 510-977, 520-1257, 539-1133, 547-1129, 548-1142, 558-1078, 579-852, 613-1099, 615-781, 616-895, 632-1316, 670-885, 679-1434, 690-955, 690-993, 692-1458, 693-958, 721-1456, 769-1028, 769-1209, 817-1086, 824-1089, 833-1089, 838-1315, 857- 1128, 857-1196, 857-1363, 857-1365, 857-1446, 857-1461, 858-1298, 879-1178, 879-1324, 885-1764, 887-1422, 893-1168, 909-1012, 911- 1735, 914-1533, 941-1416, 947-1570, 959-1384, 967-1200, 974-1648, 983-1674, 988-1627, 995-1286, 1006-1229, 1011-1356, 1011-1472, 1020-1391, 1036-1288, 1040-1674, 1069-1219, 1076-1718, 1115-1779, 1116-1339, 1117-1519, 1124-1782, 1153-1671, 1157-1368, 1172- 1683, 1193-1958, 1195-1417, 1201-1363, 1208-1482, 1228-1479, 1228-1684, 1233-1506, 1240-1511, 1253-1572, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 1256-1509, 1256-1518, 1256-1542, 1256-1543, 1256-1544, 1256-1549, 1256-1551, 1256-1553, 1256-1554, 1256-1556, 1256-1562, 1256- 1563, 1256-1565, 1256-1569, 1256-1572, 1256-1580, 1256-1583, 1256-1592, 1256-1874, 1257-1580, 1273-1979, 1307-1958, 1320-1875, 1320-1877, 1320-1893, 1321-1597, 1323-1896, 1334-1880, 1338-1994, 1357-1610, 1372-1991, 1375-1654, 1378-1946, 1380-1897, 1384- 2042, 1412-2075, 1415-1698, 1415-1973, 1415-1995, 1415-2036, 1433-2005, 1435-1995, 1436-1977, 1442-1715, 1447-2081, 1447-2107, 1447-2123, 1483-1828, 1490-1846, 1490-1928, 1493-1992, 1493-2134, 1502-1802, 1504-1760, 1516-2052, 1517-1995, 1527-1986, 1558- 1873, 1561-1770, 1562-1852, 1566-1766, 1575-1848, 1575-1854, 1583-2318, 1587-2261, 1594-2258, 1617-2236, 1618-1818, 1622-2172, 1627-1761, 1636-1889, 1646-1834, 1647-2223, 1651-1914, 1652-1972, 1656-1940, 1664-2143, 1666-1932, 1672-1958, 1677-2323, 1682- 2217, 1683-2265, 1700-2258, 1714-2257, 1721-2387, 1740-2011, 1742-1941, 1782-2089, 1804-2088, 1805-2080, 1805-2083, 1806-2025, 1830-2362, 1834-2041, 1855-2020, 1859-2077, 1859-2111, 1869-2101, 1878-2361, 1887-2527, 1892-2511, 1897-2302, 1904-2254, 1906-2511, 1907- 2211, 1909-2541, 1916-2352, 1920-2452, 1924-2160, 1926-2560, 1930-2523, 1943-2523, 1951-2062, 1958-2163, 1961-2558, 1963-2185, 1963-2269, 1970-2191, 1971-2245, 1972-2578, 1976-2479, 1982-2242, 1982-2514, 2005-2183, 2005-2196, 2005-2219, 2005-2257, 2013- 2515, 2015-2575, 2020-2559, 2034-2580, 2034-2588, 2035-2506, 2038-2579, 2038-2584, 2040-2588, 2042-2297, 2051-2264, 2051-2588, 2060-2511, 2061-2262, 2069-2349, 2073-2413, 2083-2343, 2088-2585, 2090-2360, 2110-2520, 2111-2583, 2114-2588, 2117-2583, 2133- 2588, 2141-2583, 2145-2585, 2145-2588, 2146-2586, 2147-2585, 2147-2588, 2149-2582, 2150-2383, 2150-2581, 2154-2588, 2161-2588, 2165-2587, 2168-2588, 2169-2376, 2169-2413, 2173-2413, 2174-2413, 2174-2537, 2175-2577, 2176-2413, 2178-2586, 2180-2413, 2181- 2581, 2185-2534, 2190-2517, 2195-2588, 2196-2413, 2204-2575, 2207-2413, 2211-2585, 2220-2476, 2236-2583, 2239-2413, 2240-2413, 2240-2479, 2246-2413, 2266-2541, 2267-2585, 2285-2413, 2287-2585, 2291-2584, 2293-2585, 2299-2517, 2302-2588, 2307-2583, 2308-2579, 2309- 2569, 2316-2584, 2319-2585, 2322-2581, 2327-2413, 2341-2578, 2370-2585, 2382-2585, 2414-2585, 2428-2583, 2430-2578, 2434-2584, 2478-2585, 2521-2588 84/7513960CB1 1-1147, 1-1155, 19-684, 201-1030, 305-1030, 308-1029, 347-1030, 369-1029 1155 85/7513984CB1 1-553, 1-588, 1-648, 1-668, 1-673, 1-721, 1-786, 1-827, 1-865, 2-2127, 808-1635, 808-1638, 837-1638, 979-1638, 1016-1638, 1027-1638, 2127 1041-1638 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 86/7512992CB1 1-2318, 155-325, 260-354, 261-576, 261-792, 296-347, 382-573, 445-947, 537-1180, 667-851, 1058-1314, 1091-1736, 1128-1386, 1141- 2326 1660, 1150-1407, 1150-1414, 1150-1570, 1150-1627, 1150-1636, 1150-1656, 1150-1660, 1150-1667, 1150-1669, 1162-1830, 1198-1794, 1210-1546, 1249-1499, 1249-1500, 1249-1571, 1249-1633, 1249-1708, 1249-1764, 1273-1777, 1277-1880, 1282-1884, 1307-1573, 1307- 1577, 1308-1775, 1311-1570, 1321-1885, 1327-1839, 1329-1896, 1335-1871, 1339-1880, 1345-1625, 1345-1901, 1368-1899, 1369-1916, 1386-1610, 1390-1845, 1412-1670, 1417-2268, 1421-1643, 1428-1640, 1429-2122, 1431-1689, 1431-1823, 1431-1862, 1432-1901, 1458- 1734, 1464-1980, 1466-2089, 1476-2020, 1479-2195, 1481-2034, 1486-2125, 1487-1751, 1507-1679, 1521-2189, 1525-1965, 1526-1615, 1555-2232, 1571-2231, 1578-2107, 1589-2272, 1593-1647, 1607-1882, 1609-2118, 1612-1920, 1612-2094, 1615-1863, 1629-1909, 1629- 1916, 1629-1933, 1630-1774, 1638-2005, 1640-2234, 1647-1874, 1659-2292, 1685-2284, 1689-1889, 1692-1968, 1696-2293, 1697-2293, 1698-2239, 1700-2248, 1704-2251, 1706-2179, 1718-2213, 1742-2234, 1744-1965, 1745-2288, 1751-2290, 1755-1958, 1769-2253, 1771- 2186, 1776-2039, 1797-2200, 1803-2230, 1805-2247, 1806-2197, 1809-2082, 1826-2281, 1829-2290, 1829-2292, 1833-2290, 1837-2293, 1843-2326, 1847-2292, 1862-2231, 1864-2290, 1867-2293, 1876-2261, 1879-2315, 1880-2290, 1884-2223, 1886-2326, 1889-2293, 1890- 2290, 1903-2290, 1903-2326, 1911-2294, 1933-2286, 1943-2292, 1946-2313, 1953-2221, 1954-2251, 1983-2211, 1990-2320, 1992-2098, 1994-2313, 1999-2274, 2009-2289, 2016-2277, 2023-2292, 2038-2209, 2062-2293, 2080-2326, 2115-2293, 2203-2293, 2252-2318 87/7512994CB11-2363, 155-325, 260-354, 261-576, 261-792, 296-347, 382-573, 445-947, 667-851, 881-1257, 967-1211, 967-1405, 967-1472, 967-1489, 2373 967-1556, 987-1233, 998-1261, 1031-1222, 1040-1294, 1051-1227, 1060-1433, 1060-1441, 1064-1438, 1107-1607, 1187-1443, 1257-1515, 1279-1536, 1279-1543, 1378-1607, 1411-1685, 1623-2152, 1632-2277, 1634-2317, 1638-1692, 1652-1830, 1657-1965, 1657-2139, 1660- 1908, 1674-1954, 1674-1961, 1674-1978, 1675-1819, 1683-1944, 1685-2279, 1692-1919, 1704-2337, 1730-2329, 1734-1934, 1737-2013, 1741-2338, 1742-2338, 1743-2284, 1745-2293, 1749-2296, 1751-2224, 1753-2163, 1753-2276, 1787-2279, 1789-2010, 1796-2335, 1800- 2003, 1814-2298, 1816-2231, 1821-2084, 1842-2245, 1848-2275, 1850-2292, 1851-2242, 1854-2127, 1871-2326, 1874-2335, 1874-2337, 1878-2335, 1882-2338, 1888-2373, 1892-2337, 1907-2276, 1909-2335, 1912-2338, 1921-2306, 1924-2360, 1925-2335, 1929-2268, 1931- 2373, 1934-2338, 1935-2335, 1948-2335, 1948-2373, 1956-2339, 1963-2258, 1978-2331, 1988-2337, 1991-2358, 1998-2266, 1999-2296, 2028-2256, 2035-2365, 2037-2143, 2039-2358, 2044-2319, 2054-2334, 2061-2322, 2068-2337, 2083-2254, 2107-2338, 2125-2371, 2160- 2336, 2248-2338, 2297-2363 88/7513547CB 1 1-846, 414-1121, 634-1522, 818-1733, 1152-2156, 1575-2350 2350 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 89/7513357CB1 1-170, 1-204, 1-1343, 2-147, 20-145, 25-200, 26-204, 27-524, 43-199, 61-171, 65-204, 66-180, 66-198, 66-204, 67-166, 67-200, 67-204, 68- 1464 158, 68-188, 72-204, 73-160, 73-201, 74-202, 74-204, 75-156, 75-168, 75-204, 81-204, 84-204, 200-225, 200-229, 200-236, 200-333, 200- 416, 200-418, 200-419, 200-459, 200-462, 200-474, 200-486, 200-499, 200-563, 200-565, 200-681, 200-757, 200-781, 201-238, 201-673, 201-868, 202-759, 203-447, 203-454, 206-497, 207-478, 211-330, 213-492, 214-667, 218-748, 220-371, 221-575, 224-744, 226-538, 226- 830, 230-791, 232-491, 235-355, 236-497, 236-507, 237-420, 239-352, 240-528, 241-322, 243-479, 248-781, 249-530, 255-503, 255-548, 255-706, 256-501, 256-508, 256-511, 256-550, 259-537, 260-517, 261-784, 261-866, 263-401, 263-848, 267-869, 268-732, 269-518, 270- 532, 272-544, 274-800, 278-540, 293-535, 296-439, 296-501, 301-624, 301-784, 306-738, 307-628, 310-466, 311-579, 312-875, 314-543, 315-630, 337-809, 339-526, 339-573, 340-582, 340-627, 343-594, 344-732, 345-1007, 348-1026, 350-627, 351-1049, 352-607, 359-585, 360-633, 361-542, 362-895, 363-629, 363-636, 363-640, 363-941, 363-1034, 364-621, 364-919, 369-956, 370- 711, 372-640, 372-664, 374-630, 375-612, 378-480, 378-619, 378-637, 378-818, 378-886, 379-948, 379-1124, 381-593, 382-758, 383-913, 385-640, 385-647, 386-577, 386-734, 388-987, 394-683, 395-604, 396-635, 398-1057, 400-677, 402-577, 402-606, 402-870, 403-870, 405- 755, 407-901, 407-935, 408-677, 409-958, 411-802, 411-846, 412-1024, 413-966, 415-927, 415-930, 417-772, 417-832, 419-663, 419-681, 419-927, 420-646, 425-722, 426-633, 427-836, 427-854, 427-930, 429-747, 430-741, 430-930, 431-909, 432-606, 432-734, 434-713, 439- 690, 443-1079, 445-672, 446-925, 447-607, 449-709, 450-993, 452-681, 453-745, 453-767, 453-1007, 455-701, 455-705, 456-1093, 457- 765, 458-960, 459-794, 461-786, 464-688, 464-732, 467-867, 469-756, 471-745, 471-849, 471-1007, 475-952, 476-1145, 479-742, 479- 1085, 480-743, 481-713, 486-624, 486-744, 486-752, 486-772, 486-773, 486-790, 490-1036, 491-730, 491-780, 494-639, 495-705, 499-614, 499-743, 500-967, 500-1010, 501-732, 502-765, 502-1124, 504-773, 505-754, 505-799, 507-732, 507-798, 507- 810, 507-988, 509-925, 509-1054, 511-1037, 513-626, 513-778, 515-735, 515-1157, 517-990, 519-778, 521-715, 521-777, 522-1014, 524- 771, 525-952, 525-976, 527-952, 528-661, 528-1123, 528-1132, 531-1014, 534-1096, 535-677, 535-731, 538-763, 539-747, 539-835, 539- 1118, 540-738, 540-1042, 543-727, 543-790, 543-829, 544-830, 545-1077, 545-1125, 547-825, 548-756, 550-1174, 552-793, 552-796, 553- 795, 554-805, 554-842, 554-910, 554-1167, 556-739, 556-824, 558-855, 558-1134, 560-1207, 560-1257, 561-1126, 561-1127, 562-1221, 564-836, 564-855, 564-1151, 565-773, 565-818, 566-852, 567-751, 567-812, 567-862, 568-681, 569-812, 569-871, 572-817, 572-864, 575- 668, 575-714, 575-841, 575-846, 575-857, 576-844, 579-834, 579-1094, 582-830, 582-831, 582-841, 582-856, 582-869, 585-805, 585-825, 585-856, 586-807, 591-883, 591-903, 593-725, 597-835, 598-1197, 599-815, 599-1051, 602-840, 602-846, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 603-1174, 606-835, 606-837, 607-847, 611-1014, 611-1079, 611-1098, 613-868, 617-881, 617-905, 617-1256, 619-1004, 620-789, 620-797, 621-1036, 622-941, 625-925, 632-733, 634-1076, 635-817, 635-922, 636-908, 637-730, 637-894, 637-914, 637-920, 637-947, 638-730, 638- 884, 638-1063, 642-1194, 643-956, 644-887, 644-1066, 645-869, 645-1287, 646-1405, 648-935, 648-953, 649-922, 649-941, 649-1140, 650- 1027, 651-862, 651-1336, 653-890, 656-902, 656-910, 664-939, 665-1207, 670-1052, 671-942, 677-833, 678-925, 679-833, 679-945, 679- 950, 683-912, 683-1179, 683-1362, 684-921, 684-952, 686-915, 687-967, 687-970, 689-920, 689-1311, 691-1172, 693-914, 693-940, 693- 1142, 694-986, 694-993, 697-1032, 698-1220, 698-1300, 700-1302, 704-1122, 710-916, 710-986, 710-995, 711-938, 711-966, 712-962, 712- 998, 713-1067, 714-910, 714-1182, 719-988, 720-1087, 722-1185, 723-1013, 724-1347, 724-1381, 728-1253, 730-974, 730-1007, 732- 1172, 733-1400, 734-1052, 735-898, 735-1228, 735-1384, 736-874, 736-884, 736-986, 736-988, 736-989, 736-992, 736-1002, 736-1022, 736-1168, 736-1229, 737-955, 738-971, 738-1330, 740-990, 746-1153, 746-1275, 746-1312, 748-1241, 749-951, 749- 1018, 750-1022, 751-988, 751-1015, 751-1024, 752-1026, 755-1208, 757-995, 757-1037, 760-1012, 760-1028, 761-889, 764-1000, 765- 901, 765-962, 765-1208, 767-980, 768-1013, 768-1054, 768-1320, 768-1333, 768-1362, 769-1240, 769-1373, 770-1395, 776-1032, 776- 1199, 777-892, 777-1037, 777-1101, 779-1003, 779-1073, 779-1230, 779-1391, 781-984, 782-1015, 782-1234, 783-1044, 785-1022, 786- 1010, 786-1059, 786-1111, 788-1239, 790-1046, 790-1047, 793-1053, 793-1235, 794-1172, 795-1048, 795-1104, 795-1251, 795-1252, 795- 1350, 797-1001, 797-1464, 800-1346, 806-1024, 806-1351, 808-1065, 808-1312, 812-1083, 812-1102, 812-1112, 812-1165, 812-1219, 819- 1343, 822-1117, 824-911, 825-1113, 827-1206, 829-1015, 829-1050, 832-1252, 834-1104, 834-1105, 834-1106, 834-1123, 834-1138, 834- 1142, 834-1163, 837-1278, 839-1161, 839-1162, 841-1049, 842-1092, 842-1098, 842-1154, 842-1357, 845-1070, 847-1120, 847-1344, 848-1129, 849-964, 850-1064, 850-1111, 850-1113, 850-1189, 852-1099, 852-1128, 853-1008, 855-1246, 855-1295, 856-1127, 858-1154, 858-1201, 862-1048, 862-1105, 863-1305, 868-1283, 872-1077, 874-1120, 874-1165, 880-1154, 886-1167, 887-1092, 888-1154, 893-1184, 895-1047, 903-1346, 905-987, 905-1214, 908-1373, 909-1206, 912-1184, 918-1197, 919-1166, 920-1168, 920-1174, 921-1278, 924-1139, 924-1464, 929-1177, 929-1376, 930-1260, 933-1109, 940-1191, 940-1194, 948-1154, 950-1190, 951-1154, 951-1197, 951-1199, 951-1214, 951-1346, 954-1208, 955-1192, 955-1198, 955-1236, 955-1244, 957-1124, 959-1242, 961-1210, 962-1229, 962-1233, 973-1188, 980-1253, 987-1259, 988-1240, 988-1275, 988-1429, 990-1288, 993-1191, 993-1194, 993-1212, 993-1236, 993-1255, 993-1352, 994-1225, 994-1262, 995-1225, 995-1275, 997-1275, 1001-1148, 1003-1444, 1006-1238, 1006-1273, 1007-1254, 1007-1267, 1008-1288, 1013-1284, 1020-1329, 1022-1360, 1028-1309, 1033-1261, 1039-1327, 1043-1223, 1043-1291, 1047-1302, 1047-1316, 1048-1325, 1053-1254, 1053-1274, 1053-1276, 1059-1276, 1061-1288, 1064-1363, 1078-1338, 1087-1355, 1091-1317, 1095-1364, 1096-1226, 1097- 1289, 1100-1331, 1101-1343, 1101-1398, 1102-1292, 1102-1323, 1102-1344, 1103-1292, 1106-13Q8, 1112-1300, 1118-1326, 1124-1411, 1144-1321, 1152-1413, 1212-1307, 1233-1433 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 90/7513329CB1 1-2658, 198-649, 198-674, 204-458, 204-517, 204-525, 204-646, 204-647, 206-786, 207-706, 241-629, 287-498, 329-598, 378-944, 396- 2690 917, 417-685, 418-967, 454-948, 490-582, 491-826, 951-1491, 982-1512, 993-1456, 996-1456, 1003-1279, 1003-1387, 1003-1409, 1003- 1469, 1003-1545, 1003-1594, 1003-1625, 1003-1634, 1003-1650, 1011-1550, 1030-1658, 1051-1617, 1054-1605, 1056-1678, 1061-1673, 1079-1677, 1091-1546, 1142-1993, 1171-1403, 1171-1640, 1171-1751, 1192-1715, 1193-1456, 1211-1471, 1211-1490, 1211-1755, 1226- 1723, 1226-1785, 1227-1948, 1251-1993, 1259-1947, 1270-1537, 1278-1808, 1286-1937, 1289-1947, 1295-1540, 1296-1883, 1297-1883, 1306-1733, 1307-1952, 1308-1779, 1314-1419, 1320-1916, 1322-1830, 1324-1993, 1334-1918, 1339-1617, 1348-1912, 1367-1986, 1370- 1994, 1375-1937, 1391-2061, 1392-1683, 1395-1705, 1395-2022, 1402-1967, 1407-1994, 1411-1875, 1414-1993, 1414-2024, 1415-1699, 1445-1657, 1455-1979, 1477-1727, 1485-1774, 1498-1993, 1502-1948, 1503-2033, 1505-1951, 1526-1998, 1529-1980, 1529-2016, 1529- 2140, 1545-2134, 1547-2147, 1548-1952, 1561-1845, 1568-1952, 1571-1993, 1574-1827, 1575-1848, 1575-1850, 1584-1952, 1587-2200, 1599- 2232, 1601-2199, 1603-1879, 1608-1771, 1608-1798, 1608-2249, 1621-2302, 1626-1954, 1632-1840, 1633-1948, 1657-2302, 1658-2307, 1659-2264, 1663-2331, 1665-2003, 1670-1907, 1671-2344, 1677-1947, 1677-2258, 1682-1925, 1689-2186, 1693-2333, 1697-1992, 1698- 1921, 1698-1945, 1739-1983, 1749-2016, 1773-2371, 1792-2384, 1793-1942, 1803-2081, 1821-2020, 1825-2412, 1825-2413, 1829-2441, 1837-2307, 1852-2096, 1858-2113, 1865-1970, 1901-2519, 1902-2491, 1903-2126, 1915-2234, 1932-2586, 1970-2582, 1974-2624, 1993- 2464, 2006-2227, 2014-2574, 2016-2544, 2020-2231, 2035-2316, 2038-2485, 2042-2192, 2042-2251, 2042-2522, 2057-2635, 2064-2273, 2064-2337, 2065-2341, 2085-2658, 2094-2332, 2100-2551, 2104-2342, 2105-2589, 2106-2308, 2109-2519, 2161-2405, 2162-2646, 2182- 2650, 2186-2646, 2188-2463, 2190-2653, 2195-2646, 2196-2648, 2212-2649, 2218-2581, 2221-2647, 2221-2659, 2225-2650, 2245-2647, 2246-2644, 2250-2645, 2252-2644, 2253-2640, 2257-2642, 2259-2646, 2271-2644, 2274-2647, 2281-2649, 2284-2647, 2298-2666, 2303-2647, 2311- 2641, 2311-2647, 2333-2580, 2333-2638, 2383-2640, 2393-2647, 2435-2545, 2450-2603, 2450-2690, 2456-2602, 2456-2606, 2456-2631, 2456-2637, 2459-2644, 2465-2600, 2465-2659 91/7517777CB11-648, 1-711, 1-821, 2-1700, 298-1071, 370-1070, 677-1429, 679-1658, 988-1702 1702 92/7519126CB 1 1-609 609 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 93/7519175CB1 93/7519175CB1 1-409, 80-652, 607-980, 728-980, 928-1356, 1142-1356, 1161-1356, 1170-3348, 1204-1532, 1705-2166, 1709-2158, 1714-2176, 1715- 5710 2158, 1795-2003, 1854-2158, 1916-2333, 1916-2524, 2078-2443, 2079-2443, 2079-2541, 2079-2587, 2079-2630, 2079-2649, 2079-2651, 2079-2667, 2079-2735, 2079-2760, 2079-2879, 2083-2658, 2114-2655, 2389-3058, 2500-3064, 2516-3223, 2531-3231, 2538-3197, 2560- 3064, 2564-3196, 2571-3114, 2579-3233, 2592-3064, 2593-3064, 2603-3064, 2605-3064, 2619-3064, 2620-3064, 2645-3124, 2645-3144, 2647-3064, 2664-3064, 2677-3175, 2691-3064, 2695-3423, 2701-3265, 2716-3484, 2721-3484, 2739-3368, 2748-3064, 2754-3064, 2759- 3239, 2761-3064, 2764-3282, 2767-3461, 2768-3064, 2769-3373, 2771-3446, 2780-3345, 2791-3064, 2807-3064, 2813-3410, 2857-3556, 2875-3459, 2883-3451, 2920-3409, 2960-3546, 2963-3417, 2999-3498, 3020-3424, 3058-3711, 3058-3723, 3114-3788, 3175-3726, 3203- 3376, 3233-3817, 3285-3431, 3285-3809, 3301-3817, 3312-3817, 3335-3817, 3339-3817, 3345-3817, 3400-3746, 3446-3808, 3458-4039, 3593-3817, 3639-3816, 3641-3817, 3681-3817, 3689-3817, 3738-4089, 3960-4085, 3998-4233, 4004-4664, 4005-4281, 4005-4526, 4005-4553, 4009- 4619, 4134-4353, 4227-4879, 4244-4457, 4251-5092, 4279-5093, 4451-4516, 4453-4522, 4670-5247, 4680-5407, 4698-5299, 4729-5565, 4755-5467, 4763-5348, 4785-5710, 4812-5497, 4946-5391 94/7514648CB1 1-1103, 69-823 1103 95/7517904CB1 1-528, 2-2994, 5-229, 796-1601, 846-1440, 866-1143, 930-1163, 955-1532, 977-1268, 992-1271, 1044-1302, 1044-1324, 1053-1459, 1091- 3398 1323, 1128-1389, 1128-1410, 1128-1416, 1139-1764, 1151-1279, 1167-1407, 1172-1733, 1182-1455, 1184-1726, 1190-1467, 1191-1603, 1232-1491, 1238-1359, 1248-1565, 1268-1529, 1268-1624, 1269-1522, 1291-1563, 1318-1577, 1351-1836, 1399-1609, 1399-1621, 1422- 1733, 1428-1764, 1440-1709, 1451-1677, 1586-1824, 1607-1907, 1608-1892, 1615-1850, 1615-1858, 1633-1878, 1684-2114, 1702-2237, 1706-1971, 1717-2001, 1786-2053, 1787-2340, 1789-2213, 1790-2333, 1792-1992, 1799-2370, 1822-2100, 1827-2209, 1828-2160, 1841- 2104, 1846-2112, 1863-1996, 1880-2137, 1880-2334, 1899-2194, 1902-2524, 1927-2209, 1937-2112, 1938-2284, 1943-2244, 1945-2567, 1952-2203, 1965-2478, 1969-2213, 1984-2270, 1995-2328, 1999-2273, 2002-2261, 2017-2307, 2025-2268, 2049-2258, 2089-2679, 2091- 2898, 2106-2412, 2138-2373, 2149-2600, 2159-2305, 2160-2356, 2160-2628, 2163-2788, 2178-2444, 2178-2445, 2178-2451, 2178-2548, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 2178-2570, 2178-2744, 2182-2735, 2184-2603, 2215-2453, 2218-2978, 2240-2701, 2267-2507, 2279-2528, 2297-2406, 2310-2598, 2314- 2931, 2317-2604, 2317-2606, 2321-2569, 2324-2577, 2362-2977, 2363-2748, 2365-2602, 2379-2607, 2380-2970, 2380-2979, 2381-2654, 2393-2620, 2394-2679, 2400-2925, 2403-2925, 2404-2710, 2423-2599, 2423-2692, 2423-2982, 2424-2687, 2433-2710, 2434-2955, 2436- 2727, 2440-2765, 2455-3013, 2458-3013, 2462-2920, 2467-2715, 2489-2994, 2506-2760, 2509-2982, 2527-2685, 2532-2918, 2538-2785, 2542-2982, 2548-2841, 2549-3013, 2553-2982, 2558-2820, 2558-2991, 2562-2972, 2562-2985, 2564-2982, 2565-2982, 2568-2974, 2568- 2983, 2569-2974, 2571-2982, 2577-2982, 2581-2985, 2582-2966, 2588-2858, 2589-3013, 2591-2863, 2592-2974, 2598-2971, 2607-2974, 2617-2974, 2625-2982, 2627-2840, 2627-2919, 2629-2982, 2629-2985, 2634-2982, 2655-2974, 2660-2983, 2672-2982, 2674-2972, 2684- 2982, 2689-2945, 2693-2982, 2696-2967, 2707-2973, 2719-2994, 2740-2973, 2757-2996, 2757-3009, 2765-2982, 2775-3013, 2795-2972, 2813-3308, 2816-2998, 2834-3398, 2871-3016, 2886-2982, 2909-2974 96/7518798CB1 1-345, 1-522, 1-773, 1-779, 2-831, 105-832, 186-832 832 97/7519109CB1 1-904, 122-1119, 316-1144 1144 98/7519227CB1 1-786, 1-793, 167-793, 198-793 793 99/7519262CB1 1-905, 379-1355 1355 100/7519371CB1 1-765, 430-1296, 441-1297, 515-1296 1297 101/7519442CB11-156, 2-655, 3-894, 149-894, 255-894, 323-894, 338-888 894 102/7519123CB11-735, 175-912 912 103/7519522CB 1 1-924, 470-1240, 546-1239 1240 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte Sequence Length 104/7520023CB 1 1-742, 2-1156, 263-1157 1157 105/7519518CB11-198, 2-664, 3-138, 3-532, 19-990 990 106/7519955CB1 1-614, 1-680, 1-696, 1-733, 1-767, 1-776, 1-792, 1-794, 1-816, 1-818, 1-819, 1-848, 6-798, 404-1283 1283 107/7514925CB1 1-415, 1-1464, 9-211, 212-415, 288-909, 288-980, 289-1114, 289-1165, 301-960, 319-1174, 321-1110, 351-415, 381-1128, 386-1174, 415- 1478 580, 419-942, 430-1111, 430-1134, 430-1144, 430-1145, 434-1145, 434-1147, 435-1146, 439-565, 440-630, 449-1122, 449-1123, 449- 1125, 492-979, 495-1140, 504-979, 504-1174, 510-1145, 512-979, 513-926, 524-643, 524-644, 524-815, 524-888, 524-973, 524-989, 524- 999, 524-1025, 524-1031, 524-1052, 524-1091, 524-1095, 524-1108, 526-1081, 539-1128, 555-1108, 578-1117, 590-1174, 592-1174, 621- 1116, 656-1126, 657-1174, 661-1174, 689-1292, 714-1174, 733-1312, 752-1174, 764-1174, 776-1170, 788-1174, 796-979, 802-1079, 808- 1174, 860-1437, 882-1122, 899-1159, 937-1174, 1001-1174, 1002-1174, 1022-1174, 1022-1478, 1029-1174, 1068-1174, 1075-1174, 1077- 1174, 1093-1174, 1137-1174, 1143-1174 108/7518514CB1 1-345, 1-561, 1-584, 2-1130 1130 109/7519481CB11-557, 1-727, 234-727 727 110/7519529CB11-711, 1-727, 2-726, 142-727, 184-727, 197-727 727 111/7519549CB1 1-203, 1-237, 1-359, 1-859, 2-784, 3-138, 3-727, 616-1337 1337 112/7520124CB1 1-550, 2-549 550 113/7515245CB1 1-784, 2-1008, 2-1014, 413-1008 1014 114/7519933CB1 1-373, 1-675, 1-680, 2-679, 4-680, 372-466 680 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 115/7520101CB1 1-553, 1-560, 1-686, 1-760, 2-761, 28-762, 184-762, 560-594, 560-624, 560-645 762 116/7520145CB1 1-565, 2-564, 61-565 565 117/7520174CB11-631, 2-630 631 118/7520191CB11-746, 1-810, 1-811, 2-811, 4-810, 181-811, 218-811 811 119/7520243CB11-747, 1-848, 2-700, 334-1300 1300 120/7521695CB1 1-348, 56-560, 342-560, 353-3555, 354-947, 390-560, 427-661, 580-1006, 581-1006, 594-1006, 731-1503, 797-871, 797-1542, 797-1771, 4141 818-1186, 887-1635, 932-1346, 946-1792, 974-1836, 984-1750, 1162-1537, 1351-2093, 1351-2151, 1351-2160, 1351-2165, 1351-2186, 1353-2182, 1360-1758, 1393-1849, 1393-1971, 1393-1984, 1400-2019, 1579-2110, 1663-2375, 1684-2379, 1687-2375, 1695-2375, 1710- 2375, 1714-2290, 1715-1942, 1716-2012, 1716-2196, 1718-2136, 1723-2375, 1767-2375, 1770-2309, 1773-2375, 1789-2447, 1801-2125, 1805-2471, 1823-2188, 1824-1942, 1878-2415, 1887-2292, 1898-2630, 1908-2478, 1928-2589, 1958-2375, 1962-2699, 1974-2526, 1998- 2610, 2019-2543, 2060-2780, 2063-2340, 2063-2427, 2063-2484, 2063-2533, 2063-2541, 2063-2599, 2063-2608, 2063-2640, 2063-2687, 2063-2695, 2063-2698, 2063-2713, 2063-2716, 2063-2746, 2065-2246, 2065-2634, 2065-2698, 2066-2208, 2066-2249, 2066-2252, 2066- 2253, 2069-2252, 2107-2865, 2136-2802, 2146-2723, 2161-2706, 2220-2911, 2221-2597, 2229-2476, 2236-2909, 2237-2388, 2262-2946, 2293-2792, 2296-2924, 2301-3030, 2316-2871, 2338-2894, 2339-2894, 2352-2868, 2358-3026, 2365-2917, 2373-3001, 2392-2501, 2392- 2557, 2403-2932, 2404-2942, 2405-2946, 2405-2976, 2425-2995, 2427-2939, 2428-2974, 2445-2581, 2445-2938, 2446-3005, 2458-3007, 2461-3066, 2465-3001, 2482-3150, 2483-3075, 2506-3164, 2513-3211, 2531-2925, 2532-3072, 2542-3238, 2557-3136, 2558-3086, 2569- 3236, 2573-3211, 2574-3163, 2575-3085, 2583-3007, 2584-3112, 2588-3204, 2593-3451, 2603-2900, 2603-3006, 2603-3147, 2603-3192, 2604-2908, 2608-3096, 2608-3161, 2617-2856, 2621-3119, 2628-3451, 2636-3247, 2636-3451, 2652-3292, 2654-3271, 2661-3076, 2661- 3300, 2662-3451, 2663-3373, 2665-3094, 2666-3168, 2668-3329, 2670-3248, 2677-3300, 2677-3361, 2686-3410, 2698-3224, 2699-2938, 2703-3399, 2709-3215, 2714-3342, 2715-3107, 2715-3241, 2729-3393, 2736-3445, 2737-3395, 2738-3458, 2740-3365, 2748-3341, 2752- 3375, 2753-3100, 2754-3252, 2755-3445, 2757-3327, 2761-3394, 2761-3509, 2773-3257, 2776-3364, 2784-3458, 2786-3416, 2792-3394, 2793-3225, Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 2794-3327, 2801-3340, 2804-3045, 2810-3327, 2811-2982, 2811-3420, 2813-3179, 2815-3089, 2815-3102, 2818-3353, 2823-3366, 2825- 3459, 2832-3352, 2832-3431, 2832-3527, 2835-3345, 2844-3542, 2846-3089, 2854-3491, 2855-3547, 2857-3453, 2858-3400, 2864-3543, 2866-3519, 2866-3558, 2868-3514, 2869-3045, 2876-3576, 2885-3544, 2887-3522, 2889-3555, 2893-3559, 2900-3546, 2900-3565, 2904- 3499, 2906-3543, 2907-3426, 2911-3555, 2912-3464, 2914-3556, 2919-3481, 2922-3525, 2923-3443, 2923-3490, 2932-3546, 2933-3473, 2935-3450, 2939-3459, 2942-3460, 2943-3252, 2945-3630, 2949-3609, 2952-3555, 2958-3567, 2959-3493, 2960-3553, 2961-3451, 2964- 3390, 2964-3634, 2969-3534, 2969-3611, 2971-3553, 2971-3586, 2975-3525, 2975-3531, 2975-3544, 2976-3624, 2983-3679, 2987-3372, 2990-3539, 2991-3557, 2991-3678, 2993-3623, 2993-3638, 3000-3543, 3002-3376, 3002-3691, 3002-3700, 3008-3535, 3014-3558, 3016- 3630, 3024-3559, 3025-3563, 3028-3450, 3030-3554, 3033-3541, 3036-3709, 3038-3583, 3040-3671, 3044-3709, 3046-3502, 3049-3697, 3053-3678, 3064-3715, 3069-3710, 3072-3339, 3072-3539, 3074-3552, 3079-3788, 3083-3781, 3089-3618, 3089-3741, 3089-3759, 3093-3751, 3097- 3558, 3097-3670, 3100-3619, 3109-3642, 3118-3743, 3121-3488, 3134-3814, 3135-3549, 3135-3650, 3137-3739, 3150-3784, 3158-3405, 3168-3796, 3175-3732, 3175-3837, 3181-3642, 3183-3823, 3186-3727, 3186-3760, 3198-3849, 3202-3910, 3206-3796, 3219-3754, 3289- 3809, 3323-3549, 3323-3863, 3329-3909, 3354-3453, 3383-3832, 3386-3992, 3390-4006, 3424-4074, 3454-3999, 3465-3929, 3475-3701, 3482-3911, 3504-3838, 3539-3903, 3543-4069, 3555-4069, 3562-4036, 3723-4037, 3814-4136, 3894-4141 121/7520801CB11-668, 2-799, 53-800 800 122/7520817CB11-801, 6-819, 31-300, 43-295, 43-313, 43-656, 44-678, 563-1243, 675-1243 1243 123/7520937CB1 1-823, 2-677, 280-1020 1020 Table 4 Polynucleotide Sequence Fragments SEQ ID NO :/ Incyte ID/Sequence Length 124/7521694CB1 1-860, 41-902, 211-4591, 230-262, 230-799, 230-1017, 330-837, 331-896, 331-1048, 573-lu36, 585-1042, 593-1049, 606-1049, 639-1049, 4714 639-1435, 639-1457, 716-1650, 735-1523, 735-1625, 736-1433, 745-1638, 750-1642, 751-1450, 758-1656, 765-1648, 766-1405, 766-1628, 772-1581, 797-1648, 799-1631, 799-1665, 813-1763, 845-1547, 845-1686, 867-1815, 1140-1959, 1141-1568, 1141-1839, 1141-2068, 1143- 1969, 1146-1933, 1146-1985, 1148-2028, 1210-1968, 1210-2071, 1270-1968, 1277-2164, 1400-2055, 1496-2171, 1496-2289, 2162-3153, 2163-3072, 2176-3125, 2205-3072, 2228-3098, 2270-3127, 2273-2312, 2284-2312, 2329-3103, 2329-3129, 2356-3100, 2365-3171, 2402- 3251, 2467-3215, 2643-3257, 2648-3613, 2679-3596, 2704-3386, 2704-3422, 2704-3470, 2704-3503, 2726-3625, 2790-3619, 2833-3619, 2860-2968, 2877-3791, 2897-3422, 2903-3802, 2941-3595, 2951-3398, 2951-3411, 2951-3419, 2951-3441, 2951-3445, 2951-3544, 2951- 3583, 2951-3633, 2951-3668, 2951-3691, 2951-3716, 2951-3738, 2951-3739, 2951-3741, 2951-3751, 2951-3764, 2951-3801, 2951-3847, 2951-3872, 2951-3906, 2953-3813, 2955-3603, 2955-3685, 2957-3736, 2962-3537, 2971-3701, 2986-3813, 2988-3875, 2989-3691, 2996- 3813, 2997-3812, 3012-3556, 3012-3572, 3017-3791, 3033-3791, 3041-3817, 3044-3791, 3054-3870, 3054-3891, 3058-3891, 3063-3894, 3064-3884, 3084-3765, 3117-3791, 3120-3844, 3122-3678, 3129-3876, 3139-3802, 3144-3875, 3153-4122, 3162-4119, 3168-3905, 3171- 4122, 3178-3762, 3267-4228, 3287-3854, 3316-3942, 3319-3858, 3324-3972, 3329-4126, 3368-4195, 3385-4230, 3453-4230, 3463-4118, 3481-4118, 3483-4039, 3502-4342, 3502-4377, 3514-4031, 3514-4107, 3517-4353, 3523-4107, 3530-4239, 3531-4036, 3574-4083, 3602- 4078, 3603-3636, 3625-4118, 3631-4118, 3645-4117, 3645-4118, 3690-4545, 3722-4545, 3732-4276, 3735-4545, 3766-4545, 3796-4409, 3800-4425, 3800-4642, 3802-4668, 3884-4713, 3890-4545, 3891-4714, 3902-4714, 3906-4545, 3915-4668, 3922-4714, 3971-4714, 3972- 4714, 4022-4714, 4038-4714, 4052-4694, 4058-4545, 4302-4362, 4302-4374, 4302-4417, 4302-4421 Table 5 Polynucleotide SEQ Incyte Project ID : Representative Library ID NO : 63 7511804CB 1 DUODNOT02 64 7512233CB1 LIVRTUT13 65 7512557CB 1 LIVRTUT 13 66 7512559CB1 LIVRTUT13 67 6534745CB1 PITUNON01 68 7512625CB1 LIVRTUT13 69 7512761CB1 ENDIUNT01 70 7512802CB1 SINTFET03 71 7512824CB1 PKINDNV13 72 7512760CB1 SININOT04 73 7512798CB1 BRACNOK02 74 7512799CB 1 THYMNOE02 75 7512840CB1 SMCCNON03 76 7512889CB 1 BRSTNOT09 77 7512901CB1 THYMNOT02 78 7512949CB 1 BRAITUT26 79 7512660CB 1 DUODNOT01 80 7512741CB 1 PROSTUS23 E 81 7513099CB1 CONUTUT01 82 7511908CB1 BRSTTUT18 83 7513074CB 1 PROSTUS23 86 7512992CB 1 BRSTNOT14 87 7512994CB 1 BRSTNOT14 89 7513357CB 1 ARTANOT06 90 7513329CB 1 CERVNOT01 93 7519175CB1 UTRSNOT05 95 7517904CB 1 THYMNOT02 107 7514925CB1 PITUDIR01 120 7521695CB1 SINTNOR01 247521694CB1 FTUBTUR01 Table 6 Library Vector Library Description ARTANOT06 pINCY Library was constructed using RNA isolated from aortic adventitia tissue removed from a 48-year-old Caucasian male. BRACNOK02 PSPORT1 This amplified and normalized library was constructed using RNA isolated from posterior cingulate tissue removed from an 85 year-old Caucasian female who died from myocardial infarction and retroperitoneal hemorrhage. Pathology indicated atherosclerosis, moderate to severe, involving the circle of Willis, middle cerebral, basilar and vertebral arteries; infarction, remote, left dentate nucleus; and amyloid plaque deposition consistent with age. There was mild to moderate leptomeningeal fibrosis, especially over the convexity of the frontal lobe. There was mild generalized atrophy involving all lobes. The white matter was mildly thinned. Cortical thickness in the temporal lobes, both maximal and minimal, was slightly reduced. The substantia nigra pars compacta appeared mildly depigmented. Patient history included COPD, hypertension, and recurrent deep venous thrombosis. 6.4 million independent clones from this amplified library were normalized in one round using conditions adapted from Soares et al. , PNAS (1994) 91: 9228-9232 and Bonaldo et al. , Genome Research 6 (1996): 791. BRAITUT26 pINCY Library was constructed using RNA isolated from brain tumor tissue removed from the right posterior fossa, occipital convexity of a 70-year-old Caucasian male during cerebral meninges lesion excision. Pathology indicated meningioma. Patient history included a benign colon neoplasm and unspecified personality disorder. Family history included chronic proliferative nephritis, acute myocardial infarction, atherosclerotic coronary artery disease, and chronic proliferative nephritis. BRSTNOT09 pINCY Library was constructed using RNA isolated from breast tissue removed from a 45-year-old Caucasian female during unilateral extended simple mastectomy. Pathology for the associated tumor tissue indicated invasive nuclear grade 2-3 adenocarcinoma, with 3 of 23 lymph nodes positive for metastatic disease. Immunostains for estrogen/progesterone receptors were positive, and uninvolved tissue showed proliferative changes. The patient concurrently underwent a total abdominal hysterectomy. Patient history included valvuloplasty of mitral valve without replacement, rheumatic mitral insufficiency, and rheumatic heart disease. Family history included acute myocardial infarction, atherosclerotic coronary artery disease, and type II diabetes.

Table 6 Library Vector Library Description BRSTNOT14 pINCY Library was constructed using RNA isolated from breast tissue removed from a 62-year-old Caucasian female during a unilateral extended simple mastectomy. Pathology for the associated tumor tissue indicated an invasive grade 3 (of 4), nuclear grade 3 (of 3) adenocarcinoma, ductal type. Ductal carcinoma in situ, comedo type, comprised 60% of the tumor mass. Metastatic adenocarcinoma was identified in one (of 14) axillary lymph nodes with no perinodal extension. The tumor cells were strongly positive for estrogen receptors and weakly positive for progesterone receptors. Patient history included a benign colon neoplasm, hyperlipidemia, cardiac dysrhythmia, and obesity. Family history included atherosclerotic coronary artery disease, myocardial infarction, colon cancer, ovarian cancer, lung cancer, and cerebrovascular disease. BRSTTUT18 pINCY Library was constructed using RNA isolated from right breast tumor tissue removed from a 68-year-old female during right modified radical mastectomy. Pathology indicated infiltrating, high grade, ductal carcinoma of the breast. The breast parenchyma revealed a firm tumor mass surrounded by an abundant amount of thick fibrous breast tissue. CERVNOT01 PSPORT1 Library was constructed using RNA isolated from the uterine cervical tissue of a 35-year-old Caucasian female during a vaginal hysterectomy with dilation and curettage. Pathology indicated mild chronic cervicitis. Family history included atherosclerotic coronary artery disease and type II diabetes. CONUTUT01 pINCY Library was constructed using RNA isolated from sigmoid mesentery tumor tissue obtained from a 61-year-old female during a total abdominal hysterectomy and bilateral salpingo-oophorectomy with regional lymph node excision. Pathology indicated a metastatic grade 4 malignant mixed mullerian tumor present in the sigmoid mesentery at two sites. DUODNOT01 pINCY Library was constructed using RNA isolated from duodenal tissue obtained from a 41-year-old Caucasian female during a radical pancreaticoduodenectomy. Family history included benign hypertension and malignant skin neoplasm. DUODNOT02 pINCY Library was constructed using RNA isolated from duodenal tissue of a 8-year-old Caucasian female, who died from head trauma. Serology was positive for cytomegalovirus (CMV). ENDIUNT01 pINCY The library was constructed using RNA isolated from untreated iliac artery endothelial cell tissue removed from a Black female. The cells were exposed to normoxic conditions (atmospheric levels of oxygen).

Table 6 Library Vector Library Description FTUBTUR01 PCDNA2.1 This random primed library was constructed using RNA isolated from fallopian tube tumor tissue removed from an 85-year-old Caucasian female during bilateral salpingo-oophorectomy and hysterectomy. Pathology indicated poorly differentiated mixed endometrioid (80%) and serous (20%) adenocarcinoma, which was confined to the mucosa without mural involvement. Endometrioid carcinoma in situ was also present. Pathology for the associated uterus tumor indicated focal endometrioid adenocarcinoma in situ and moderately differentiated invasive adenocarcinoma arising in an endometrial polyp. Metastatic endometrioid and serous adenocarcinoma was present at the cul-de-sac tumor. Patient history included medullary carcinoma of the thyroid and myocardial infarction. LIVRTUT13 pINCY Library was constructed using RNA isolated from liver tumor tissue removed from a 62-year-old Caucasian female during partial hepatectomy and exploratory laparotomy. Pathology indicated metastatic intermediate grade neuroendocrine carcinoma, consistent with islet cell tumor, forming nodules ranging in size, in the lateral and medial left liver lobe. The pancreas showed fibrosis, chronic inflammation and fat necrosis consistent with pseudocyst. The gall bladder showed mild chronic cholecystitis. Patient history included malignant neoplasm of the pancreas tail, pulmonary embolism, hyperlipidemia, thrombophlebitis, joint pain in multiple joints, type II diabetes, benign hypertension, and cerebrovascular disease. Family history included pancreas cancer, secondary liver cancer, benign hypertension, and hyperlipidemia. PITUDIR01 PCDNA2.1 This random primed library was constructed using RNA isolated from pituitary gland tissue removed from a 70-year-old female who died from metastatic adenocarcinoma. PITUNON01 pINCY This normalized pituitary gland tissue library was constructed from 6.92 million independent clones from a pituitary gland tissue library. Starting RNA was made from pituitary gland tissue removed from a 55-year-old male who died from chronic obstructive pulmonary disease. Neuropathology indicated there were no gross abnormalities, other than mild ventricular enlargement. There was no apparent microscopic abnormality in any of the neocortical areas examined, except for a number of silver positive neurons with apical dendrite staining, particularly in the frontal lobe. The significance of this was undetermined. The only other microscopic abnormality was that there was prominent silver staining with some swollen axons in the CA3 region of the anterior and posterior hippocampus. Microscopic sections of the cerebellum revealed mild Bergmann's gliosis in the Purkinje cell layer. Patient history included schizophrenia. The library was normalized in two rounds using conditions adapted from Scares et al. , PNAS (1994) 91: 9228-9232 and Bonaldo et al. , Genome Research (1996) 6: 791, except that a significantly longer (48 hours/round) reannealing hybridization was used.

Table 6 Library Vector Library Description PKINDNV13 PCR2-TOPOTA Library was constructed using pooled cDNA from different donors. cDNA was generated using mRNA isolated from pooled skeletal muscle tissue removed from ten 21 to 57-year-old Caucasian male and female donors who died from sudden death; from pooled thymus tissue removed from nine 18 to 32-year-old Caucasian male and female donors who died from sudden death; from pooled liver tissue removed from 32 Caucasian male and female fetuses who died at 18-24 weeks gestation due to spontaneous abortion; from kidney tissue removed from 59 Caucasian male and female fetuses who died at 20-33 weeks gestation due to spontaneous abortion; and from brain tissue removed from a Caucasian male fetus who died at 23 weeks gestation due to fetal demise. PROSTUS23 pINCY This subtracted prostate tumor library was constructed using 10 million clones from a pooled prostate tumor library that was subjected to 2 rounds of subtractive hybridization with 10 million clones from a pooled prostate tissue library. The starting library for subtraction was constructed by pooling equal numbers of clones from 4 prostate tumor libraries using mRNA isolated from prostate tumor removed from Caucasian males at ages 58 (A), 61 (B), 66 (C), and 68 (D) during prostatectomy with lymph node excision. Pathology indicated adenocarcinoma in all donors. History included elevated PSA, induration and tobacco abuse in donor A; elevated PSA, induration, prostate hyperplasia, renal failure, osteoarthritis, renal artery stenosis, benign HTN, thrombocytopenia, hyperlipidemia, tobacco/alcohol abuse and hepatitis C (carrier) in donor B; elevated PSA, induration, and tobacco abuse in donor C; and elevated PSA, induration, hypercholesterolemia, and kidney calculus in donor D. The hybridization probe for subtraction was constructed by pooling equal numbers of cDNA clones from 3 prostate tissue libraries derived from prostate tissue, prostate epithelial cells, and fibroblasts from prostate stroma from 3 different donors. Subtractive hybridization conditions were based on the methodologies of Swaroop et al., NAR 19 (1991): 1954 and Bonaldo, et al. Genome Research 6 (1996): 791. SININOT04 pINCY Library was constructed using RNA isolated from diseased ileum tissue obtained from a 26-year-old Caucasian male during a partial colectomy, permanent colostomy, and an incidental appendectomy. Pathology indicated moderately to severely active Crohn's disease. Family history included enteritis of the small intestine. SINTFET03 pINCY Library was constructed using RNA isolated from small intestine tissue removed from a Caucasian female fetus, who died at 2 weeks'gestation. SINTNOR01 PCDNA2.1 This random primed library was constructed using RNA isolated from small intestine tissue removed from a 31-year-old Caucasian female during Roux-en-Y gastric bypass. Patient history included clinical obesity.

Table 6 Library Vector Library Description SMCCNON03 pINCY This normalized smooth muscle cell library was constructed from 7.56 million independent clones from a smooth muscle cell library. Starting RNA was made from smooth muscle cell tissue removed from the coronary artery of a 3-year-old Caucasian male. The normalization and hybridization conditions were adapted from Soares et al. , (PNAS (1994) 91: 9228-9232); Swaroop et al. , (NAR (1991) 19: 1954); and Bonaldo et al. , (Genome Research (1996) 6: 791-806), using a significantly longer (48 hour) reannealing hybridization period. THYMNOE02 PCDNA2.1 This 5'biased random primed library was constructed using RNA isolated from thymus tissue removed from a 3-year-old Hispanic male during a thymectomy and closure of a patent ductus arteriosus. The patient presented with severe pulmonary stenosis and cyanosis. Patient history included a cardiac catheterization and echocardiogram. Previous surgeries included Blalock-Taussig shunt and pulmonary valvotomy. The patient was not taking any medications. Family history included benign hypertension, osteoarthritis, depressive disorder, and extrinsic asthma in the grandparent (s). THYMNOT02 PBLUESCRIPT Library was constructed using polyA RNA isolated from thymus tissue removed from a 3-year-old Caucasian male, who died from drowning. Serologies were negative. UTRSNOT05 pINCY The library was constructed using RNA isolated from the uterine tissue of a 45-year-old Caucasian female during a total abdominal hysterectomy and total colectomy. Pathology for the associated tumor tissue indicated multiple leiomyomas of the myometrium and a grade 2 colonic adenocarcinoma of the cecum. Patient history included multiple sclerosis and mitral valve disorder. Family history included type I diabetes, cerebrovascular disease, atherosclerotic coronary artery disease, malignant skin neoplasm, hypertension, and malignant neoplasm of the colon.

Table 7 Program Description Reference Parameter Threshold ABI FACTURA A program that removes vector sequences and masks Applied Biosystems, Foster City, CA. ambiguous bases in nucleic acid sequences. ABI/PARACEL FDF A Fast Data Finder useful in comparing and Applied Biosystems, Foster City, CA; Mismatch <50% annotating amino acid or nucleic acid sequences. Paracel Inc. , Pasadena, CA. ABI AutoAssembler A program that assembles nucleic acid sequences. Applied Biosystems, Foster City, CA. BLAST A Basic Local Alignment Search Tool useful in Altschul, S. F. et al. (1990) J. Mol. Biol. ESTs : Probability value = 1. OE- sequence similarity search for amino acid and nucleic 215: 403-410; Altschul, S. F. et al. (1997) 8 or less; Full Length sequences: acid sequences. BLAST includes five functions: Nucleic Acids Res. 25: 3389-3402. Probability value = 1. OE-10 or blastp, blastn, blastx, tblastn, and tblastx. less FASTA A Pearson and Lipman algorithm that searches for Pearson, W. R. and D. J. Lipman (1988) Proc. ESTs : fasta E value = 1.06E-6 ; similarity between a query sequence and a group of Natl. Acad Sci. USA 85: 2444-2448; Pearson, Assembled ESTs : fasta Identity sequences of the same type. FASTA comprises as W. R. (1990) Methods Enzymol. 183: 63-98; = 95% or greater and Match least five functions: fasta, tfasta, fastx, tfastx, and and Smith, T. F. and M. S. Waterman (1981) length = 200 bases or greater; ssearch. Adv. Appl. Math. 2: 482-489. fastx E value = 1. OE-8 or less; Full Length sequences: fastx score = 100 or greater BLIMPS A BLocks IMProved Searcher that matches a Henikoff, S. and J. G. Henikoff (1991) Probability value =1. 0E-3 or sequence against those in BLOCKS, PRINTS, Nucleic Acids Res. 19: 6565-6572; Henikoff, less DOMO, PRODOM, and PFAM databases to search J. G. and S. Henikoff (1996) Methods for gene families, sequence homology, and structural Enzymol. 266: 88-105; and Attwood, T. K. et fingerprint regions. al. (1997) J. Chem. Inf. Comput. Sci. 37: 417- 424.

Table 7 Program Description Reference Parameter Threshold HMMER An algorithm for searching a query sequence against Krogh, A. et al. (1994) J. Mol. Biol. PFAM, INCY, SMART or hidden Markov model (HMM)-based databases of 235: 1501-1531; Sonnhammer, E. L. L. et al. TIGRFAM hits: Probability protein family consensus sequences, such as PFAM, (1988) Nucleic Acids Res. 26: 320-322; value = 1. OE-3 or less; Signal INCY, SMART and TIGRFAM. Durbin, R. et al. (1998) Our World View, in peptide hits: Score = 0 or greater a Nutshell, Cambridge Univ. Press, pp. 1- 350. ProfileScan An algorithm that searches for structural and Gribskov, M. et al. (1988) CABIOS 4: 61-66; Normalized quality score zu GCG sequence motifs in protein sequences that match Gribskov, M. et al. (1989) Methods specified"HIGH"value for that sequence patterns defined in Prosite. Enzymol. 183: 146-159; Bairoch, A. et al. particular Prosite motif. (1997) Nucleic Acids Res. 25: 217-221. Generally, score = 1.4-2. 1. Phred A base-calling algorithm that examines automated Ewing, B. et al. (1998) Genome Res. 8: 175- sequencer traces with high sensitivity and probability. 185; Ewing, B. and P. Green (1998) Genome Res. 8: 186-194. Phrap A Phils Revised Assembly Program including Smith, T. F. and M. S. Waterman (1981) Adv. Score = 120 or greater; Match SWAT and CrossMatch, programs based on efficient Appl. Math. 2: 482-489; Smith, T. F. and length = 56 or greater implementation of the Smith-Waterman algorithm, M. S. Waterman (1981) J. Mol. Biol. 147: 195- useful in searching sequence homology and 197; and Green, P. , University of assembling DNA sequences. Washington, Seattle, WA. Consed A graphical tool for viewing and editing Phrap Gordon, D. et al. (1998) Genome Res. 8: 195- assemblies. 202. SPScan A weight matrix analysis program that scans protein Nelson, H. et al. (1997) Protein Engineering Score = 3. 5 or greater sequences for the presence of secretory signal 10: 1-6; Claverie, J. M. and S. Audic (1997) peptides. CABIOS 12: 431-439. TMAP A program that uses weight matrices to delineate Persson, B. and P. Argos (1994) J. Mol. Biol. transmembrane segments on protein sequences and 237: 182-192; Persson, B. and P. Argos determine orientation. (1996) Protein Sci. 5: 363-371.

Table 7 Program Description Reference Parameter Threshold TMHMMER A program that uses a hidden Markov model (HMM) Sonnhammer, E. L. et al. (1998) Proc. Sixth to delineate transmembrane segments on protein Intl. Conf. On Intelligent Systems for Mol. sequences and determine orientation. Biol., Glasgow et al., eds., The Am. Assoc. for Artificial Intelligence (AAAI) Press, Menlo Park, CA, and MIT Press, Cambridge, MA, pp. 175-182. Motifs A program that searches amino acid sequences for Bairoch, A. et al. (1997) Nucleic Acids Res. patterns that matched those defined in Prosite. 25: 217-221; Wisconsin Package Program Manual, version 9, page M51-59, Genetics Computer Group, Madison, WI.

Table 8 SEQ PID EST ID SNP ID EST CB 1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 63 7511804 1359840H1 SNP00074796 18 592 T T G G190 n/a n/a n/a n/a 63 7511804 1361523H1 SNP00011014 100 787 T T C P255 n/a n/a n/a n/a 63 7511804 1749008F6 SNP00023897 77 787 C C G P255 n/d n/d 0. 97 n/d 63 7511804 1749008H1 SNP00023897 77 786 C C G P255 n/d n/d 0. 97 n/d 64 7512233 085309H1 SNP00128469 65 2031 C C T noncoding n/a n/a n/a n/a 64 7512233 086095H1 SNP00101038 80 1734 C C G noncoding n/d n/d n/d n/d 64 7512233 086315H1 SNP00025719 169 1478 C C T noncoding n/a n/a n/a n/a 64 7512233 086523H1 SNP00025720 164 1784 A A G noncoding n/a n/a n/a n/a 64 7512233 086523H1 SNP00128468 165 1785 G G A noncoding n/a n/a n/a n/a 64 7512233 087733H1 SNP00148142 28 1920 C C A noncoding n/a n/a n/a n/a 64 7512233 089149H1 SNP00133128 125 1472 C C T noncoding n/a n/a n/a n/a 64 7512233 089523H1 SNP00025721 101 2134 T T C noncoding n/d n/a n/a n/a 64 7512233 089523H1 SNP00136333 95 2128 T T C noncoding n/a n/a n/a n/a 64 7512233 089557H1 SNP00131197 53 1735 C C T noncoding n/a n/a n/a n/a 64 7512233 1007258H1 SNP00133127 21 1418 T T C noncoding n/a n/a n/a n/a 64 7512233 1264859T6 SNP00025721 191 2135 T T C noncoding n/d n/a n/a n/a 64 7512233 1264859T6 SNP00136333 197 2129 T T C noncoding n/a n/a n/a n/a 64 7512233 1352295H1 SNP00034062 251 2265 T T C noncoding n/d n/d n/d n/d 64 7512233 138457H1 SNP00153493 215 2021 T T C noncoding n/a n/a n/a n/a 64 7512233 138908T6 SNP00034062 45 2300 T T C noncoding n/d n/d n/d n/d 64 7512233 139427H1 SNP00101039 222 1862 G G A noncoding n/d n/d n/d n/d 64 7512233 139427H1 SNP00150105 107 1747 G G C noncoding n/a n/a n/a n/a 64 7512233 139922H1 SNP00025718 68 1287 G G A noncoding n/a n/a n/a n/a 64 7512233 166645H1 SNP00096914 159 1352 A G A noncoding n/a n/a n/a n/a 64 7512233 168107H1 SNP00150105 102 2857 G G C noncoding n/a n/a n/a n/a 64 7512233 1716454T6 SNP00034062 52 2273 T T C noncoding n/d n/d n/d n/d 64 7512233 1740386T6 SNP00034062 79 2267 T T C noncoding n/d n/d n/d n/d 64 7512233 1740386T6 SNP00101039 482 1864 G G A noncodin n/d n/d n/d n/d Table 8 SEQ PID EST ID SNP ID EST CB 1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 64 7512233 1757216H1 SNP00101037 252 2823 T T G noncoding n/a n/a n/a n/a 64 7512233 1781229T6 SNP00034062 63 2268 T T C noncoding n/d n/d n/d n/d 64 7512233 1781438T6 SNP00034062 52 2293 T T C noncoding n/d n/d n/d n/d 64 7512233 2430790H1 SNP00025720 71 2894 A A G noncoding n/a n/a n/a n/a 64 7512233 2430790H1 SNP00101038 21 2844 C C G noncoding n/d n/d n/d n/d 64 7512233 2430790H1 SNP00128468 72 2895 G G A noncoding n/a n/a n/a n/a 64 7512233 2513425H2 SNP00025721 59 898 T T C F294 n/d n/a n/a n/a 64 7512233 2514908H1 SNP00136332 144 810 G G A Q264 n/a n/a n/a n/a 64 7512233 2515964H1 SNP00150104 66 1329 C C T noncoding n/a n/a n/a n/a 64 7512233 271203H1 SNP00136333 7 892 T T C L292 n/a n/a n/a n/a 64 7512233 271768H1 SNP00034062 154 1029 T T C noncoding n/d n/d n/d n/d 64 7512233 272518H1 SNP00136332 81 2046 A G A noncoding n/a n/a n/a n/a 64 7512233 272518H1 SNP00153492 45 2010 T C T noncoding n/a n/a n/a n/a 64 7512233 279593T6 SNP00025721 212 2133 T T C noncoding n/d n/a n/a n/a 64 7512233 279593T6 SNP00136333 218 2127 T T C noncoding n/a n/a n/a n/a 64 7512233 293485H1 SNP00025718 87 1110 G G A noncoding n/a n/a n/a n/a 64 7512233 294931T6 SNP00034062 50 2289 T T C noncoding n/d n/d n/d n/d 64 7512233 4416883H1 SNP00023086 98 98 T T C M27 n/a n/a n/a n/a 64 7512233 4416883H1 SNP00096914 191 191 G G A R58 n/a n/a n/a n/a 64 7512233 4418323H1 SNP00055533 210 1200 A A G noncoding n/a n/a n/a n/a 64 7512233 4418617H1 SNP00057456 115 1535 C C T noncoding n/a n/a n/a n/a 64 7512233 4420092H1 SNP00153492 139 774 C C T N252 n/a n/a n/a n/a 64 7512233 5395280T1 SNP00148142 423 1921 C C A noncoding n/a n/a n/a n/a 64 7512233 5395296T1 SNP00034062 75 2270 T T C noncoding n/d n/d n/d n/d 64 7512233 5395296T1 SNP001Q1039 479 1866 G G A noncoding n/d n/d n/d n/d 64 7512233 5395374T1 SNP00034062 58 2266 T T C noncoding n/d n/d n/d n/d 64 7512233 5395402T1 SNP00153493 288 2028 T T C noncoding n/a n/a n/a n/a 64 7512233 5395436T1 SNP00101039 467 1863 G G A noncoding n/d n/d n/d n/d Table 8 SEQ PID EST ID SNP ID EST CB1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 64 7512233 5395960T1 SNP00034062 74 2269 T T C noncoding n/d n/d n/d n/d 64 7512233 5396101T1 SNP00034062 28 2296 T T C noncoding n/d n/d n/d n/d 64 7512233 5396101T1 SNP00101039 431 1893 G G A noncoding n/d n/d n/d n/d 64 7512233 5396144T1 SNP00025720 527 2906 A A G noncoding n/a n/a n/a n/a 64 7512233 5396144T1 SNP00128468 526 2907 G G A noncoding n/a n/a n/a n/a 64 7512233 5396269T1 SNP00025720 540 2898 A A G noncoding n/a n/a n/a n/a 64 7512233 5396269T1 SNP00128468 539 2899 G G A noncoding n/a n/a n/a n/a 64 7512233 5396302T1 SNP00025721 126 2204 C T C noncoding n/d n/a n/a n/a 64 7512233 5396302T1 SNP00136333 132 2198 T T C noncoding n/a n/a n/a n/a 64 7512233 5396494T1 SNP00101039 429 1912 G G A noncoding n/d n/d n/d n/d 64 7512233 5396517T1 SNP00025721 147 2176 T T C noncoding n/d n/a n/a n/a 64 7512233 5396517T1 SNP00136333 153 2170 T T C noncoding n/a n/a n/a n/a 64 7512233 5396793T1 SNP00034062 53 2276 T T C noncoding n/d n/d n/d n/d 64 7512233 5396907T1 SNP00034062 42 2272 C T C noncoding n/d n/d n/d n/d 64 7512233 5396907T1 SNP00101039 445 1869 G G A noncoding n/d n/d n/d n/d 64 7512233 5397024T1 SNP00034062 9 2294 T T C noncoding n/d n/d n/d n/d 64 7512233 5397024T1 SNP00101039 412 1891 G G A noncoding n/d n/d n/d n/d 64 7512233 5398089F6 SNP00025719 489 242 C C T P75 n/a n/a n/a n/a 64 7512233 6895941H1 SNP00150104 29 2565 C C T noncoding n/a n/a n/a n/a 64 7512233 7026553H1 SNP00057456 67 299 C C T A94 n/a n/a n/a n/a 64 7512233 7026783H1 SNP00131197 131 2845 C C T noncoding n/a n/a n/a n/a 64 7512233 7056901H1 SNP00057457 370 410 C C T A131 n/a n/a n/a n/a 64 7512233 8108613J1 SNP00055533 31 2613 A A G noncoding n/a n/a n/a n/a 65 7512557 138343H1 SNP00047285 160 2111 C C A P698 n/a n/a n/a n/a 65 7512557 2512814H1 SNP00040707 99 1774 C C A V585 n/d n/a n/a n/a 65 7512557 2683926H1 SNP00010494 94 94 C C T T25 n/a n/a n/a n/a 65 7512557 4285203F6 SNP00122818 409 409 A G A V130 0. 75 0. 73 0. 69 0. 54 65 7512557 4419328H1 SNP00119698 131 2201 T T C C728 n/d 0. 91 n/d n/d Table 8 SEQ PID EST ID SNP ID EST CB1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 65 7512557 6214167H1 SNP00119699 521 2347 T T C noncoding n/d 0. 63 n/d n/d 66 7512559 138343H1 SNP00047285 160 2111 C C A P698 n/a n/a n/a n/a 66 7512559 2512814H1 SNP00040707 99 1774 C C A V585 n/d n/a n/a n/a 66 7512559 2683926H1 SNP00010494 94 94 C C T T25 n/a n/a n/a n/a 66 7512559 4285203F6 SNP00122818 409 409 A G A V130 0. 75 0. 73 0. 69 0. 54 68 7512625 4420814F7 SNP00152603 181 1591 A G A noncoding n/a n/a n/a n/a 69 7512761 1004631H1 SNP00008006 97 111 G G A S13 0. 66 n/a n/a n/a 69 7512761 1371086H1 SNP00103800 121 443 C C T noncoding n/d 0. 99 n/d n/d 69 7512761 1696532F6 SNP00066484 363 1141 C C T noncoding n/a n/a n/a n/a 69 7512761 1696532T6 SNP00066484 308 1142 C C T noncoding n/a n/a n/a n/a 69 7512761 2201447H1 SNP00008007 32 240 C C T noncoding n/a n/a n/a n/a 69 7512761 2344826F6 SNP00008006 117 117 G G A G15 0. 66 n/a n/a n/a 69 7512761 6841255H1 SNP00139599 10 1060 T T C noncoding n/a n/a n/a n/a 70 7512802 1540012H1 SNP00143088 160 2224 G G A noncoding n/a n/a n/a n/a 70 7512802 1886726H1 SNP00143087 157 1712 A A G noncoding n/a n/a n/a n/a 70 7512802 2061125R6 SNP00143087 201 1713 A A G noncoding n/a n/a n/a n/a 70 7512802 2215457F6 SNP00060530 202 1123 G G A noncoding 0. 96 n/d n/d n/d 70 7512802 2215457H1 SNP00060530 201 1122 G G A noncoding 0. 96 n/d n/d n/d 70 7512802 773073 Ul SNP00143087 308 1728 A A G noncoding n/a n/a n/a n/a 72 7512760 1285527H1 SNP00013117 196 1299 A A G 1430 n/d n/a n/a n/a 72 7512760 1444373T6 SNP00046470 505 1386 G G C D459 n/a n/a n/a n/a 72 7512760 1513882F6 SNP00013117 134 1298 G A G M429 n/d n/a n/a n/a 72 7512760 1574488H1 SNP00046470 119 1385 G G C L458 n/a n/a n/a n/a 72 7512760 2796040H1 SNP00046469 70 1154 A G A Q381 n/a n/a n/a n/a 73 7512798 3947337H1 SNP00100385 201 1043 C C T noncoding Q. 85 0. 94 0. 95 0. 95 73 7512798 6953321H1 SNP00100384 20 524 C T C noncoding n/a n/a n/a n/a 73 7512798 8613606J1 SNP00100384 283 527 T T C noncoding n/a n/a n/a n/a 74 7512799 3947337H1 SNP00100385 201 978 C C T F326 0. 85 0. 94 0. 95 0. 95 Table 8 SEQ PID EST ID SNP ID EST CB 1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele I NO : frequency frequency frequency frequency 74 7512799 7735169J1 SNP00100384 269 603 T T C I201 n/a n/a n/a n/a 75 7512840 366250H1 SNP00054172 35 1518 A A G noncoding n/d n/a n/a n/a 77 7512901 1358518H1 SNP00068729 172 1189 A A G noncoding n/a n/a n/a n/a 77 7512901 1358518H1 SNP00068730 111 1250 A A G noncoding n/a n/a n/a n/a 77 7512901 1377839H1 SNP00022706 21 372 T T C Llll n/a n/a n/a n/a 77 7512901 1377839H1 SNP00022707 149 500 C C T noncoding n/a n/a n/a n/a 77 7512901 4301338H1 SNP00143779 216 777 G G A noncoding n/a n/a n/a n/a 77 7512901 7610787H1 SNP00022707 133 514 C C T noncoding n/a n/a n/a n/a 78 7512949 3236013F6 SNP00131365 126 164 G G A K27 n/a n/a n/a n/a 79 7512660 3151484H1 SNP00017464 86 349 G G T V96 n/a n/a n/a n/a 79 7512660 6130593H1 SNP00017464 160 341 G G T D94 n/a n/a n/a n/a 80 7512741 1379965F6 SNP00114801 155 3635 A A G noncoding n/a n/a n/a n/a 80 7512741 2632730H1 SNP00146109 157 2048 A A G S676 n/a n/a n/a n/a 80 7512741 2758103H1 SNP00019895 76 2909 T C T P963 n/d n/d n/d n/d 80 7512741 2842560T6 SNP00114801 143 3641 A A G noncoding n/a n/a n/a n/a 80 7512741 348270T6 SNP00019895 193 2912 C C T Y964 n/d n/d n/d n/d 81 7513099 3249177H1 SNP00023138 263 1700 T T C noncoding n/a n/a n/a n/a 81 7513099 7611233J1 SNP00023138 570 1680 T T C noncoding n/a n/a n/a n/a 82 7511908 1880062F6 SNP00023025 159 793 A A G noncoding 0. 03 n/d 0. 07 n/d 83 7513074 1868521T6 SNP00037248 28 2493 G G A noncoding n/a n/a n/a n/a 83 7513074 274662T6 SNP00037248 32 2492 A G A noncoding n/a n/a n/a n/a 83 7513074 3800416T6 SNP00037248 31 2507 G G A noncoding n/a n/a n/a n/a 83 7513074 4380691H1 SNP00100395 144 400 G G T Q115 0. 75 0. 84 0. 71 n/a 83 7513074 4599393F7 SNP00037247 530 2489 C C T noncoding n/a n/a n/a n/a 83 7513074 6382193H1 SNP00100396 14 579 A A G D175 n/d n/d n/d n/d 83 7513074 7638225H1 SNP00100395 104 440 G G T G129 0. 75 0. 84 0. 71 n/a 83 7513074 7692525J1 SNP00100395 147 376 G G T P107 0. 75 0. 84 0. 71 n/a 83 7513074 7692525J1 SNP00100396 326 555 A A G N167 n/d n/d n/d n/d Table 8 SEQ PID EST ID SNP ID EST CB 1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 84 7513960 1840616H1 SNP00011726 81 573 C C T L184 n/a n/a n/a n/a 85 7513984 2772903F6 SNP00120575 250 1514 G G A noncoding n/d n/d n/d n/d 86 7512992 1429127F7 SNP00142702 515 600 A A G Gill n/a n/a n/a n/a 86 7512992 1876060T6 SNP00005185 22 2213 G G A noncoding 0. 98 n/a n/a n/a 86 7512992 1877614F6 SNP00023191 272 1702 G G C noncoding n/a n/a n/a n/a 86 7512992 2098152H1 SNP00098532 17 1623 T T C N452 0. 61 0. 81 0. 77 0. 65 86 7512992 6534732H1 SNP00003472 75 1532 C C T T422 n/a n/a n/a n/a 87 7512994 1429127F7 SNP00142702 515 600 A A G Gill n/a n/a n/a n/a 87 7512994 1876060T6 SNP00005185 22 2258 G G A noncoding 0. 98 n/a n/a n/a 87 7512994 1877614F6 SNP00023191 272 1747 G G C noncoding n/a n/a n/a n/a 87 7512994 2098152H1 SNP00098532 17 1668 T T C N467 0. 61 0. 81 0. 77 0. 65 87 7512994 8567919T1 SNP00003472 685 1583 C C T A439 n/a n/a n/a n/a 88 7513547 1990694H1 SNP00153017 111 1767 C C T H452 n/a n/a n/a n/a 88 7513547 3044934F6 SNP00067306 123 1534 G G A G374 0. 88 0. 79 n/d 0. 95 88 7513547 3044934H1 SNP00067306 122 1533 G G A A374 0. 88 0. 79 n/d 0. 95 88 7513547 3873947H1 SNP00007107 41 2269 G G T noncoding n/a n/a n/a n/a 88 7513547 3873947H1 SNP00098317 90 2318 T T C noncoding n/d n/a n/a n/a 88 7513547 4144368T6 SNP00032212 167 2138 A C A 1575 n/a n/a n/a n/a 88 7513547 4144368T6 SNP00097089 87 2218 T T G noncoding n/a n/a n/a n/a 88 7513547 4422182F6 SNP00153016 121 1418 C C A N335 n/a n/a n/a n/a 89 7513357 116233H1 SNP00121347 33 470 T T C T117 0. 68 n/a n/a n/a 89 7513357 1214170H1 SNPOQ013177 51 1043 T C T Y308 n/a n/a n/a n/a 89 7513357 1347328H1 SNP00097462 27 34 C C A noncoding n/a n/a n/a n/a 89 7513357 1347328H1 SNP00128550 49 56 T T C noncoding n/a n/a n/a n/a 89 7513357 1400061H1 SNP00128551 153 789 A A G R224 n/a n/a n/a n/a 89 7513357 1400061H1 SNP00128552 193 829 T T C V237 n/a n/a n/a n/a 89 7513357 1422603H1 SNP00093096 59 295 T T C M59 n/a n/a n/a n/a 89 7513357 1422603H1 SNP00134927 36 272 C C T D51 n/a n/a n/a n/a Table 8 SEQ PID EST ID SNP ID EST CB1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 89 7513357 3213120T6 SNP00013177 346 1050 C C T Q311 n/a n/a n/a n/a 89 7513357 3527072T6 SNP00013177 298 1078 T C T M320 n/a n/a n/a n/a 89 7513357 4535064T1 SNP00013177 307 1082 C C T L321 n/a n/a n/a n/a 89 7513357 7153213H1 SNP00128551 353 732 A A G 1205 n/a n/a n/a n/a 89 7513357 7413670T2 SNP00013177 329 1041 C C T H308 n/a n/a n/a n/a 90 7513329 1581645H1 SNP00074575 13 1620 G G C S540 n/a n/a n/a n/a 90 7513329 2868202H1 SNP00074574 70 1410 C C T N470 n/a n/a n/a n/a 91 7517777 1468683F6 SNP00147908 294 661 T C T V204 n/a n/a n/a n/a 91 7517777 1468683F6 SNP00147909 435 802 T C T 1251 n/a n/a n/a n/a 91 7517777 5550934F7 SNP00136569 134 319 T T C Y90 n/a n/a n/a n/a 91 7517777 7677316J1 SNP00136569 21 298 C T C N83 n/a n/a n/a n/a 91 7517777 7677316J1 SNP00147908 363 640 C C T H197 n/a n/a n/a n/a 94 7514648 2476277H1 SNP00127476 107 47 A A G noncoding n/a n/a n/a n/a 94 7514648 5306785H1 SNP00144970 17 582 C C T A171 n/a n/a n/a n/a 94 7514648 5979601H1 SNP00127477 58 325 G G A Q85 n/a n/a n/a n/a 94 7514648 8626537H1 SNP00144970 490 581 C C T P171 n/a n/a n/a n/a 95 7517904 1538120H1 SNP00024718 40 2566 C C T noncoding n/a n/a n/a n/a 95 7517904 1903432F6 SNP00074271 279 2456 A A G noncoding n/d n/d n/d n/d 95 7517904 2302790H1 SNP00149887 43 2509 C C T noncoding n/a n/a n/a n/a 95 7517904 2602020F6 SNP00122174 258 1525 G G C noncoding n/a n/a n/a n/a 95 7517904 3593071T6 SNP00024718 345 2573 C C T noncoding n/a n/a n/a n/a 95 7517904 3777007H1 SNP00123535 160 164 A A G D55 0. 99 n/d n/d n/d 95 7517904 5021254T1 SNP00024718 352 2569 C C T noncoding n/a n/a n/a n/a 95 7517904 5021254T1 SNP00074271 462 2459 A A G noncoding n/d n/d n/d n/d 95 7517904 5044629H1 SNP00136617 83 532 T T C noncoding n/a n/a n/a n/a 95 7517904 7750796J1 SNP00122174 442 15Q2 G G C noncoding n/a n/a n/a n/a 95 7517904 7754296H1 SNP00123535 79 132 G A G Q44 0. 99 n/d n/d n/d 98 7519227 1316093H1 SNP00126327 159 436 G G C noncoding n/a n/a n/a n/a Table 8 SEQ PID EST ID SNP ID EST CB 1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 98 7519227 1316093H1 SNP00126328 178 455 T T C noncoding n/a n/a n/a n/a 98 7519227 1438803H1 SNP00092529 236 354 A A G H115 0. 93 0. 90 0. 99 0. 83 98 7519227 1821938F6 SNP00121237 116 641 C C T noncoding n/a n/a n/a n/a 98 7519227 1821938F6 SNP00121238 196 721 C C T noncoding n/d n/a n/a n/a 98 7519227 1821938H1 SNP00121237 117 642 C C T noncoding n/a n/a n/a n/a 98 7519227 1821938H1 SNP00121238 197 722 C C T noncoding n/d n/a n/a n/a 98 7519227 1821938T6 SNP00121237 354 663 C C T noncoding n/a n/a n/a n/a 98 7519227 1821938T6 SNP00121238 275 742 C C T noncoding n/d n/a n/a n/a 98 7519227 1988568H1 SNP00043742 6 65 C C T L19 n/a n/a n/a n/a 98 7519227 3402729H1 SNP00009424 220 329 G G C G107 n/a n/a n/a n/a 98 7519227 545951R6 SNP00138842 125 306 C C T A99 n/a n/a n/a n/a 98 7519227 7638514J1 SNP00092529 467 355 A A G Q115 0. 93 0. 90 0. 99 0. 83 103 7519522 3290128H1 SNP00065780 14 764 A G A T250 n/a n/a n/a n/a 103 7519522 3406256H1 SNP00105281 158 446 G G A V144 n/a n/a n/a n/a 103 7519522 3406256H1 SNP00105282 189 477 G G C V155 n/d n/d n/a n/a 103 7519522 6285941H2 SNP00049516 24 407 T T C C131 n/a n/a n/a n/a 103 7519522 7050174H1 SNP00105283 163 599 G A G G195 n/d n/a n/a n/a 103 7519522 7051785H1 SNP00103291 393 829 G A G R272 n/d n/a n/a n/a 103 7519522 7676358H1 SNP00065780 364 756 G G A G248 n/a n/a n/a n/a 103 7519522 7676358H1 SNP00105281 46 438 G G A D142 n/a n/a n/a n/a 103 7519522 7676358H1 SNP00105282 77 469 G G C G152 n/d n/d n/a n/a 103 7519522 7676358H1 SNP00105283 199 591 A A G 1193 n/d n/a n/a n/a 104 7520023 4741811F6 SNP00031768 172 802 G A G L267 0. 92 0. 99 0. 94 n/d 105 7519518 1271557H1 SNP00025229 188 602 A A G noncoding n/a n/a n/a n/a 105 7519518 1339625H1 SNP00025230 14 831 C C T noncoding n/d n/d n/d n/d 105 7519518 1439733H1 SNP00025227 184 85 C C T V20 n/a n/a n/a n/a 106 7519955 2239738F6 SNP00069622 48 1200 T T G noncoding n/d n/d n/d n/d 106 7519955 3747978H1 SNP00040242 61 328 T C T noncoding n/a n/a n/a n/a Table 8 SEQ PID EST ID SNP ID EST CB 1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 106 7519955 3747978H1 SNP00128300 52 319 T T C noncoding nla n/a n/a n/a 106 7519955 7694520J1 SNP00069622 256 1201 T T G noncoding n/d n/d n/d n/d 107 7514925 6039162H1 SNP00069936 364 13Q6 G T G noncoding n/a n/a n/a n/a 109 7519481 1316093H1 SNP00126327 159 642 G G C noncoding n/a n/a n/a n/a 109 7519481 1316093H1 SNP00126328 178 661 T T C noncoding n/a n/a n/a n/a 109 7519481 1438803H1 SNP00092529 236 560 A A G noncoding 0. 93 0. 90 0. 99 0. 83 109 7519481 1703707H1 SNP00000525 149 207 C C T C66 n/a n/a n/a n/a 109 7519481 1728710H1 SNP00043742 6 64 C C T L19 n/a n/a n/a n/a 109 7519481 1984208R6 SNP00043742 256 65 C C T P19 n/a n/a n/a n/a 109 7519481 2356170H1 SNP00130926 3 54 A G A A15 n/a n/a n/a n/a 109 7519481 3107811H1 SNP00069722 67 126 T T C V39 n/a n/a n/a n/a 109 7519481 545951R6 SNP00138842 125 512 C C T noncoding n/a n/a n/a n/a 110 7519529 5593787F6 SNP00116533 233 143 T T G W47 n/a n/a n/a n/a 110 7519529 6798890H1 SNP00116528 173 25 C C T R7 n/a n/a n/a n/a 110 7519529 6798890H1 SNP00116529 272 124 A A G P40 n/a n/a n/a n/a 110 7519529 7756639H1 SNP00116528 78 26 C C T Q8 n/a n/a n/a n/a 110 7519529 7756639H1 SNP00116529 177 125 A A G 141 n/a n/a n/a n/a 111 7519549 1271557H1 SNP00025229 188 949 A A G Q308 n/a n/a n/a n/a 111 7519549 1339625H1 SNP00025230 14 1178 C C T H385 n/d n/d n/d n/d Ill 7519549 1439733H1 SNP00025227 184 85 C C T V20 n/a n/a n/a n/a 112 7520124 1559465H1 SNP00135042 90 79 C C T D26 n/a n/a n/a n/a 112 7520124 7752525J1 SNP00135042 52 42 C C T T14 n/a n/a n/a n/a 113 7515245 1210324H1 SNP00149379 127 917 G G A A301 n/a n/a n/a n/a 113 7515245 1366605H1 SNP00120139 121 741 A A G 1243 n/d n/d n/d n/d 114 7519933 1000192H1 SNP00135491 38 301 T T G V99 n/a n/a n/a n/a 114 7519933 8617948H1 SNP00018083 105 9 G G A G2 n/a n/a n/a n/a 114 7519933 8651412H1 SNP00155110 79 77 T C T L24 n/a n/a n/a n/a 115 7520101 1000192H1 SNP00067745 137 400 T T C 1132 n/d n/d n/d n/d Table 8 SEQ PID EST ID SNP ID EST CB1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 115 7520101 1000192H1 SNP00135491 38 301 T T G V99 n/a n/a n/a n/a 115 7520101 1862259F6 SNP00067745 185 401 T T C 1132 n/d n/d n/d n/d 115 7520101 1862259F6 SNP00135491 86 302 T T G V99 n/a n/a n/a n/a 115 7520101 7622019H1 SNP00155110 504 77 C C T L24 n/a n/a n/a n/a 116 7520145 176598R6 SNP00050746 354 292 G G A R84 n/a n/a n/a n/a 116 7520145 1879670F6 SNP00050746 306 291 G G A R84 n/a n/a n/a n/a 116 7520145 3881478H1 SNP00123287 45 325 C C T I95 n/a n/a n/a n/a 117 7520174 176598R6 SNP00050746 354 292 G G A R84 n/a n/a n/a n/a 117 7520174 1879670F6 SNP00050746 306 291 G G A R84 n/a n/a n/a n/a 117 7520174 4345749H1 SNP00123287 81 325 C C T I95 n/a n/a n/a n/a 118 7520191 1001420H1 SNP00036591 240 623 G G A noncoding n/a n/a n/a n/a 119 7520243 027707H1 SNP00017180 119 447 C C T noncoding n/a n/a n/a n/a 119 7520243 027707H1 SNP00143256 186 514 T T C noncoding n/a n/a n/a n/a 119 7520243 1513346T6 SNP00143257 454 1156 A A G noncoding n/a n/a n/a n/a 119 7520243 7740349J1 SNP00143256 583 517 T T C noncoding n/a n/a n/a n/a 119 7520243 8609083J1 SNP00017180 641 449 C C T noncoding n/a n/a n/a n/a 120 7521695 4110656H1 SNP00072981 143 3780 C C T noncoding n/a n/a n/a n/a 121 7520801 1274568F6 SNP00116611 135 437 T T C V131 n/a n/a n/a n/a 121 7520801 1600263H1 SNP00012716 33 158 A A G Q38 n/d n/a n/a n/a 121 7520801 1886686H1 SNP00045966 184 737 C C T noncoding n/d n/d n/d n/d 121 7520801 1886686H1 SNP00045967 233 786 T T C noncoding n/a n/a n/a n/a 123 7520937 1316093H1 SNP00126327 159 681 G G C R226 n/a n/a n/a n/a 123 7520937 1316093H1 SNP00126328 178 700 T T C P232 n/a n/a n/a n/a 123 7520937 1438803H1 SNP00092529 236 599 A A G T199 0. 93 0. 90 0. 99 0. 83 123 7520937 1821938F6 SNP00121237 116 886 C C T C294 n/a n/a n/a n/a 123 7520937 1821938F6 SNP00121238 196 966 C C T S321 n/d n/a n/a n/a 123 7520937 1821938H1 SNP00121237 117 887 C C T L295 n/a n/a n/a n/a 123 7520937 1821938H1 SNP00121238 197 967 C C T Y321 n/d n/a n/a n/a Table 8 SEQ PID EST ID SNP ID EST CB 1 EST Allele Allele Amino Acid Caucasian African Asian Hispanic ID SNP SNP Allele 1 2 Allele 1 Allele 1 Allele 1 Allele 1 NO : frequency frequency frequency frequency 123 7520937 1821938T6 SNP00121237 354 908 C C T R302 n/a n/a n/a n/a 123 7520937 1821938T6 SNP00121238 275 987 C C T S328 n/d n/a n/a n/a 123 7520937 3402729H1 SNP00009424 220 574 G G C K190 n/a n/a n/a n/a 123 7520937 5100506F6 SNP00069722 109 274 T T C V90 n/a n/a n/a n/a 123 7520937 545951R6 SNP00138842 125 551 C C T L183 n/a n/a n/a n/a 123 7520937 6083743H1 SNP00043742 40 213 C C T P70 n/a n/a n/a n/a 123 7520937 7638514J1 SNP00092529 467 600 A A G N199 0. 93 0. 90 0. 99 0. 83