DIAGNOSIS OF DISEASES AND CONDITIONS BY ANALYSIS OF

HISTOPATHOLOGICALLY PROCESSED BIOLOGICAL SAMPLES USING

LIQUDD TISSUE ^® PREPARATIONS

Related application [0001] This application claims priority to USSN 60/684,183, filed May 25, 2005, pending, the contents of which are incorporated by reference in their entirety.

Field of the Invention

[0002] The invention generally relates to diagnosis of a disease or condition in a subject by analysis of a biological sample obtained from the subject.

Background

[0003] For over a hundred years, public and academic medical universities and institutions, pathology clinics, private biomedical institutions, tissue archives, hospitals, and museums have been preserving biological specimens with formalin and other chemical fixatives such as formaldehyde and ethyl alcohol. The most common fixative is formalin. Formalin is used as a fixative because of it superior ability to preserve both tissue structure and cellular morphology. This has resulted in the wide use of formalin for the successful preservation of histologic sections for traditional microscopic analysis. Formalin fixation is so effective in preserving tissue structure and cellular morphology that the formalin archive is a veritable treasure trove containing millions of samples. Within this archive are biological samples of healthy tissue, tissue samples from virtually every known human disease, and a multitude of preserved life forms.

[0004] Formalin induces extensive cross-linking of the proteins within the biological specimen. These protein cross links, while providing excellent cellular morphology preservation, also renders the fixed sample relatively insoluble. Because of these protein cross-links, the types of assays that can be performed on a formalin-fixed sample are limited in number, unable to provide quantitative results and lack sensitivity. In fact, formalin fixed biological samples are virtually unusable in many modern assay techniques, which are both highly quantitative and sensitive.

[0005] Thus, there is an unmet need in the industry to use histologically processed samples in the diagnosis of diseases such as cancer, Alzheimer's Disease, and Parkinson's Disease, as well as other conditions.

Summary of the Invention

[0006] The present invention provides compositions and methods for detecting diseases such as cancer by analysis of proteins contained in Liquid Tissue preparations obtained from histologically processed samples, such as formalin-fixed tissue.

[0007] In one aspect, the invention provides a method of diagnosing the presence of a disease, condition, or syndrome in a subject (e.g., a human subject), by detecting the presence of at least one protein analyte in a Liquid Tissue preparation from a biological sample obtained from a subject suspected of suffering from a disease, condition, or syndrome, wherein the biological sample comprises formalin-fixed tissue or paraffin-fixed tissue, wherein the presence of the analyte indicates that the subject has the disease, condition, or syndrome.

[0008] The invention also includes a step of comparing the one or more detected analytes with one or more reference analytes obtained from a subject known to have or not have the disease, condition, or syndrome. In some embodiments the invention provides the step of quantitating the at least one analyte, such as by isotopic labeling of the proteins or AQUA peptides.

[0009] In embodiments of the invention, the detection is mass spectrometry, immunohistochemistry, ELISA, Western blotting, polyacrylamide gel electrophoresis, synthetic aptamer binding analysis, or isoelectric focusing analysis. In certain embodiments the Liquid Tissue preparation is in the form of an array. The protein analyte is generally not substantially cross-linked. Mass spectrometric analysis is matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF), liquid chromatography electrospray ionization tandem mass spectrometry (LC-ES I-MS/MS), or surface enhanced laser desorption ionization (SELDI) mass spectrometry. The analyte is one of the analytes listed in Table 1.

[0010] In another aspect, the invention provides a method of detecting cancer in a subject by detecting the presence of at least one protein analyte in a Liquid Tissue preparation from a biological sample obtained from a subject suspected of suffering from a disease, condition, or syndrome, wherein the biological sample contains formalin-fixed tissue or paraffin-fixed tissue, wherein the presence of the analyte indicates that the subject has cancer. The analyte is a peptide derived from Her2, an estrogen receptor, a progesterone receptor, PSA or an androgen receptor. The cancer is, for example, prostate cancer and the analyte is a peptide derived from PSA, PAP, PEBP or GDF 15.

[0011] The invention provides for the additional step of comparing the protein analytes with one or more reference analytes obtained from a subject known to have or not have the disease, condition, or syndrome (e.g., cancer).

[0012] In another aspect, the invention provides a method of determining the predisposition to develop a disease or condition in a subject, by detecting the presence of at least one protein analyte in a Liquid Tissue preparation from a biological sample obtained from a subject suspected of suffering from a disease, condition, or syndrome, wherein the biological sample comprises formalin-fixed tissue or paraffin-fixed tissue; and comparing the one or more detected protein analytes with one or more reference analytes obtained from a subject known to have the disease or condition, wherein the presence of the one or more analytes indicates that the subject has an increased predisposition to develop the disease or condition as compared to a subject not having said one or more analytes. The analyte is a peptide derived from Her2, an estrogen receptor, a progesterone receptor, PSA or an androgen receptor. The cancer is, for example,, prostate cancer and the analyte is a peptide derived from PSA, PAP, PEBP or GDF 15. Alternatively, the disease is Alzheimer's disease and the analyte is a peptide derived from CSF beta-amyloid protein or tau protein. Alternatively, the disease is Parkinson's disease and the analyte is a peptide derived from alpha synuclein, parkin, ubiquitin C-terminal hydrolase L (UCH-Ll), or NR4A2. Alternatively, the condition is a benign hyperplastic condition.

[0013] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other

references mentioned herein are incorporated by reference in their entirety. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.

[0014] These and other objects of the present invention will be apparent from the detailed description of the invention provided below.

Brief Description of the Drawings

[0015] The foregoing and other features and advantages of the invention will be apparent from the following more particular description of preferred embodiments of the invention, as illustrated in the accompanying drawings in which like reference characters refer to the same parts throughout the different views. The drawings are not necessarily to scale, emphasis instead being placed upon illustrating the principles of the invention.

[0016] Figure 1 is a flow chart illustrating the method to achieve a diagnosis and/or prognosis of one or more diseases, or conditions, by analysis of proteins present in a Liquid Tissue preparation. The analysis is performed by, e.g., mass spectrometry, or any number of other affinity-based assays where one or more analytes are detected within the complex Liquid Tissue preparation.

[0017] Figure 2 is a series of images and a line graph demonstrating the detection of prostate cancer using the methods of the present invention. Liquid Tissue preparations were prepared from a fixed tissue section of a diseased prostate, where one extract was prepared from a region of the tissue containing prostate cancer ("Cancer") and the other extract was prepared from a region of the tissue containing normal cells ("Normal"). The extracts were spotted onto a membrane where differential expression of the protein Prostate Specific Antigen (PSA) was determined by a standard immunoassay. The graph shows that a high level of PSA protein is detected in the cancer region, while PSA is undetected in the normal region of the tissue.

[0018] Figure 3 is a photographic image and three mass spectral analyses of three

Liquid Tissue preparations prepared from the same fixed tissue section: one preparation is from a region of cancer (upper left), one preparation is from a region benign prostatic hyperplasia (BPH) (lower left), and a third preparation is from a region of normal stroma (right). Mass spectrometry protein expression results (shown as mass spectrometry base peak chromatograms and summarily indicated by an abbreviated protein expression list) indicate

relatively equivalent expression on known prostate cancer biomarkers between cancer and BPH. One protein, GDF- 15, was demonstrated to be differentially expressed between these two types of prostate disease or conditions.

Detailed Description [0019] The present invention provides methods for diagnosing diseases or conditions using biological samples that are generally present as histopathologically processed tissue sections.

[0020] Previously, the present inventors have found that histopathologically processed biological samples can be heated in a reaction buffer, followed by protease treatment, to provide materials, herein termed Liquid Tissue preparations, that are rich in molecular information regarding the original biological sample. See U.S. S.N. 10/796,288, filed March 10, 2004, the contents of which are incorporated by reference in their entirety. The inventors now have found that these preparations are useful for diagnosing disease, conditions and/or syndromes in patients from whom the samples are taken.

[0021] As used herein and in the appended claims, the singular forms "a," "and," and

"the" include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to "a protein" is a reference to one or more proteins and includes equivalents thereof known to those skilled in the art, and so forth.

[0022] Biological Samples [0023] Histopathologically processed biological samples can include whole organisms, samples obtained from biopsy, diagnostic surgical pathology, tissue samples, body fluids {e.g., blood, plasma, serum, saliva, semen, cervical secretions, saliva, urine, tears, sweat, breast milk, and amniotic fluids), cellular or viral material, or any other biological sample that has been histopathologically processed.

[0024] Examples of histopathological processing of biological samples include, but are not limited, to: formalin fixation of whole organisms; formalin fixation of tissues or cells; formalin fixation/paraffin embedding of tissues or cells; and formalin fixation and/or paraffin embedding of tissue culture cells.

[0025] Histopathological processing typically occurs through the use of a formalin fixative. Formalin is used widely because it is relatively inexpensive, easy to handle, and once the formalin-fixed sample is embedded in paraffin the sample is stored easily.

Additionally, formalin is often the fixative of choice because it preserves both tissue structure and cellular morphology. Although the exact mechanism may not be understood fully, fixation occurs by formalin-induced cross-linking of the proteins within the biological specimen. Due to these protein cross-links, formalin fixation has found wide success in the traditional microscopic analysis of histologic sections.

[0026] The sheer volume of formalin-fixed specimens cannot be overstated. For nearly the last one hundred years, biological specimens have been commonly fixed in formalin or formalin fixed/paraffin wax-embedded (FFPE) blocks. Universities and museums have vast archives of plants and animals that are formalin-fixed. Hospitals, in the course of diagnostic surgical pathology, have established large formalin-fixed collections that contain tissues from nearly every known disease in addition to normal, healthy tissue. Due to the need to retain these clinical tissue samples in case further testing is required, these archives around the world now contain millions of FFPE samples.

[0027] Liquid Tissue preparations [0028] The invention described herein provides new and surprising uses for Liquid

Tissue preparations obtained from histopathologically processed biological samples. Generally, the Liquid Tissue preparations contain substantially all of the biomolecules contained within the sample, including but not limited to proteins, glycoproteins, nucleic acids (e.g., DNA, RNA), lipids, glycolipids, and cell organelle-derived molecules. As used herein, the term "protein" encompasses all proteins, including polypeptides, protein fragments, oligopeptides, and peptides containing two or more amino acids connected by peptide bonds.

[0029] The biomolecules contained within the Liquid Tissue preparation are useful as

"analytes", either in a whole and intact form or and component thereof, if the biomolecule is detectable, such as by mass spectroscopy or by binding to a reagent of specific binding affinity. By way of non-limiting example, analytes useful herein include peptides generated by proteolytic digestion of proteins contained in the Liquid Tissue preparation.

[0030] In addition, the Liquid Tissue preparations described and used herein can be subjected to additional manipulations, such as fractionation by chromatography or other means, dilution, treatment with enzymes or other modifying agents.

[0031] Methods of Preparing Liquid Tissue preparations

[0032] In general, Liquid Tissue preparations are generated by contacting all or a portion of a biological sample (e.g., a formalin-fixed tissue section) with a buffer solution. The sample in solution is heated for a time and at a temperature sufficient to negatively affect (e.g., reverse) the formalin-induced protein cross-links. For example, the heating is performed at a temperature of about 80 ⁰ C to about 100°C (e.g., at about 85°C, 9O ⁰ C, 95°C, 98 ⁰ C, 100 ⁰ C, 102 ⁰ C, or 105 ⁰ C) from about 30 seconds to about 24 hours or more (e.g., for 5, 10, 15, 30, 45 seconds, or 1, 2, 3, 4, 5, 10, 15, 30 or 45 minutes or 1, 2, 3, 4, 5, 7, 10, 14, 18, or 24 hours). Without being bound by any theory, the present inventors believe that the negative affect of temperature on the protein cross-links appears to involve some form of releasing, reversing, or partial modification of the cross-links. Generally, as used herein, the term "buffer" refers to a buffer which has a specific pH in the range of 1.0 to 9.0. Both specific pH and buffer types are selected based upon the required conditions, such as the proteolytic enzyme used. Suitable buffer type and specific pH requirements are described in patent application U.S.S.N. 10/796,288.

[0033] The heated solution is then modified by adding at least one enzyme to the histopathologically processed biological sample. Enzymes include proteases, nucleases, glycosidases, lipases, phospholipases, phosphatases, and sulfatases. In a preferred embodiment, the enzyme is a proteolytic enzyme. Proteolytic enzymes are believed to augment the negative effect of heating on formalin-induced protein cross-links. Examples of proteolytic enzymes that are suitable for use in the present invention include but are not limited to trypsin, proteinase K, chymotrypsin, papain, pepsin, pronase, and endoproteinase Lys-C. Advantageously, the protease treatment is carried out following the heating step described above. The protease treatment is advantageously carried out at a temperature that is optimal for maximum activity of the protease, such as about 3O ⁰ C to about 60 ⁰ C.

[0034] In one embodiment of the current invention, the Liquid Tissue preparation is fractionated into distinct and separate biomolecules that may be collected separately. Examples of biomolecule fractions that can be collected include but are not limited to protein, glycoproteins, nucleic acids (e.g., DNA, RNA), glycolipids, and lipids. Fractionation techniques are well known in the arts and include but are not limited to, spin column fractionation, immunoprecipitation, gradient centrifϊigation, HPLC and drip column fractionation. Other fractionation methods are well known in the art.

[0035] In another embodiment of the current invention, the Liquid Tissue preparation is modified by the addition of one or more detergents, including for example Nonidet-P-40, SDS, Tween-20, Triton-X, and sodium deoxycholate. The detergent is added prior to the protease treatment step (before or after heating), in which case the nature of the detergent and its concentration is selected so as to not substantially inhibit the activity of the protease. Alternatively, the detergent is added after addition of the protease.

[0036] Analyte detection and quantitation

[0037] Detection of one or more analytes is accomplished by any suitable means known to those skilled in the art. A preferred detection means is mass spectroscopy, such as matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF), liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), or surface enhanced laser desorption ionization (SELDI) mass spectrometry. When analyte detection is performed using mass spectrometry, the biological sample is generally contacted with a buffer containing a volatile ammonium salt. For example the buffer can contain 10OmM ammonium bicarbonate, although the skilled artisan will recognize that the concentration of the solution may be varied.

[0038] Exemplary analytes are provided in Table 1. Other analytes can be obtained from one of the following databases: Online Mendelian Inheritance of Man (OMIM), the Tumor Gene Database, or the Gene Cards database.

[0039] Other detection means include but are not limited to are column chromatography, protein arrays, Western blotting, immunoprecipitation, affinity columns, alternative splicing assays, mutation analysis, nucleic acid amplification (for example PCR, LCR, and T7-based RNA amplification), labeled probes for microarray analysis, RFLP analysis, Southern blotting, and high-through put assays such as but not limited to one- and two-dimensional polyacrylamide gel electrophoresis (2D-P AGE), serial analysis of gene expression (SAGE), HPLC, FPLC, liquid chromatography, ELISA assays, Quantitative RT- PCR, Single Nucleotide Polymorphism detection, genotyping and protein and nucleic acid sequencing. See, Shi et ah, Antigen retrieval techniques: current perspectives. J Histochem Cytochem. 2001 49(8): 931-73; Espina et ah, Protein microarrays: molecular profiling technologies for clinical specimens. Proteomics. 2003 3(11):2091-100; Bons et ah, Protein profiling as a diagnostic tool in clinical chemistry: a review. Clin Chem Lab Med. 2005 43(12): 1281-90; Loor et al., Evaluation of a human pancreas-specific antigen by enzyme-

linked immunosorbent assay. Clin Chim Acta. 1981 117(3):251-8; and Ikeda et ah, Extraction and analysis of diagnostically useful proteins from formalin-fixed, paraffin- embedded tissue sections. J Histochem Cytochem. 1998 46(3): 397-403.

[0040] When the analyte of interest is a protein or peptide, the Liquid Tissue preparation is generally in a soluble liquid form and, surprisingly, is representative of the total protein content of the cells procured from the starting histopathologically processed biological sample. The preparation is used in any number of protein identification, analysis and expression assays described herein or known to the skilled practitioner.

[0041] When the analyte of interest is DNA, the Liquid Tissue preparation is in a soluble liquid form and is representative of the total DNA content of the cells procured from the starting histopathologically processed biological sample. The DNA extract can be placed in any number of DNA and/or RNA gene identification analyses and monitoring assays designed to determine variations in DNA including but not limited to the analysis of gene structure, genetic variability, single nucleotide polymorphisms and mutation analyses.

[0042] When the analyte of interest is RNA, the Liquid Tissue preparation is in a soluble liquid form and is representative of the total RNA content of the cells procured from the starting histopathologically processed biological sample. The RNA extract can be used in any suitable method of RNA and/or gene identification analysis and gene expression analysis and quantitative RT-PCR analysis

[0043] In certain embodiments it is useful to quantitate the detected analytes. This quantitation is performed by, e.g., isotopic labeling of the proteins; methods for isotope labelling include SILAC (stable isotope labelling with amino acids in cell culture), ICAT (isotope coded affinity tagging), and ITRAQ (isotope tags for relative and absolute quantitation). Alternatively, quantitation is performed by the use of AQUA peptides (See, Stemmann et al, Dual inhibition of sister chromatid separation at metaphase, Cell 107: 715- 726 (2001)). AQUA peptides are commercially available from Sigma-Aldrich (St. Louis, MO) and methods for their use are known in the art. See Gerber et al. Proc. Nat 'I Acad. Set USA. 100:6940 (2003). See also U.S.S.N. 09/839,884, filed April 20, 2001. The contents of these references are herein incorporated by reference in their entireties.

[0044] In certain embodiments the analyte detected in the Liquid Tissue preparation is compared with a reference analyte. A reference analyte may be any analyte obtained from

a subject known to have or not have the disease, condition, or syndrome. In certain embodiments, a reference analyte comprises a database. The database contains data on a plurality of analytes obtained from one or more subjects suffering from or at risk of developing one or more diseases or conditions. The database contains one or more data units corresponding to the one or more analytes, each of the data units including an identifier that includes two or more fields, each field for storing a value corresponding to one or more properties of the analytes (such as one or more mass spectral properties, frequency of appearance in various tumor types, and quantity of the protein in a plurality of tissues).

[0045] Liquid Tissue arrays

[0046] Multiple Liquid Tissue preparations obtained from multiple different histopathologically processed biological samples can be placed in an array format. A specific example of a high-throughput assay is the protein array. Protein arrays are highly parallel (multiplexed) and can be conducted in miniature (microarray). Protein arrays are quick, usually automated, highly sensitive, and capable of generating an enormous amount of data in a single experiment. The protein array is essentially a miniaturized version of the familiar

ELISA or dot blotting immunoassay. Similar to ELISA and dot blots, protein array results are usually obtained using optical detection methods, for example fluorescent detection. The data generated by a single protein array experiment often is so voluminous that specialized computer software is useful to read and analyze the data that is generated.

[0047] In one type of protein array analysis, specific capture reagents of known binding affinity, such as antibodies, are immobilized or spotted onto a support surface in a known positional manner, thus forming the protein array. The Liquid Tissue preparation is then contacted with the protein array. Because the immobilized binding proteins on the support surface have a specific affinity for an individual protein or marker, protein arrays are able to detect target molecules or marker proteins in the Liquid Tissue preparation. By immobilizing the specific capture reagents in known locations on the support surface, protein identification and the presence of marker proteins can be determined by x, y positional information. In addition, since differences in protein levels within complex samples can be easily measured, accurate quantitative differential analysis can also be performed. Detection is achieved through a number of methods known to those well versed in the art. Examples include but are not limited to: secondary antibodies in sandwich assays, direct labeling of

analytes, dual color labeling, mass spectrometry, surface plasmon resonance, and atomic force microscopy.

[0048] An alternative type of protein array analysis places tissue/cell lysates in an arrayed format, for example on a solid support. Multiple lysates from different samples may be arrayed on a single surface in a positionally identifiable manner. Reagents of known binding specificity, such as antibodies, that bind to target biomolecules or markers are then added. The main difference between the two major types of array analyses described herein is that in the first type of protein array, the expression of many different proteins across a single source of protein (a single cancer tissue for example) can be determined. In contrast, by the other type of protein array analysis, one can assay for the expression of one protein at a time across many different sources of protein (many different cases of cancer tissues for example). The lysate may be fractionated prior to immobilization on the array, and protein containing fractions of the lysates may be used to prepare the array. The skilled artisan will recognize also that other fractions of the lysates can be used to prepare arrays. For example, DNA and/or RNA containing fractions can be immobilized on suitable surfaces to prepare nucleic acid arrays.

[0049] Specific reagents of known binding affinity in protein arrays advantageously are antibodies or antibody fragments, but may also be single domain antibodies, engineered scaffolds, peptides, nucleic acid aptamers, small molecules such as drugs, for example, protein ligands, or other specific binding proteins known in the relevant art. Antibodies may be either polyclonal or monoclonal, or a portion or fragment of an antibody capable of binding antigenic sites, and are available from the usual commercial sources such as Sigma- Aldrich Co. (St. Louis, Mo.).

[0050] Protein array support surfaces include but are not limited to glass (such as slides), silicon, porous silicon, nylon, PVDF or nitrocellulose membranes and the like, or beads and are available from a variety of commercial sources. Alternatively, specialized chips have been developed for protein assays and are commercially available from, for example, Biotrove (Woburn, Mass.), Zyomyx (Hayward, Calif.) and Pontilliste (Mountain View, Calif.). [0051] Specific capture reagents or Liquid Tissue preparations are spotted or immobilized onto the support surface by a number of techniques familiar to those knowledgeable in the arts. Examples include, but are not limited to, robotic contact printing,

robotic non-contact printing, ink jetting, and piezoelectric spotting. If the capture reagent is a polymer that may be synthesized on a solid support, such as a nucleic acid, the capture reagent may be prepared directly on the support by, for example, photolithography. A number of automated commercial spotters are available from, for example, Packard Bioscience (Meriden, Conn.) and manual spotting equipment also is commercially available from, e.g. V & P Scientific (San Diego, Calif.).

[0052] Diagnosis of diseases or conditions

[0053] In order to diagnose a disease or condition in a subject, a biological sample is used to generate a Liquid Tissue preparation as described herein. Detection of one or more analytes in the preparation indicates that the subject as the disease or condition.

[0054] The subject is generally a mammalian subject, such as a human or non-human primate. However, also included as subjects are other non-human animals including mammals (such as rodents, sheep, dogs, cats, cows, and goats) amphibians (such as members of the Xenopus genus), and avians.

[0055] Diseases and conditions include any phenotype characterized by the presence of a given analyte. Examples include: cancer (such as prostate cancer, breast cancer, colorectal cancer, Hodgkin's disease, leukemias, lymphomas, metastases, myelomas, ovarian cancer, and lung cancer, inflammatory or degenerative disease such as Alzheimer's Disease, Parkinson's Disease and Amylotropic Lateral Sclerosis (ALS), cardiovascular diseases (and associated conditions and symptoms, including atherosclerosis; autoimmune myocarditis, chronic cardiac hypoxia, congestive heart failure, coronary artery disease, cardiomyopathy and cardiac cell dysfunction; diabetes, HIV infection (and associated conditions and symptoms, including degenerative responses, neurodegenerative responses, and HIV associated Hodgkin's Disease), osteoporosis; resistance to infectious diseases such as Leishmaniasis, Leprosy, Lyme Disease, Lyme Carditis, malaria, cerebral malaria, meningititis, tubulointestitial nephritis associated with malaria), which are caused by bacteria, viruses (e.g. cytomegalovirus, encephalitis, Epstein-Barr Virus, Human Immunodeficiency Virus, Influenza Virus) or protozoans (e.g., Plasmodium falciparum, trypanosomes); benign conditions such as benign prostatic hyperplasia, and preneoplastic conditions such as prostatic intraepithelial neoplasia.

EXAMPLES

[0056] The following examples are provided to further illustrate and to facilitate the understanding of the invention. These specific examples are intended to be illustrative of the invention and are not intended to be limiting.

[0057] Example 1: Preclinical diagnosis of prostate cancer using an antibody-based immunodetection assay analysis of Liquid Tissue preparation.

[0058] A plurality of Liquid Tissue preparations were prepared from a biological sample obtained from the prostate of a human subject. A first Liquid Tissue preparation was prepared from a region of the tissue containing prostate cancer (upper box), and a second Liquid Tissue preparation was prepared from a region of the tissue containing normal cells (lower box). The preparations were spotted onto a membrane, and differential levels of the protein Prostate Specific Antigen (PSA) were determined by a standard immunoassay. PSA is used in current clinical analyses as a diagnostic indicator of prostate cancer. As shown in the line graph of Figure 2, a high level of PSA was detected in the cancer region was observed, whereas no detectable level of PSA was seen in the normal region of the tissue.

[0059] A plurality of Liquid Tissue preparations were prepared from a biological sample obtained from the prostate of a human subject. A first Liquid Tissue preparation was prepared from a region of the tissue containing prostate cancer (upper left box), a second Liquid Tissue preparation was prepared from a region of the tissue containing benign prostate hyperplasia (BPH) (upper left box),and a third Liquid Tissue preparation was prepared from a region of the tissue containing normal cells (lower right box). Figure 3 illustrates the results of a mass spectrometry-based assay of the three Liquid Tissue preparations described above. Mass spectrometry protein expression results (shown as mass spectrometry base peak chromatograms and summarily indicated by an abbreviated protein expression list) indicate relatively equivalent expression on known prostate cancer biomarkers between both cancer and BPH while one protein was demonstrated to be differentially expressed between these two very different types of prostate disease and/or conditions. These results demonstrate that the protein GDF- 15 is useful used to give a distinguishing diagnosis between prostate cancer and BPH.

[0060] While this invention has been particularly shown and described with references to preferred embodiments thereof, it will be understood by those skilled in the art

that various changes in form and details may be made therein without departing from the spirit and scope of the invention as defined by the appended claims. Those skilled in the art will recognize or be able to ascertain using no more than routine experimentation, many equivalents to the specific embodiments of the invention described specifically herein. Such equivalents are intended to be encompassed in the scope of the claims.

Table 1.

GenBank Accession

Collagen alpha 3(VI) chain precursor Filamin A (Alpha-filamin) (Filamin 1) (Endothelial actin-binding protein) (ABP-280) (Nonmuscle filamin)

25 Myosin heavy chain, smooth muscle isoform (SMMHC) 22 Myosin heavy chain, cardiac muscle alpha isoform (MyHC-alpha) 20 Titin 19 Myosin heavy chain, skeletal muscle, adult 1 (Myosin heavy chain Ilx/d) (MyHC-IIx/d) 19 Desmin 16 Myosin heavy chain, cardiac muscle beta isoform (MyHC-beta) 14 Actin, aortic smooth muscle (Alpha-actin 2) 13 Serum albumin precursor 12 Vimentin 12 Alpha-actinin 2 (Alpha actinin skeletal muscle isoform 2) (F-actin cross linking protein) 12 Filamin C (Gamma-filamin) (Filamin 2) (Protein FLNc) (Actin-binding like protein) (ABP-L) (ABP-280-like protein)

P12109 11 Collagen alpha l(VI) chain precursor P12814 11 Alpha-actinin 1 (Alpha-actinin cytoskeletal isoform) (Non-muscle alpha-actinin 1) (F-actin cross linking protein)

10 Vinculin (Metavinculin) 9 Tropomyosin 1 alpha chain (Alpha-tropomyosin) 9 Hemoglobin beta chain 9 Undulin 1 (Fragment)

Lamin A/C (70 kDa lamin)

Tubulin beta-1 chain (OK/SW-cl.56)

Collagen alpha 2(VI) chain precursor

Desmuslin

ATP synthase beta chain, mitochondrial precursor (EC 3.6.3.14)

Laminin beta-2 chain precursor (S-laminin) (Laminin BIs chain)

Myosin heavy chain, skeletal muscle, adult 2 (Myosin heavy chain Ha) (MyHC-IIa)

Creatine kinase, M chain (EC 2.7.3.2) (M-CK)

Basement membrane-specific heparan sulfate proteoglycan core protein precursor (HSPG) (Perlecan) (PLC)

Transgelin (Smooth muscle protein 22-alpha) (SM22-alpha) (WS3-10) (22 kDa actin- binding protein)

P02647 Apolipoprotein A-I precursor (Apo-AI) (ApoA-I) P04792 Heat-shock protein beta-1 (HspBl) (Heat shock 27 kDa protein) (HSP 27) (Stress- responsive protein 27) (SRP27) (Estrogen-regulated 24 kDa protein) (28 kDa heat shock protein)

P05976 Myosin light chain 1, skeletal muscle isoform (MLClF) (Al catalytic) (Alkali myosin light chain 1)

Annexin A2 (Annexin II) (Lipocortin π) (Calpactin I heavy chain) (Chromobindin 8) (p36) (Protein I) (Placental anticoagulant protein IV) (PAP-IV)

5 Elastin precursor (Tropoelastin)

5 Tenascin X precursor (TN-X) (Hexabrachion-like) 5 Myosin heavy chain, nonmuscle type A (Cellular myosin heavy chain, type A)

(Nonmuscle myosin heavy chain-A) (NMMHC-A)

P51884 5 Lumican precursor (Keratan sulfate proteoglycan lumican) (KSPG lumican) P68366 5 Tubulin alpha-1 chain (Alpha-tubulin 1) (Testis-specific alpha-tubulin) (Tubulin H2-aIpha)

Laminin alpha-5 chain precursor

Hemoglobin alpha chain

Tropomyosin beta chain (Tropomyosin 2) (Beta-tropomyosin)

Laminin gamma- 1 chain precursor (Laminin B2 chain)

Creatine kinase, B chain (EC 2.7.3.2) (B-CK)

Mimecan precursor (Osteoglycin) (Osteoinductive factor) (OIF)

ATP synthase alpha chain, mitochondrial precursor (EC 3.6.3.14)

Titin (Fragment)

Talin 1

Heat-shock protein beta-6 (HspB6) (Heat-shock 20 kDa like-protein p20)

Complement C3 precursor [Contains: C3a anaphylatoxin]

Ig gamma-1 chain C region

Myoglobin

Collagen alpha 1(1) chain precursor

Fibronecu ^' n precursor (FN) (Cold-insoluble globulin) (CIG)

Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Muscle-type aldolase) (Lung cancer antigen NY-LU-I)

P04083 Annexin Al (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin 9) (P35) (Phospholipase A2 inhibitory protein)

Glyceraldehyde-3-phosphate dehydrogenase, liver (EC 1.2.1.12) (GAPDH) Gelsolin precursor (Actin-depolymerizing factor) (ADF) (Brevin) (AGEL) Tropomyosin alpha 3 chain (Tropomyosin 3) (Tropomyosin gamma) (hTM5) Heat shock 70 kDa protein 1 (HSP70.1) (HSP70-1/HSP70-2) Collagen alpha 2(1) chain precursor Myosin light polypeptide 3 (Myosin light chain 1, slow-twitch muscle B/ventricular isoform) (MLClSB) (Ventricular/slow twitch myosin alkali light chain) (Cardiac myosin light chain- I) (CMLCl)

P08758 Annexin A5 (Annexin V) (Lipocortin V) (Endonexin II) (Calphobindin I) (CBP-I) (Placental anticoagulant protein I) (PAP-I) (PP4) (Thromboplastin inhibitor) (Vascular anticoagulant-alpha) (VAC-alpha) (Anchorin CII)

P11217 3 Glycogen phosphorylase, muscle form (EC 2.4.1.1) (Myophosphorylase)

P13645 3 Keratin, type I cytoskeletal 10 (Cytokeratin 10) (KlO) (CK 10)

P14618 3 Pyruvate kinase, isozymes M1/M2 (EC 2.7.1.40) (Pyruvate kinase muscle isozyme) (Cytosolic thyroid homione-binding protein) (CTHBP) (THBPl)

P16615 3 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 (EC 3.6.3.8) (Calcium pump 2) (SERCA2) (SR Ca(2+)-ATPase 2) (Calcium-transporting ATPase sarcoplasmic reticulum type, slow twitch skeletal muscle isoform) (Endoplasmic reticulum class 1/2 Ca(2+) ATPase)

P20929 Nebulin

P28001 3 Histone H2A.a (H2A/a) (H2A.2)

P51888 3 Prolargin precursor (Proline-arginine-rich end leucine-rich repeat protein)

P60174 3 Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)

P60709 3 Actin, cytoplasmic 1 (Beta-actin)

P62805 3 Histone H4

QQ0872 3 Myosin-binding protein C, slow-type (Slow MyBP-C) (C-protein, skeletal muscle slow- isoform)

Q05682 3 Caldesmon (CDM)

015124 3 Phosphoglucomutase-like protein 5 (Phosphoglucomutase-related protein) (PGM-RP) (Aciculin)

015149 3 Plectin 1 (PLTN) (PCN) (Hemidesmosomal protein 1) (HDl)

015746 3 Myosin light chain kinase, smooth muscle and non-muscle isozymes (EC 2.7.1.117) (MLCK) [Contains: Telokin (Kinase related protein) (KRP)]

Q6NZI2 3 Polymerase I and transcript release factor (PTRF protein) (FKSG13 protein)

Q96C67 3 COL 14Al protein

014904 2 Wnt-9a protein precursor (Wnt-14)

014983 2 Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCAl) (SR Ca(2+)-ATPase 1) (Calcium-transporting ATPase sarcoplasmic reticulum type, fast twitch skeletal muscle isoform) (Endoplasmic reticulum class 1/2 Ca(2+) ATPase)

ADAMTS-2 precursor (EC 3.4.24.14) (A disintegrin and metalloproteinase with thrombospondin motifs 2) (ADAM-TS 2) (ADAM-TS2) (Procollagen I/TI amino- propeptide processing enzyme) (Procollagen I N-proteinase) (PC I-NP) (Procollagen N- endopeptidase) (pNPI)

095613 2 Pericentrin 2 (Pericentral B) (Kendrin)

P00338 2 L-lactate dehydrogenase A chain (EC 1.1.1.27) (LDH-A) (LDH muscle subunit) (LDH-M)

P01834 2 Ig kappa chain C region

P01876 2 Ig alpha- 1 chain C region

P02511 2 Alpha crystallin B chain (Alpha(B)-crystallin) (Rosenthal fiber component) (Heat-shock protein beta-5) (HspB5)

P02671 2 Fibrinogen alpha/alpha-E chain precursor [Contains: Fibrinopeptide A]

P02766 2 Transthyretin precursor (Prealbumin) (TBPA) (TTR) (ATTR)

P02787 2 Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1-metal binding globulin) (PRO1400)

Keratin, type II cytoskeletal 1 (Cytokeratin 1) (Kl) (CK 1) (67 kDa cytokeratin) (Hair alpha protein)

P05787 2 Keratin, type II cytoskeletal 8 (Cytokeratin 8) (K8) (CK 8)

P06702 2 Calgranulin B (Migration inhibitory factor-related protein 14) (MRP- 14) (P 14) (Leukocyte Ll complex heavy chain) (SlOO calcium-binding protein A9) (Calprotectin LlH subunit)

P07451 2 Carbonic anhydrase HI (EC 4.2.1.1) (Carbonate dehydratase πi) (CA-III)

P07737 2 Profilin-1 (Profilin I)

P08133 2 Annexin A6 (Annexin VI) (Lipocortin VI) (P68) (P70) (Protein HI) (Chromobindin 20) (67 kDa calelectrin) (Calphobindin-II) (CPB-H)

P10916 2 Myosin regulatory light chain 2, ventricular/cardiac muscle isoform (MLC-2) (MLC-2v) P14649 2 Myosin light chain 1, slow-twitch muscle A isoform (MLC lsa) (Alkali)

P17174 2 Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transaminase-1)

P17540 2 Creatine kinase, sarcomeric mitochondrial precursor (EC 2.7.3.2) (S-MtCK) (Mib-CK) (Basic-type mitochondrial creatine kinase)

P21810 Biglycan precursor (Bone/cartilage proteoglycan T) (PG-Sl) P24844 Myosin regulatory light chain 2, smooth muscle isoform (Myosin RLC) (LC20) P29536 Leiomodin 1 (Leiomodin, muscle form) (64 kDa autoantigen Dl) (64 kDa autoantigen ID) (64 kDa autoantigen 1D3) (Thyroid-associated ophthalmopathy autoantigen) (Smooth muscle leiomodin) (SM-Lmod)

P3S555 Fibrillin 1 precursor P35580 Myosin heavy chain, nonmuscle type B (Cellular myosin heavy chain, type B) (Nonmuscle myosin heavy chain-B) (NMMHC-B)

Malate dehydrogenase, cytoplasmic (EC 1.1.1.37)

Calponin 1 (Calponin Hl, smooth muscle) (Basic calponin)

Heat shock-related 70 IcDa protein 2 (Heat shock 70 kDa protein 2)

Troponin C, slow skeletal and cardiac muscles (TN-C)

Actin, alpha skeletal muscle (Alpha-actin 1)

Tubulin beta-2 chain A-kinase anchor protein 12 (A-kinase anchor protein 250 kDa) (AKAP 250) (Myasthenia gravis autoantigen gravin) (Desmoyokin) (Fragments)

and a half LIM domains protein 1)

Tubulin alpha-2 chain (Alpha-tubulin 2) Nidogen-2 precursor (NID-2) (Osteonidogen) Myosin light chain 2 Transforming growth factor-beta induced protein IG-H3 precursor (Beta IG-H3) (Kerato- epithelin) (RGD-containing collagen associated protein) (RGD-CAP)

Mitogen-activated protein kinase 6 (EC 2.7.1.37) (Extracellular signal-regulated kinase 3) (ERK-3) (MAP kinase isoform p97) (p97-MAPK)

O6DV90 2 Sarcomeric tropomyosin kappa

Q6P0O1 2 Alpha 2 type VI collagen, isofotm 2C2

O96RL7 2 Vacuolar protein sorting 13A (Chorein) (Chorea-acanthocytosis protein)

Q9BVJ6 2 UTP14, U3 small nucleolar ribonucleoprotein, homolog A

O9BX66 2 Sorbin and SH3 domain-containing protein 1 (Ponsin) (c-Cbl-associated protein) (CAP) (SH3 domain protein 5) (SH3P12)

O9NO75 2 HEF-like protein

O9NZN4 2 EH-domain containing protein 2

Q9Y4Z4 2 ZASP protein (Fragment)

000232 1 26S proteasome non-ATPase regulatory subunit 12 (26S proteasome regulatory subunit _P 55)

000260 1 Collagen type XIV precursor (Fragment)

000281 1 D9 splice variant A

000295 1 Tubby related protein 2 (Tubby-like protein 2)

000321 1 Ets translocation variant 2 (Ets-related protein 71 )

000555 1 Voltage-dependent P/Q-type calcium channel alpha-1 A subunit (Voltage-gated calcium channel alpha subunit Cav2.1) (Calcium channel, L type, alpha-1 polypeptide isoform 4) (Brain calcium channel I) (BI)

014497 1 SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin subfamily F member 1 (SWI-SNF complex protein p270) (B 120)

1 FrpHE

1 Calsequestrin, cardiac muscle isoform precursor (Calsequestrin 2)

1 KIAA0308 protein (Fragment)

1 PTPLl -associated RhoGAP 1 N-glycosylase/DNA lyase [Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-

(apurinic or apyrimidinic site) lyase (EC 4.2.99.18) (AP lyase)]

043167 1 Zinc finger and BTB domain containing protein 24 (Zinc finger protein 450) 043174 1 Cytochrome P45026 (EC 1.14.-.-) (Retinoic acid-metabolizing cytochrome) (P450 retinoic acid-inactivating 1) (P450RAI) (hP450RAI) (Retinoic acid 4-hydroxylase)

1 Paired box protein Pax-4

1 Alpha-actinin 4 (Non-muscle alpha-actinin 4) (F-actin cross linking protein) 1 Putative pre-mRNA splicing factor RNA helicase (ATP-dependent RNA helicase #3)

(DEAH-box protein 16)

Q60232 1 Sjogren's syndrome/scleroderma autoantigen 1 (Autoanύ ^' gen p27) Q60279 1 KIAA0527 protein (Fragment) O60423 1 Potential phospholipid-transporting ATPase IK (EC 3.6.3.1) (ATPase class I type 8B member 3)

1 Long-chain-fatty-acid~CoA ligase 4 (EC 6.2.1.3) (Long-chain acyl-CoA synthetase 4)

(LACS 4)

Q60662 1 Kelch repeat and BTB domain containing protein 10 (Kelch-related protein 1) (Kel-like protein 23) (Sarcosin)

Q75019 1 Leukocyte immunoglobulin-like receptor subfamily A member 1 precursor (Leucocyte immunoglobulin-like receptor 6) (LIR-6) (CD85i antigen)

1 KIAA0451 protein (Fragment)

1 KIAA0633 protein (Fragment)

1 KIAA0657 protein (Fragment) 1 Filamin B (FLN-B) (Beta-fϊlamin) (Actin-binding like protein) (Thyroid autoantigen)

(Truncated actin-binding protein) (Truncated ABP) (ABP-280 homolog) (ABP-278) (Filamin 3) (Filamin homolog 1) (FhI)

1 Zinc finger protein (Fragment)

1 KE04p (Chromosome 10 open reading frame 69) (Novel protein) (FLJ32012) 1 U5 small nuclear ribonucleoprotein 200 kDa helicase (EC 3.6.1.-) (U5 snRNP-specifϊc 200 kDa protein) (U5-200KD) (Activating signal cointegrator 1 complex subunit 3-like 1)

factor 3 subunit 1 (eIF-3 alpha) (eIF3 p35) (eIF3j) 3 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 3)

075891 1 10-formyltetrahydrofolate dehydrogenase (EC 1.5.1.6) (10-FTHFDH)

075912 1 Diacylglycerol kinase, iota (EC 2,7.1.107) (Diglyceride kinase) (DGK-iota) (DAG kinase iota)

076064 1 Ubiquitin ligase protein RNF8 (EC 6.3.2.-) (RING finger protein 8)

094788 1 Aldehyde dehydrogenase 1A2 (EC 1.2.1.3) (Retinaldehy de-specific dehydrogenase type 2) (RALDH(II)) (RALDH-2)

094807 1 Telomerase transcriptase (Fragment)

094818 1 Nucleolar protein 4 (Nucleolar-Iocalized protein) (HRIHFB2255)

094819 1 Protein KIAA0711

094851 1 Protein MICAL-2

094863 1 KIAA0763 protein (Fragment)

094921 1 Serine/threonine-protein kinase PFTAIRE-I (EC 2.7.1.37)

094936 1 KIAA0853 protein (Fragment)

095153 1 Peripheral-type benzodiazepine receptor-associated protein 1 (PRAX-I) (Peripheral benzodiazepine receptor interacting protein) (PBR-IP) (RIM binding protein 1) (RIM- BPl)

095185 1 Netrin receptor UNC5C precursor (Unc-5 homolog C) (Unc-5 homolog 3)

095218 1 Zinc finger protein 265 (Zinc finger, splicing)

095477 1 ATP-binding cassette, sub-family A, member 1 (ATP-binding cassette transporter 1) (ATP-binding cassette 1) (ABC-I) (Cholesterol efflux regulatory protein)

Amyloid beta A4 precursor protein-binding family B member 3 (Fe65-like protein 2) (Fe65L2)

095714 1 HERC2 protein

095872 1 Protein BAT4 (HLA-B-associated transcript 4) (G5)

P00352 1 Aldehyde dehydrogenase IAl (EC 1.2.1.3) (Aldehyde dehydrogenase, cytosolic) (ALDH class 1) (Retinal dehydrogenase 1) (ALHDII) (ALDH-El)

P00354 1 GIy ceraldehyde-3-phosphate dehydrogenase, muscle (EC 1.2.1.12) (GAPDH)

P00441 1 Superoxide dismutase [Cu-Zn] (EC 1.15.1.1)

P00450 1 Ceruloplasmin precursor (EC 1.16.3.1) (Ferroxidase)

P00747 1 Plasminogen precursor (EC 3.4.21.7) [Contains: Angiostatin]

P01009 1 Alpha- 1 -antitrypsin precursor (Alpha-1 protease inhibitor) (Alpha-1-antiproteinase) (PRO0684/PRO2209)

PO1023 1 Alpha-2-macroglobulin precursor (Alpha- 2-M)

PO1028 1 Complement C4 precursor [Contains: C4a anaphylatoxin; C4b]

PO1620 1 Ig kappa chain V-III region SIE

PO1737 1 T-cell receptor alpha chain V region PYl 4 precursor

PO1765 1 Ig heavy chain V-III region TIL

P01780 1 Ig heavy chain V-III region JON

PO1842 1 Ig lambda chain C regions

P02042 1 Hemoglobin delta chain

P02461 1 Collagen alpha l(III) chain precursor

P02533 1 Keratin, type I cytoskeletal 14 (Cytokeratin 14) (K14) (CK 14)

P02585 1 Troponin C, skeletal muscle

P02679 1 Fibrinogen gamma chain precursor (PRO2061)

P02760 1 AMBP protein precursor [Contains: Alpha-1-microglobιilin (Protein HC) (Complex- forming glycoprotein heterogeneous in charge) (Alpha- 1 microglycoprotein); Inter-alpha- trypsin inhibitor light chain (ITI-LC) (Bikunin) (HI-30)]

Hemopexin precursor (Beta-lB-glycoprotein) Ferritin light chain (Ferritin L subunit) Vitronectin precursor (Serum spreading factor) (S-protein) (V75) [Contains: Vitronectin V65 subunit; Vitronectin VlO subunit; Somatomedin B]

P04179 1 Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)

P04196 1 Histidine-rich glycoprotein precursor (Histidine-proline rich glycoprotein) (HPRG)

P04220 1 Ig mu heavy chain disease protein (BOT)

P05155 1 Plasma protease Cl inhibitor precursor (Cl Inh) (Cllnh)

P06733 1 Alpha enolase (EC 4.2.1.11) (2-ρhospho-D-glycerate hydro-lyase) (Non-neural enolase) (NNE) (Enolase 1) (Phosphopyruvate hydratase) (C-myc promoter-binding protein) (MBP-I) (MPB-I) (Plasminogen-binding protein)

P06737 1 Glycogen phosphorylase, liver form (EC 2.4.1.1)

P06744 1 Glucose-6-phosphate isomerase (EC 5.3.1.9) (GPI) (Phosphoglucose isomerase) (PGI) (Phosphohexose isomerase) (PHI) (Neuroleukin) (NLK) (Sperm antigen-36) (SA-36)

P07195 1 L-lactate dehydrogenase B chain (EC 1.1.1.27) (LDH-B) (LDH heart subunit) (LDH-H)

P07288 1 Prostate specific antigen precursor (EC 3.4.21.77) (PSA) (Gamma-seminoprotein) (Kallikrein 3) (Semenogelase) (Seminin) (P-30 antigen)

P07358 1 Complement component C8 beta chain precursor

07602 Proactivator polypeptide precursor [Contains: Saposin A (Protein A); Saposin B (Sphingolipid activator protein 1) (SAP-I) (Cerebroside sulfate activator) (CSAct) (Dispersin) (Sulfatide/GMl activator); Saposin C (Co-beta-glucosidase) (Al activator) (Glucos

P07900 1 Heat shock protein HSP 90-alpha (HSP 86)

P08238 1 Heat shock protein HSP 90-beta (HSP 84) (HSP 90)

P08572 1 Collagen alpha 2(IV) chain precursor

P09211 1 Glutathione S-transferase P (EC 2.5.1.18) (GST class-pi) (GSTPl-I) P09382 1 Galectin-1 (Beta-galactoside-binding lectin L-14-I) (Lactose-binding lectin 1) (S-Lac lectin 1) (Galaptin) (14 kDa lectin) (HPL) (HBL)

Glutathione S-transferase Mu 1 (EC 2.5.1.18) (GSTMl-I) (GST class-mu 1) (GSTMIa- Ia) (GSTMlb-lb) (HB subunit 4) (GTH4)

P09525 Annexin A4 (Annexin IV) (Lipocortin IV) (Endonexin I) (Chromobindin 4) (Protein II) (P32.5) (Placental anticoagulant protein II) (PAP-II) (PP4-X) (35-beta calcimedin) (Carbohydrate-binding protein P33/P41) (P33/41)

2',3'-cyclic-nucleotide 3'-phosphodiesterase (EC 3.1.4.37) (CNP) (CNPase)

Interferon-induced protein with tetratricopeptide repeats 2 (IFIT- 2) (Interferon-induced 54 IdDa protein) (IFI-54K) (ISG-54 K)

P09972 Fructose-bisphosphate aldolase C (EC 4.1.2.13) (Brain-type aldolase) P10155 60-kDa SS-A/Ro ribonucleoprotein (60 kDa Ro protein) (60 kDa ribonucleoprotein Ro) (RoRNP) (Ro 60 kDa autoantigen) (Sjogren syndrome type A antigen) (SS-A) (Sjogren syndrome antigen A2)

P10909 Clusterin precursor (Complement-associated protein SP-40,40) (Complement cytolysis inhibitor) (CLI) (NA1/NA2) (Apolipoprotein J) (Apo-J) (Testosterone-repressed prostate message 2) (TRPM-2)

Pl 1021 1 78 kDa glucose-regulated protein precursor (GRP 78) (Immunoglobulin heavy chain binding protein) (BiP) (Endoplasmic reticulum lumenal Ca(2+) binding protein grp78)

Pl 1055 1 Myosin heavy chain, fast skeletal muscle, embryonic (Muscle embryonic myosin heavy chain) (SMHCE)

Pl 1142 Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8) Pl 1474 Steroid hormone receptor ERRl (Estrogen-related receptor, alpha) (ERR-alpha) (Estrogen receptor-like 1)

Pl 1498 Pyruvate carboxylase, mitochondrial precursor (EC 6.4.1.1) (Pyruvic carboxylase) (PCB)

Pl 2273 Prolactin-inducible protein precursor (Secretory actin-binding protein) (SABP) (Gross cystic disease fluid protein 15) (GCDFP-15) (gpl7)

Keratin, type I cytoskeletal 13 (Cytokeratin 13) (K13) (CK 13) Keratin, type II cytoskeletal 5 (Cytokeratin 5) (K5) (CK 5) (58 kDa cytokeratin) Troponin T, slow skeletal muscle isoforms (Slow skeletal muscle troponin T) Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoceptor) Nidogen precursor (Entactin) Alcohol dehydrogenase [NADP+] (EC 1.1.1.2) (Aldehyde reductase) (Aldo-keto reductase family 1 member Al)

Ezrin (p81) (Cytovillin) (ViIHn 2)

Zinc finger protein 40 (Human immunodeficiency virus type I enhancer-binding protein 1) (HIV-EPl) (Major histocompatibility complex binding protein 1) (MBP-I) (Positive regulatory domain π binding factor 1) (PRDII-BFl)

Erythroid transcription factor (GATA-I) (Eryfl) (GF-I) (NF-El)

Atrial natriuretic peptide receptor A precursor (ANP-A) (ANPRA) (GC-A) (Guanylate cyclase) (EC 4.6.1.2) (NPR-A) (Atrial natriuretic peptide A-type receptor)

Zinc finger protein ZFP-36 (Fragment) Homeobox protein Hox-B4 (Hox-2F) (Hox-2.6) Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) (12-LOX) (Platelet-type lipoxygenase 12)

Phosphoglycerate mutase 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme B) (PGAM-B) (BPG-dependent PGAM 1)

Neural-cadherin precursor (N-cadherin) (Cadherin-2) Myosin regulatory light chain 2, nonsarcomeric (Myosin RLC) Casein kinase π, alpha' chain (CK II) (EC 2.7.1.37) Bile-salt-activated lipase precursor (EC 3.1.1.3) (EC 3.1.1.13) (BAL) (Bile-salt-stimulated lipase) (BSSL) (Carboxyl ester lipase) (Sterol esterase) (Cholesterol esterase) (Pancreatic lysophospholipase)

Annexin A7 (Annexin VII) (Synexin) (OK/SW-cl.95)

Tryptase beta-2 precursor (EC 3.4.21.59) (Tryptase 2) (Tryptase H)

Ras-related protein Rab-5A

Collagen alpha l(V) chain precursor Glutathione S-transferase Mu 3 (EC 2.5.1.18) (GSTM3-3) (GST class-mu 3) (hGSTM3-3)

P21291 1 Cysteine and glycine-rich protein 1 (Cysteine-rich protein 1) (CRPl) (CRP)

P21359 1 Neurofibromin (Neurofibromatosis-related protein NF-I) [Contains: Neurofibromin truncated]

P21817 1 Ryanodine receptor 1 (Skeletal muscle-type ryanodine receptor) (RyRl) (RYR-I) (Skeletal muscle calcium release channel)

Lactoperoxidase precursor (EC 1.11.1.7) (LPO) (Salivary peroxidase) (SPO)

Ubiquinol-cytochrome-c reductase complex core protein 2, mitochondrial precursor (EC 1.10.2.2) (Complex III subunit II)

P23142 Fibulin-1 precursor P23468 Receptor-type tyrosine-protein phosphatase delta precursor (EC 3.1.3.48) (Protein-tyrosine phosphatase delta) (R-PTP-delta)

P23528 Cofilin, non-muscle isoform (Cofilin-1) (18 kDa phosphoprotein) (ρl8) P24752 Acetyl-CoA acetyllransferase, mitochondrial precursor (EC 2.3.1.9) (Acetoacetyl-CoA thiolase) (T2)

Alpha- ID adrenergic receptor (Alpha lD-adrenoceptor) (Alpha lD-adrenoreceptor) (Alpha- IA adrenergic receptor) (Alpha adrenergic receptor Ia)

P25311 I Zinc-alpha-2-glycoprotein precursor (Zn-alpha-2-glycoprotein) (Zn-alpha-2-GP)

P25940 1 Collagen alpha 3(V) chain precursor

P26196 1 Probable ATP-dependeπt RNA helicase p54 (Oncogene RCK) (DEAD-box protein 6)

P26640 1 Valyl-tRNA synthetase 2 (EC 6.1.1.9) (Valine-tRNA ligase 2) (VaIRS 2) (G7a)

P27105 1 Erythrocyte band 7 integral membrane protein (Stomatin) (Protein 7.2b)

P27708 1 CAD protein [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate carbamoyltransferase (EC 2.1.3.2); Dihydroorotase (EC 3.5.2.3)]

P27824 1 Calnexin precursor (Major histocompatibility complex class I antigen-binding protein p88) (p90) (IP90)

P27986 1 Phosphatidylinositol 3-kinase regulatory alpha subunit (PI3-kinase p85-alpha subunit) (PtdIns-3-kinase p85-alpha) (PI3K)

P28289 1 Tropomodulin 1 (Erythrocyte tropomodulin) (E-Tmod)

P28331 1 NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Complex 1-75Kd) (CI-75Kd)

P28749 1 Retinoblastoma-like protein 1 (107 kDa retinoblastoma-associated protein) (PRBl) (P107)

P30041 1 Peroxiredoxin 6 (EC 1.11.1.-) (Antioxidant protein 2) (1-Cys peroxiredoxin) (1-Cys PRX) (Acidic calcium-independent phospholipase A2) (EC 3.1.1.-) (aiPLA2) (Non-selenium glutathione peroxidase) (EC 1.11.1.7) (NSGPx) (24 kDa protein) (Liver 2D page spot 40

P30048 Thioredoxin-dependent peroxide reductase, mitochondrial precursor (EC 1.11.1.-) (Peroxiredoxin 3) (Antioxidant protein 1) (AOP-I) (MER5 protein homolog) (HBC189) (PRX III)

1 ATP synthase delta chain, mitochondrial precursor (EC 3.6.3.14)

1 UMP-CMP kinase (EC 2.7.4.14) (Cytidylate kinase) (Deoxycytidylate kinase) (Cytidine monophosphate kinase)

P30086 1 Phosphatidylethanolamine-binding protein (PEBP) (Prostatic binding protein) (HCNPpp)

(Neuropolypeptide h.3) (Raf kinase inhibitor protein) (RKIP) [Contains: Hippocampal cholinergic neurostimulating peptide (HCNP)]

P30101 1 Protein disulfide-isomerase A3 precursor (EC 5.3.4.1) (Disulfide isomerase ER-60)

(ERp60) (58 kDa microsomal protein) (p58) (ERp57) (58 kDa glucose regulated protein)

P30443 1 HLA class I histocompatibility antigen, A-I alpha chain precursor (MHC class I antigen

A* l)

P30518 1 Vasopressin V2 receptor (Renal-type arginine vasopressin receptor) (Antidiuretic hormone receptor) (AVPR V2)

P3053Q 1 Tyrosine-protein kinase receptor UFO precursor (EC 2.7.1.112) (AXL oncogene)

P30532 1 Neuronal acetylcholine receptor protein, alpha-5 chain precursor

P30712 1 Glutathione S-transferase theta 2 (EC 2.5.1.18) (GST class-theta 2)

P30837 1 Aldehyde dehydrogenase X, mitochondrial precursor (EC 1.2.1.3) (ALDH class 2)

P31025 1 Von Ebner's gland protein precursor (VEG protein) (Tear prealbumin) (TP) (Tear lipocalin) (Lipocalin 1)

Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (EC 1.3.5.1) (Fp) (Flavoprotein subunit of complex II)

P31150 1 Rab GDP dissociation inhibitor alpha (Rab GDI alpha) (GDI-I) (XAP-4) (Oligophrenin 2)

P31323 1 cAMP-dependent protein kinase type II-beta regulatory subunit

P32119 1 Peroxiredoxin 2 (EC 1.11.1.-) (Thioredoxin peroxidase 1) (Thioredoxin-dependent peroxide reductase 1) (Thiol-specific antioxidant protein) (TSA) (PRP) (Natural killer cell enhancing factor B) (NKEF-B)

P32242 1 Homeobox protein OTXl

P32243 1 Homeobox protein 0TX2

P33981 1 Dual specificity protein kinase TTK (EC 2.7.1.-) (Phosphotyrosine picked threonine kinase) (PYT)

Trypsin III precursor (EC 3.4.21.4) (Brain trypsinogen) (Mesotrypsinogen) (Trypsin IV)

P35237 Placental thrombin inhibitor (Cytoplasmic antiproteinase) (CAP) (Protease inhibitor 6) (PI-6)

P35270 1 Sepiapterin reductase (EC 1.1.1.153) (SPR)

P35527 1 Keratin, type I cytoskeletal 9 (Cytokeratin 9) (K9) (CK 9)

P35908 1 Keratin, type II cytoskeletal 2 epidermal (Cytokeratin 2e) (K2e) (CK 2e)

P36542 1 ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)

P37802 1 Transgelin-2 (SM22-alpha homolog)

P39059 1 Collagen alpha l(XV) chain precursor

P39060 1 Collagen alpha 1 (XVIII) chain precursor [Contains: Endostatin]

P40225 1 Thrombopoietin precursor (Megakaryocyte colony stimulating factor) (Myeloproliferative leukemia virus oncogene ligand) (C-mpl ligand) (ML) (Megakaryocyte growth and development factor) (MGDF)

P40818 1 Ubiquitin carboxyl-terminal hydrolase 8 (EC 3.1.2.15) (Ubiquitin thiolesterase 8) (Ubiquitin-specific processing protease 8) (Deubiquitinating enzyme 8) (hUBPy)

P40939 1 Trifunctional enzyme alpha subunit, mitochondrial precursor (TP-alpha) (78 kDa gastrin- binding protein) [Includes: Long-chain enoyl-CoA hydratase (EC 4.2.1.17); Long chain 3- hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35)]

P41219 1 Peripherin

P42331 1 Rho-GTPase-activating protein 25

P42357 1 Histidine ammonia-lyase (EC 4.3.1.3) (Histidase)

P42658 1 Dipeptidyl aminopeptidase-like protein 6 (Dipeptidylpeptidase VI) (Dipeptidylpeptidase 6) (Dipeptidyl peptidase IV like protein) (Dipeptidyl aminopeptidase-related protein) (DPPX)

Carnitine O-acetyltransferase (EC 2.3.1.7) (Carnitine acetylase) (CAT)

P43250 1 G protein-coupled receptor kinase 6 (EC 2.7.1.-) (G protein-coupled receptor kinase GRK6)

P48066 1 Sodium- and chloride-dependent GABA transporter 3

P48740 1 Complement-activating component of Ra-reactive factor precursor (EC 3.4.21.-) (Ra- reactive factor serine protease plOO) (RaRF) (Mannan-binding lectin serine protease 1) (Mannose-binding protein associated serine protease) (MASP-I)

P48995 1 Short transient receptor potential channel 1 (TrpCl) (TRP-I protein)

P49247 1 Ribose-5-phosphate isomerase (EC 5.3.1.6) (Phosphoriboisomerase)

P49454 1 CENP-F kinetochore protein (Centromere protein F) (Mitosin) (AH antigen)

P49746 1 Thrombospondin 3 precursor

P49748 1 Acyl-CoA dehydrogenase, very-long-chain specific, mitochondrial precursor (EC 1.3.99.-) (VLCAD)

P50461 Cysteine and glycine-rich protein 3 (Cysteine-rich protein 3) (CRP3) (LIM domain protein, cardiac) (Muscle LIM protein)

P51530 1 DNA2-like homolog (DNA replication helicase-like homolog) (Fragment)

P5153I 1 Possible global transcription activator SNF2L2 (SNF2-alpha) (SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily A member 2)

P51610 1 Host cell factor Cl (HCF) (VP16 accessory protein) (HFCl) (VCAF) (CFF)

P51828 1 Adenylate cyclase, type VII (EC 4.6.1.1) (ATP pyrophosphate-lyase 7) (Adenylyl cyclase 7)

P52179 1 Myomesin 1 (190 kDa titin-associated protein) (190 kDa connectin-associated protein)

P52306 1 Rapl GTPase-GDP dissociation stimulator 1 (SMG P21 stimulatory GDP/GTP exchange protein) (SMG GDS protein) (Exchange factor smgGDS)

P52799 Ephrin-B2 precursor (EPH-related receptor tyrosine kinase ligand 5) (LERK-5) (HTK ligand) (HTK-L)

P52907 F-actin capping protein alpha-1 subunit (CapZ alpha-1) P53007 Tricarboxylate transport protein, mitochondrial precursor (Citrate transport protein) (CTP) (Tricarboxylate carrier protein)

P53671 LM domain kinase 2 (EC 2.7.1.-) (LIMK-2) P54296 Myomesin 2 (M-protein) (165 kDa titin-associated protein) (165 kDa connectin-associated protein)

Type III iodothyronine deiodinase (EC 1.97.1.11) (Type-Ill 5'deiodinase) (DIOIII) (Type 3 DI) (5DIII)

P55083 1 Microfibril-associated glycoprotein 4 precursor

P55786 1 Puromycin-sensitive aminopeptidase (EC 3.4.11.-) (PSA)

P55854 1 Ubiquitin-like protein SMT3A

P56704 1 Wnt-3a protein precursor

P58658 1 Protein C21orf63 precursor (Protein PRED34) (SUE21) (UNQ2504/PRO5993)

P60323 1 Nanos homolog 3

P60413 1 Keratin-associated protein 10-12 (Keratin-associated protein 10.12) (High sulfur keratin- associated protein 10.12) (Keratin-associated protein KAP 18- 12) (Keratin-associated protein 18.12)

Myosin light polypeptide 6 (Myosin light chain alkali 3) (Myosin light chain 3) (MLC-3) (LC17)

P60981 Destrin (Actin-depolymerizing factor) (ADF) P61158 Actin-like protein 3 (Actin-related protein 3)

P61764 Syntaxin binding protein 1 (Unc-18 homolog) (Unc-18A) (Unc-18-1) (N-Secl) (p67) P61978 Heterogeneous nuclear ribonucleoprotein K (hnRNP K) (Transformation up-regulated nuclear protein) (TUNP) 1) (KCIP-I)

(H2B/k) (H2B/1) IA) (Ras-related protein Krev-1)

kinase C inhibitor protein-1) (KCIP-I) (Hemoglobin gamma-A chain) (Hb F Agamma)

catalytic subunit (EC 2.7.1.37) (DNA-PKcs) (DNPKl)

Crumbs protein homolog 1 precursor

Fibulin-2 precursor

Polycystin 1 precursor (Autosomal dominant polycystic kidney disease protein 1) Calcium-transporting ATPase type 2C, member 1 (EC 3.6.3.8) (ATPase 2Cl) (ATP- dependent Ca(2+) pump PMRl) (HUSSY-28)

Nuclear factor NF-kappa-B pl00/p49 submits (DNA-binding factor KBF2) (H2TF1) (Lymphocyte translocation chromosome 10) (Oncogene Lyt-10) (LytlO) [Contains: Nuclear factor NF-kappa-B p52 subunit] nuclear ribonucleoprotein U (hnRNP U) (Scaffold attachment factor A)

chain, brain 1 (Spectrin, non-erythroid beta chain 1) (Beta-II spectrin)

Transcription factor ReIB (I-Rel)

Collagen alpha 3(FV) chain precursor (Goodpasture antigen) l-phosphatidylinositol-4,5-bisphosphate phosphodiesterase beta 3 (EC 3.1.4.11) (Phosphoinositide phospholipase C) (PLC-beta-3) (Phospholipase C-beta-3)

Tyrosine-protein kinase transmembrane receptor ROR2 precursor (EC 2.7.1.112) (Neurotrophic tyrosine kinase, receptor-related 2) Contactin 2 precursor (Axonin-1) (Axonal glycoprotein TAG-I) (Transient axonal glycoprotein I) (TAX-I)

MBP-2 (MHC Binding Protein-2)

Eukaryotic translation initiation factor 4 gamma 1 (eIF-4-gamma 1) (eIF-4Gl) (eIF-4G) (p220)

Keratin, type I cytoskeletal 17 (Cytokeratin 17) (K17) (CK 17) (39.1)

Activin receptor type I precursor (EC 2.7.1.37) (ACTR-I) (Serine/threonine-protein kinase receptor Rl) (SKRl) (Activin receptor-like kinase 2) (ALK-2) (TGF-B superfamily receptor type I) (TSR-I)

14-3-3 protein eta (Protein ASl) Undulin 2 (Fragment)

006830 1 Peroxiredoxin 1 (EC 1.11.1.-) (Thioredoxin peroxidase 2) (Thioredoxin-dependent peroxide reductase 2) (Proliferation-associated protein PAG) (Natural killer cell enhancing factor A) (NKEF-A)

Q07507 1 Dermatopontin precursor (Tyrosine-rich acidic matrix protein) (TRAMP)

Q08043 1 Alpha-actinin 3 (Alpha actinin skeletal muscle isoform 3) (F-actin cross linking protein)

008170 1 Splicing factor, arginine/serine-rich 4 (Pre-mRNA splicing factor SRP75) (SRPOOlLB)

010586 1 D-site-binding protein (Albumin D box-binding protein) (TAXREB302)

012756 1 Kinesin-like protein KIFlA (Axonal transporter of synaptic vesicles)

012809 1 Potassium voltage-gated channel subfamily H member 2 (Voltage-gated potassium channel subunit KvIl.1) (Ether-a-go-go related gene potassium channel 1) (H-ERG) (Ergl) (Ether-a-go-go related protein 1) (Eag related protein 1) (eag homolog)

012815 1 Trophinin-associated protein (Tastin) (Trophinin-assisting protein)

012891 1 Hyaluronidase 2 precursor (EC 3.2.1.35) (Hyal-2) (Hyaluronoglucosaminidase 2) (LUCA- 2)

Heat shock protein 75 kDa, mitochondrial precursor (HSP 75) (Tumor necrosis factor type 1 receptor associated protein) (TRAP-I) (TNFR-associated protein 1)

Ankyrin 3 (ANK-3) (Ankyrin G)

Presynaptic protein SAP97 (Synapse-associated protein 97) (Discs, large homolog 1) (hDlg)

Heat-shock protein beta-3 (HspB3) (Heat shock 17 IcDa protein)

S-methyl-5-thioadenosine phosphorylase (EC 2.4.2.28) (5'-methylthioadenosine phosphorylase) (MTA phosphorylase) (MTAPase)

BMP and activin membrane-bound inhibitor homolog precursor (Putative transmembrane protein NMA) (Non-metastatic gene A protein)

Semaphorin 3B precursor (Semaphorin V) (Sema V) (Sema A(V)) Selenium-binding protein 1 Ras-GTPase-activating protein binding protein 1 (GAP SH3-domain binding protein 1) (G3BP-1) (DNA helicase VIII) (HDH-VIII)

Metastasis-associated protein MTAl

Phospholipase Dl (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine- hydrolyzing phospholipase Dl) (hPLDl)

Tubulin beta-4 chain (Tubulin beta-Ill) Hypothetical protein (Fragment) Spectrin alpha chain, brain (Spectrin, non-erythroid alpha chain) (Alpha-II spectrin) (Fodrin alpha chain)

Ectonucleotide pyrophosphatase/phosphodiesterase 2 (E-NPP 2) (Phosphodiesterase I/nucleotide pyrophosphatase 2) (Phosphodiesterase I alpha) (PD-Ialpha) (Autotaxin) [Includes: Alkaline phosphodiesterase I (EC 3.1.4.1); Nucleotide pyrophosphatase (EC 3.6.1.

cGMP-dependent protein kinase 1, alpha isozyme (EC 2.7.1.37) (CGK 1 alpha) (cGKI- alpha)

014151 1 Scaffold attachment factor B2

014166 1 Hypothetical protein KIAAO 153

014191 1 Werner syndrome helicase

014195 1 Dihydropyrimidinase related ρrotein-3 (DRP-3) (Unc-33-like phosphoprotein) (ULIP protein) (Collapsin response mediator protein 4) (CRMP-4)

Nebulin (Fragment)

Myosin-binding protein C, fast-type (Fast MyBP-C) (C-protein, skeletal muscle fast- isoform)

Giant larvae homologue

Hypermethylated in cancer 1 protein (Hic-1) (Zinc finger and BTB domain containing protein 29) Inter-alpha-trypsin inhibitor heavy chain H4 precursor (ITI heavy chain H4) (Inter-alpha- inhibitor heavy chain 4) (Inter-alpha-trypsin inhibitor family heavy chain-related protein) (IHRP) (Plasma kallikrein sensitive glycoprotein 120) (PK-120) (GP120) (PR Ribosome biogenesis protein BMSl homolog Prepro-alpha2(I) collagen precursor Transcription elongation factor B polypeptide 1 (RNA polymerase II transcription factor

SIII subunit C) (SIII pl5) (Elongin C) (EIoC) (Elongin 15 kDa subunit)

protein IA) (SH3P17) E2 variant 2 (MMS2) (Enterocyte differentiation associated promoting factor) (EDPF-I) (Vitamin D3 Sodium channel protein type IX alpha subunit (Voltage-gated sodium channel alpha subunit Navl.7) (Neuroendocrine sodium channel) (liNE-Na) (Peripheral sodium channel 1) Cyclic-nucleotide-gated cation channel alpha 3 (CNG channel alpha 3) (CNG-3) (CNG3)

(Cyclic nucleotide gated channel alpha 3) (Cone photoreceptor cGMP-gated channel alpha subunit) Alpha-internexin (Alpha-Inx) (66 kDa neurofilament protein) (Neurofilament-66) (NF-66)

Laminin alpha-4 chain precursor Membrane copper amine oxidase (EC 1.4.3.6) (Vascular adhesion protein-1) (VAP-I) (HPAO) Jumonji, AT rich interactive domain 2 protein (OTTHUMP00000016058) Novel protein similar to preferentially expressed antigen in melanoma (PRAME) (OTTHUMP00000044421 ) Novel protein (MGC27277) (Fragment) Nebulin-related anchoring protein Novel protein similar to preferentially expressed antigen in melanoma (PRAME) Novel protein (Fragment) OTTHUMP00000039401 Breast and ovarian cancer susceptibility protein 1 (Fragment) Rapl interacting factor 1 Multiple myeloma SET domain containing protein type III Hypothetical protein DKFZp686B07186 Hypothetical protein DKFZp781D2023 Hypothetical protein DKFZp781 D 1923

Hypothetical protein DKFZp781J054 Hypothetical protein DKFZp781C08198 Hypothetical protein DKFZp45 ILl 87 (Fragment) Cell division cycle 2-like 5 (Cholinesterase-related cell division controller) RGD, leucine-rich repeat, tropomodulin and proline-rich containing protein (Fragment) TNXB protein (Fragment) Hypothetical protein (Fragment) Hypothetical protein Interferon-inducible protein X beta 2 isoform (IFIX) Hypothetical protein PiggyBac transposable element derived 2 TAF3 protein (Fragment) Von Willebrand factor A domain-related protein, isoform 1 (WARP) Hypothetical protein FLJ21908 protein Plectin 11 Atherin Normal early placenta (Fragment) APEM9336 Echinoderm microtubule associated protein-like 5 (Fragment) L-lactate dehydrogenase A-like 6A (EC 1.1.1.27) Hypothetical protein FLJ 16614 Hypothetical protein FLJ 16517 Hypothetical protein FLJ 16186 Hypothetical protein FLJ27410 Hypothetical protein FLJ26450 Hypothetical protein FLJ46160 Hypothetical protein FLJ46705 Hypothetical protein FLJ46690 Hypothetical protein FLJ46347 Hypothetical protein FLJ46248 Hypothetical protein FLJ46180 Hypothetical protein FLJ46024 Hypothetical protein FLJ45584 Hypothetical protein FLJ45563 Hypothetical protein FLJ45248 Hypothetical protein FLJ45244 Hypothetical protein FLJ45178 Hypothetical protein FLJ44382 Hypothetical protein FLJ44342 Hypothetical protein FLJ43880 Hypothetical protein FLJ43756 Hypothetical protein FLJ43252 Hypothetical protein FLJ43213 Hypothetical protein FLJ43187 Hypothetical protein FLJ42519

O6ZVW2 1 Hypothetical protein FLJ42006

Q71U36 1 Tubulin alpha-3 chain (Alpha-tubulin 3) (Tubulin B-alpha-1)

Q76B58 1 DBCCRl -like (OTTHUMP00000060752) (DBCCRlL)

O7L5L3 1 MGC4171 protein

O7LBC6 1 Nuclear protein 5qNCA

Q7M4L6 1 Shb-like adapter protein, Shf

O7RTY9 1 Testis serine protease 1 precursor

O7Z2I9 1 ATP-binding cassette sub-family A member 10

O7Z3Y8 1 Type I inner root sheath specific keratin 25 irs3

Q7Z527 1 GMP dehydrogenase

O7Z5L5 1 Alpha 1 type XXIV collagen precursor

O7Z645 1 Collagen, type VI, alpha 1,

O7Z659 1 Hypothetical protein DKFZp779H0156 (Fragment)

O7Z7G1 1 MIST

O86SF2 1 N-acetylgalactosaminyltransferase 7 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransferase 7) (UDP-GalNAc:polypeptide N- acetylgalactosaminyltransferase 7) (Polypeptide GaINAc transferase 7) (GalNAc-T7) (pp- GaNTase 7)

1 G protein-coupled receptor PGR4 (Fragment)

1 Disheveled associated activator of morphogenesis 2 1 Full-length cDNA 5-PRIME end of clone CSODFO 13 YM24 of Fetal brain of Homo sapiens (human) (Fragment) protein 4 (Splicing factor SF2) (PP239)

(Fragment) (Novel protein) (DKFZp434A1315)

(EC 6.3.2.-) (DAZ-interacting protein 3) (RNA-binding

1 EROl-like protein beta precursor (EC 1.8.4.-) (EROl-Lbeta) (Oxidoreductin 1-lbeta) (Endoplasmic oxidoreductin 1-like protein B)

1 Abhydrolase domain containing 7

1 Steerin3 protein

1 MGC27277 protein

1 COL23A1 protein

1 Seven transmembrane helix receptor

1 Neuropathy target esterase (Fragment)

1 BTB/POZ domain containing protein 12

1 Protein C6orfl65

1 Collagen XXVII proalpha 1 chain precursor (OTTHUMP00000021970)

1 ALFY

1 Ovarian zinc finger protein

1 Hypothetical protein DKFZp762K2011

Hypothetical protein DKFZp761L1023 (Fragment) Hypothetical protein FLJ23518 Polymerase (DNA directed) iota Hypothetical protein FLJ40198 Hypothetical protein FLJ40083 Hypothetical protein FLJ37051 Hypothetical protein FLJ35393 Hypothetical protein FLJ35093 (Hypothetical protein DKFZp686M07166) Hypothetical protein FLJ34483 Hypothetical protein FLJ34056 Hypothetical protein FLJ90646 Hypothetical protein FLJ90472 Hypothetical protein FLJ90455 Hypothetical protein DKFZp547B0614 (Fragment) Hypothetical protein DKFZp434N1720 (Fragment) ATP-binding cassette, sub-family F, member 1 (ATP-binding cassette 50) (TNF-alpha stimulated ABC protein)

Chromosome 1 open reading frame 26

Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog (Histone-lysine N- methyltransferase, H3 lysine-4 specific MLL3) (EC 2.1.1.43) (Homologous to ALR protein) FLJ00406 protein (Fragment) Nesprin 1 (Nuclear envelope spectrin repeat protein 1) (Synaptic nuclear envelope protein

1) (Syne-1) (Myocyte nuclear envelope protein 1) (Myne-1) (Enaptin) Ubiquitin carboxyl-terminal hydrolase 32 (EC 3.1.2.15) (Ubiquitin thiolesterase 32)

(Ubiquitin-specific processing protease 32) (Deubiquitinating enzyme 32) (NY-REN-60 antigen) Bardet-Biedl syndrome 1 protein (BBS2-like protein 2) Neurobeachin protein (Lysosomal trafficking regulator 2) (BCL8B protein) Protein C 12orf2 (Carcinoma associated protein HOJ- 1) CDC26 subunit of anaphase promoting complex (Cell division cycle 26) Chromosome X open reading frame 38 Signal peptide peptidase-like 2B (EC 3.4.99.-) (SPP-like 2B protein) (SPPL2b protein)

(Intramembrane protease 4) (MP4) (Presenilin-like protein 1) Probable serine/threonine-protein kinase KIAA1811 (EC 2.7.1.37) Citrate lyase beta subunit (Citrate lyase beta like) Apical protein 2 Putative G-protein coupled receptor Polycystic kidney disease 1-like 1 protein (Polycystin ILl) FLJ00251 protein (Fragment) FLJOO 169 protein (Fragment) FLJOO 167 protein (Fragment) FLJOO 128 protein (Fragment) Ubiquitin carboxyl-terminal hydrolase 33 (EC 3.1.2.15) (Ubiquitin thiolesterase 33)

(Ubiquitin-specific processing protease 33) (Deubiquitinating enzyme 33) (VHL- interacting deubiquitinating enzyme 1)

O8TF 19 1 KIAA1983 protein (Fragment)

O8TF45 1 Zinc finger protein 418

Q8WTS1 1 CGI58 protein

Q8WWI1 1 LIM domain only protein 7 (LOMP) (F-box only protein 20)

O8WWM7 1 Ataxin-2-like protein (Ataxin-2 domain protein) (Ataxin-2 related protein)

Q8WXD9 1 Cask-interacting protein 1

Q8WXE9 1 Stonin 2 (Stoned B)

08WYY1 1 Hypothetical protein

092889 1 DNA repair endonuclease XPF (EC 3.1.-.-) (DNA excision repair protein ERCC-4) (DNA- repair protein complementing XP-F cell) (Xeroderma pigmentosum group F complementing protein)

Transcription factor IIIB 90 kDa subunit (TFIIIB90) (hTFIHB90) (B-related factor 1) (hBRF) (TATA box-binding protein-associated factor, RNA polymerase HI, subunit 2) (TAF3B2)

Tumor necrosis factor receptor superfamily member 25 precursor (WSL-I protein) (Apoptosis-mediating receptor DR3) (Apoptosis-mediating receptor TRAMP) (Death domain receptor 3) (WSL protein) (Apoptosis inducing receptor AIR) (Apo-3) (Lymphocyte associated

1 HSRBC protein (Protein kinase C, delta binding protein)

1 Pleckstrin homology domain containing family C member 1 (Kindlin 2) (Mitogen- inducible gene 2 protein) (Mig-2)

1 Repulsive guidance molecule A precursor (RGM domain family member A)

1 SH3-domain kinase binding protein 1 (Cbl-interacting protein of 85 IcDa) (Human Src- family kinase binding protein 1) (HSB-I) (CD2 binding protein 3) (CD2BP3)

1 MYO 1 G protein (Fragment)

1 Coiled-coil-helix-coiled-coil-helix domain containing 1

1 NT5C2L1 protein

1 Hypothetical protein (Fragment) 1 Potassium channel tetramerisation domain containing protein 12 (Pfetin) (Predominantly fetal expressed Tl domain)

(MLCK)

RNA helicase DDX27 (DEAD-box protein 27) (HSPC259)

1 Dehydrogenase El and transketolase domain containing protein 1

1 Williams-Beuren syndrome chromosome region 16 protein

1 CCGl-interacting factor B

1 KIAAl 868 protein (Fragment)

1 KIAAl 822 protein (Fragment)

1 Zinc finger protein 462

1 Hypothetical protein FLJ14909

1 Hypothetical protein FLJ14834 1 Calreticulin 3 precursor (Calreticulin 2)

ω96L34 1 MAP/microtubule affinity-regulating kinase 4 (EC 2.7.1.37) (MAP/microtubule affinity- regulating kinase like 1)

O96L96 1 Muscle alpha-kinase

O96LM3 1 Hypothetical protein FLJ25373

O96MB5 1 Hypothetical protein FLJ32682

O96MC7 1 Hypothetical protein FLJ32603

O96ML4 1 Hypothetical protein FLJ32194

O96MN5 1 Hypothetical protein FLJ32112 (Novel protein)

O96NY2 1 DEAD/DEXH helicase DDX31 (OTTHUMP00000064614)

O96P94 1 Dermatan-4-sulfotransferase-l (Dermatan 4-sulfotransferase)

O96PX5 1 KIAA1913 protein (Fragment)

O96RK0 1 Capicua protein

O96RR4 1 Calcium/calmodulin-dependent protein kinase kinase 2 (EC 2.7.1.37) (Calcium/calmodulin-dependent protein kinase kinase beta) (CaM-kinase kinase beta) (CaM-KIC beta) (CaMKK beta)

O96S08 1 Some homology with holliday junction DNA helicase RUVB like

O96S66 1 Mid-1-related chloride channel 1 (Hypothetical protein KIAA0761) (MCLC)

O96T58 1 Msx2-interacting protein (SMART/HDACl associated repressor protein)

O96TA2 1 ATP-dependent metalloprotease YMElLl (EC 3.4.24.-) (YMEl-like protein 1) (ATP- dependent metalloprotease FtsHl) (Meg-4) (Presenilin-associated metalloprotease) (PAMP) (UNQ1868/PRO4304)

099457 1 Nucleosome assembly protein 1 -like 3

099460 1 26S proteasome non-ATPase regulatory subunit 1 (26S proteasome regulatory subunit RPN2) (26S proteasome regulatory subunit Sl) (26S proteasome subunit pi 12)

B-cell receptor-associated protein BAP37 (Repressor of estrogen receptor activity) (D- prohibitin) precursor

4 precursor (TIMP-4) (Tissue inhibitor of metalloproteinases-

Aconitate hydratase, mitochondrial precursor (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase) Endothelial PAS domain protein 1 (EPAS-I) (Member of PAS protein 2) (M0P2) (Hypoxia-inducible factor 2 alpha) (HIF-2 alpha) (HIF2 alpha) (HIF-I alpha-like factor) (HLF)

A-kinase anchor protein 9 (Protein kinase A anchoring protein 9) (PRKA9) (A-kinase anchor protein 450 kDa) (AKAP 450) (A-kinase anchor protein 350 kDa) (AKAP 350) (hgAKAP 350) (AKAP 120 like protein) (Hyperion protein) (Yotiao protein) (Centrosome- and Go

(EC 3.5.3.11) (Agmatine ureohydrolase) (AUH) protein of 21 kDa precursor (hPAP21)

1 Chromosome 9 open reading frame 156

1 DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 32 (Fragment)

Q9BUP0 1 EF-hand domain-containing protein 1 (Swiprosin 2) (PP3051)

O9BUR4 1 FLJ 10385 protein

O9BUY9 1 Growth arrest-specific 2 like 1, isoform a

O9BVC6 1 Hypothetical protein MGC5508

O9BVP4 1 PDLIM3 protein (Alpha-actinin-2-associated LIM protein)

O9BX44 1 BA92K2.2 (Similar to ubiquitin)

O9BXG4 1 Spermatid perinuclear RNA-binding protein

Q9BYX7 1 FKSG30

O9C0A8 1 KIAAl 755 protein (Fragment)

O9C0D3 1 KIAA1730 protein (Fragment)

Q9C0E5 1 KIAA1718 protein (Fragment)

Q9C0J8 1 WD-repeat protein 33 (WD-repeat protein WDC 146)

O9GZM7 1 Tubulointerstitial nephritis antigen-related protein precursor (Glucocorticoid-inducible protein) (Oxidized-LDL responsive gene 2) (Hypothetical protein PSEC0088) (LCN7) (P3ECSL)

Striatum-specific G potein-coupled receptor (Striatum-specific G protein-coupled receptor)

1 Nuclear RNA export factor 2 (TAP-like protein 2) (TAPL-2)

1 Hypothetical protein DKFZp564C012

1 Calcineurin-binding protein calsarcin-2

1 Activating signal cointegrator 1 complex subunit 2 (ASC-I complex subunit plOO) (Trip4 complex subunit pi 00)

1 Serologically defined breast cancer antigen NY-BR-62 (Fragment)

1 Sarcolemmal associated protein 1

1 CTCL tumor antigen se20-9 (Ste20-related serineVthreonine kinase) (SLK) 1 Tankyrase 2 (EC 2.4.2.30) (TANK2) (Tankyrase II) (TNKS-2) (TRFl -interacting ankyrin- related ADP-ribose polymerase 2) (Tankyrase-like protein) (Tankyrase-related protein)

1 Ran-binding protein 17

1 Sorting nexin 25 (MSTP043) 1 MCMlO homolog (MCMlO minichromosome maintenance deficient 10) (S. cerevisiae)

(OTTHUMP00000045155)

1 Serine/threonine-protein kinase WNKl (EC 2.7.1.37) (Protein kinase with no lysine 1)

(Protein kinase, lysine-deficient 1) (Kinase deficient protein)

1 Serine/threonine-protein kinase PLK3 (EC 2.7.1.37) (Polo-like kinase 3) (PLK-3)

(Cytokine-inducible serine/threonine-protein kinase) (FGF-inducible kinase) (Proliferation-related kinase)

1 Salvador homolog 1 protein (45 kDa WW domain protein) (hWW45)

1 Rho-related GTP-binding protein RhoJ (TclO-like GTP-binding protein TCL)

1 PR-domain zinc finger protein 13

1 Hypothetical protein FLJ23584

1 Hypothetical protein FLJ21687

1 Hypothetical protein FLJ21665 (Tubulin, alpha-like 3)

1 Hypothetical protein FLJ21126

1 Hypothetical protein FLJ 14298 1 Hypothetical protein FLJ13848

Zinc finger protein 430 Hypothetical protein FLJ12822 Hypothetical protein FLJ12730 Phosphoinositide-specific phospholipase C PLC-epsilon Methylcrotonyl-CoA carboxylase beta chain, mitochondrial precursor (EC 6.4.1.4) (3-

Methylcrotonyl-CoA carboxylase 2) (MCCase beta subunit) (3-methylcrotonyl- CoAxarbon dioxide ligase beta subunit) Zinc finger I ⁷ YVE domain containing protein 28 GlyceroI-3-phosphate acyltransferase, mitochondrial precursor (EC 2.3.1.15) (GPAT) Ubiquitin-coηjugating enzyme isolog (HSPC 150 protein similar to ubiquitin-conjugating enzyme) (Hypothetical protein FLJ20497) (OTTHUMP00000060941) (Ubiquitin- conjugating enzyme E2) Endothelial zinc finger protein induced by tumor necrosis factor alpha (Zinc finger protein

N-methyltransferase 4 (EC 2.1.1.-) (Heterogeneous nuclear n methyltransferase-like protein 4) Eukaryotic translation initiation factor 4E transporter (eIF4E transporter) (4E-T)

(Eukaryotic translation initiation factor 4E nuclear import factor 1) Putative GTP-binding protein PTD004 (PRO2455) RNA-binding protein 12 (RNA binding motif protein 12) (SH3/WW domain anchor protein in the nucleus) (SWAN) (HRIHFB2091) Alpha-parvin (Calponin-like integrin-linked kinase binding protein) (CH-ILKBP) Hypothetical protein FLJ10572 (Hypothetical protein KLHLl 1) Hypothetical protein FLJ20505 Hypothetical protein FLJ20006 Ciliary dynein heavy chain 9 (Axonemal beta dynein heavy chain 9) MRNA-binding protein CRDBP MTRl PRO2760 Hypothetical protein PRO 1866 KIAAl 486 protein (Fragment) Serine/threonine-protein kinase PAK 7 (EC 2.7.1.37) (p21 -activated kinase 7) (PAK-7)

(PAK-5)

protein 7 (CHD-7) (Fragment)

of hairless-like protein (Transcription factor Guanine nucleotide-binding protein G(I)/G(S)/G(O) gamma- 12 subunit 7-dehydrocholesterol reductase (EC 1.3.1.21) (7-DHC reductase) (Sterol delta-7- reductase) (Putative sterol reductase SR-2) Hypothetical protein DKFZp434A2017 (Fragment) Alpha-methylacyl-CoA racemase (EC 5.1.99.4) (2-methylacyl-CoA racemase)

O9UIF9 1 Bromodomain adjacent to zinc finger domain 2A (Transcription termination factor-I interacting protein 5) (TTF-I interacting protein 5) (Tip5) (hWALp3)

O9UII5 1 Zinc finger protein ZFD25

O9UJO7 1 Protein C20orf79

O9UJY4 1 ADP-ribosylation factor binding protein GGA2 (Golgi-localized, gamma ear-containing, ARF-binding protein 2) (Gamma-adaptin related protein 2) (Vear) (VHS domain and ear domain of gamma-adaptin)

Potassium voltage-gated channel subfamily D member 3 (Voltage-gated potassium channel subunit Kv4.3)

Peroxisomal carnitine O-octanoyltransferase (EC 2.3.1.137) (COT) Integrin beta-1 binding protein 2 (Melusin) (MSTP015)

Protein kinase C and casein kinase substrate in neurons protein 3 (SH3 domain-containing protein 6511) (Endophilin I)

Squamous cell carcinoma antigen recognized by T cells 2 (SART2 protein)

Zinc finger protein 236

KIAA1241 protein (Fragment)

KIAA1200 protein (Fragment)

KIAAl 189 protein (Fragment)

KIAAl 135 protein (Fragment) Protein kinase C binding protein 1 (Rack7) (Cutaneous T-cell lymphoma associated antigen sel4-3) (CTCL tumor antigen sel4-3) (Zinc finger MYND domain containing protein 8)

Myeloid/lymphoid or mixed-lineage leukemia protein 4 (Trithorax homolog 2)

Cystine/glutamate transporter (Amino acid transport system xc-) (xCT) (Calcium channel blocker resistance protein CCBRl)

Leucine-rich repeat protein SHOC-2 (Ras-binding protein Sur-8)

PITSLRE serine/threonine-protein kinase CDC2L2 (EC 2.7.1.37) (Galactosyltransferase associated protein kinase p58/GTA) (Cell division cycle 2-like 2) (CDKl 1)

RuvB-like 2 (EC 3.6.1.-) (48-kDa TATA box-binding protein-interacting protein) (48-kDa TBP-interacting protein) (TIP 49b) (Repressing pontin 52) (Reptin 52) (51 kDa erythrocyte cytosolic protein) (ECP-51) (TIP60-associated protein 54-beta) (TAP54-beta) (CG

1 XAP-5-like protein

1 Phenylalanyl-tRNA synthetase alpha chain (EC 6.1.1.20) (Phenylalanine-tRNA ligase alpha chain) (PheRS) (CML33)

1 Transmembrane protein 5

1 KIAA0962 protein (Fragment)

1 KIAA0967 protein

1 TRS85 homolog

1 Putative deoxyribose-phosphate aldolase (EC 4.1.2.4) (Phosphodeoxyriboaldolase) (Deoxyriboaldolase) (DERA) (CGI-26)

1 Hypothetical protein CGI-96 (BK 126B4.3)

1 UPFO 198 protein CGI- 141 (HDCMA39P) (UNQ432/PRO793)

1 CGI-150 protein

1 N-acetylated-alpha-linked acidic dipeptidase π (EC 3.4.17.21) (NAALADase II) 1 ZASP protein (Fragment)

fibrosarcoma oncogene homolog APC2 protein (Fragment) Ancient ubiquitous protein 1 precursor EMILIN 1 precursor (Elastin microfibril interface-located protein 1) (Elastin microfibril interfacer 1) Brefeldin A-inhibited guanine nucleotide-exchange protein 1 (Brefeldin A-inhibited GEP

1) (p200 ARF-GEPl) (p200 ARF guanine nucleotide exchange factor) Gap junction alpha-3 protein (Connexin 46) (Cx46) Sulfide:quinone oxidoreductase, mitochondrial precursor (EC 1.-.-.-) (CGI-44) Zinc finger CW-type coiled-coil domain protein 1 Lymphocyte antigen 96 precursor (MD-2 protein) (ESOP-I)