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Title:
COMPOSITIONS FOR THE DETECTION OF GENE EXPRESSION IN DIABETIC MICROANGIOPATHY
Document Type and Number:
WIPO Patent Application WO/2009/004443
Kind Code:
A3
Abstract:
The present invention relates to a composition comprising a plurality of polynucleotide probes. The composition can be used as hybridisable array elements in a microarray. The present invention also relates to a method for selecting polynucleotide probes for the composition. The present invention further relates to a composition comprising a plurality of polynucleotide probes for use in research and diagnostic applications, in particular for the diagnosis of diabetic microangiopathy. The present invention also relates to novel bio-markers and sets thereof that are useful in the diagnosis and treatment of diabetic microangiopathy.

Inventors:
KERJASCHKI DONTSCHO (AT)
WICK NIKOLAUS (AT)
THURNER STEFAN (AT)
Application Number:
PCT/IB2008/001680
Publication Date:
March 12, 2009
Filing Date:
June 27, 2008
Export Citation:
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Assignee:
UNIV WIEN MED (AT)
KERJASCHKI DONTSCHO (AT)
WICK NIKOLAUS (AT)
THURNER STEFAN (AT)
International Classes:
C12Q1/68
Foreign References:
EP1615035A12006-01-11
EP1615036A12006-01-11
US20060019315A12006-01-26
US20060008829A12006-01-12
Other References:
"Affimetrix GeneChip Human Genome U133 Array Set HG-U133A", GEO,, 1 January 1900 (1900-01-01), XP002254749
Attorney, Agent or Firm:
IPRIS GmbH (Birsigstrasse 4, Basel, CH)
Download PDF:
Claims:

Claims

1. A composition comprising a nucleic acid probe for use in detecting the altered expression of genes in diabetic microangiopathy, wherein said nucleic acid probe comprises at least 12 continuous bases of a biomarker according to table 1 or a complement thereof.

2. The composition according to claim 1, wherein said nucleic acid probe comprises at least 24, 30, 50 or more continuous bases.

3. The composition according to claim 1 or 2, wherein said nucleic acid probe is a single stranded DNA and/or a cDNA.

4. The composition according to any of claims 1 to 3, wherein said nucleic acid probe is immobilized on a substrate.

5. The composition according to claim 4, wherein said nucleic acid probe is a hybridisable element on a microarray.

6. The composition according to any of claims 1 to 5, wherein said composition comprises at least 10, 15, 20, 50, 100, 125 or 559, or 560 biomarkers according to table 1 or a complement thereof.

7. The composition according to any of claims 1 to 5, wherein said composition comprises all biomarkers according to table 1 or a complement thereof which exhibit a p-value of less than 0.001, preferably of less than 0.0001, or most preferably of less than 0.00001, as determined by the t-test, or a combination of markers as grouped by the RVM method.

8. The composition according to any of claims 1 to 5, wherein said composition comprises the biomarkers SFRS12, RSUl, PRSS23, EPS8L2, Hs.438689, ANP32E, GBEl, CFH, Hs.159472, LDHB, SEPHSl, TBC1D4, USP33, STOM, GNAS, IFITM3, Clone MO-30 mRNA sequence, SNAP23, SNX4, ANXA2, ALGI l, AQPl, Fbxo7, WEEl, RNF13, NNMT, HNRP A3, YTHDF2, DUSP22, PRSS23, LRRC32, YWHAQ, GTPBP4, ZDHHCl 7, DAZAPl, MED4, BMX, SFRS6, ST6GALNAC3, PPP1R12A, TAF2, CD47, IFITM2, BRDl, RPL13, PTPRK, GALC, SNX2, GCA, RFCl, HERC4, GPRl 16, BRWD2, RPL13, THlL, GNAS, IARS, ELF2, ATP6V0D1, NEK7, HOXA5, GPI, UNC50, FMRl, STK17A, EWSRl, KRCCl, OSBPLlA; LZTFLl, VPS35, DNAJC3, MBD4, STT3A, AP1S2, BACE2, GAPDH, ADD3, ARF4, and TLKl or a complement thereof.

9. The composition according to any of claims 1 to 5, wherein said composition comprises the biomarkers EWSRl, KRCCl, OSBPLlA; LZTFLl, VPS35, DNAJC3, MBD4, STT3A, AP1S2, BACE2, GAPDH, ADD3, ARF4, and TLKl or a complement thereof.

10. The composition according to any of claims 1 to 5, wherein said composition comprises the biomarkers MBD4, STT3A, AP1S2, BACE2, GAPDH, ADD3, ARF4, and TLKl or a complement thereof.

11. A method for diagnosing or monitoring the treatment of diabetic microangiopathy in a sample, said method comprising: a) obtaining nucleic acids from said sample; b) contacting the nucleic acids of the sample with an array comprising a nucleic acid probe according to any of claims 1 to 10 under conditions to form one or more hybridization complexes;

c) detecting said hybridization complexes; and d) comparing the levels of the hybridization complexes detected in step (c) with the level of hybridization complexes detected in a non-diseased sample, wherein the altered level of hybridization complexes detected in step (c) compared with the level of hybridization complexes of a non-diseased sample correlates with the presence of diabetic microangiopathy.

12. A method for identifying candidate compounds for the treatment of diabetic microangiopathy, said method comprising: a) contacting a cell with at least one candidate compound, b) obtaining nucleic acids from said cell, c) contacting the nucleic acids of said sample with an array comprising a nucleic acid probe according to any of claims 1 to 10 under conditions to form one or more hybridization complexes; d) detecting said hybridization complexes; and e) comparing the levels of the hybridization complexes detected in step (d) with the level of hybridization complexes detected in a sample of a cell which has not been contacted with said at least one candidate compound, wherein the altered level of hybridization complexes detected in step (d) compared with the level of hybridization complexes detected in a sample of a cell which has not been contacted with said at least one candidate compound identifies candidate compounds for the treatment of diabetic microangiopathy.

13. The method according to claim 12, wherein said candidate compound alters the level of hybridization complexes of biomarkers according to table 1 or a complement thereof which exhibit a p-value TT of less than 0.001, preferably of less than 0.0001, or most preferably of less than 0.00001 , or a combination of markers as grouped by the RVM method.

14. The method according to claim 11 or 12, furthermore comprising the step of formulating said identified compound into a pharmaceutical preparation.

15. A method of treating diabetic microangiopathy, comprising monitoring according to claim 11 , and selecting the further treatment based, at least in part, on said monitoring.

16. A method of treating diabetic microangiopathy, comprising administering to a patient in need thereof an effective amount of a pharmaceutical preparation produced according to claim 14.

Description:

Compositions for the detection of gene expression in diabetic microangiopathy

The present invention relates to a composition comprising a plurality of polynucleotide probes. The composition can be used as hybridisable array elements in a DNA-based array. The present invention also relates to a method for selecting polynucleotide probes for the composition. The present invention further relates to a composition comprising a plurality of polynucleotide probes for use in research and diagnostic applications, in particular for the diagnosis of diabetic microangiopathy. The present invention also relates to novel bio- markers and sets thereof that are useful in the diagnosis and treatment of diabetic microangiopathy.

DESCRIPTION

DNA-based arrays can provide a simple way to explore the nucleotide sequence of a single gene for polymorphic nucleotide or the expression of a large number of genes. For the present invention only the second type is relevant.

There are two basic DNA-based array technologies known. cDNA microarrays and DNA chips. Both are especially relevant for the rapid screening of expression of a large number of genes. There is a growing awareness that gene expression is affected in a global fashion. A genetic predisposition, disease or therapeutic treatment may affect, directly or indirectly, the expression of a large number of genes. In some cases the interactions may be expected, such as where the genes are part of the same signalling pathway. In other cases, such as when the genes participate in separate or completely novel signalling pathways, the interactions may be totally unexpected. Therefore, DNA-based arrays can be used to investigate how genetic predisposition, disease, or therapeutic treatment affects the expression of a large number of genes.

Diabetes mellitus is diagnosed, when plasma fasting glucose levels rise > 126 mg/dl. The number of diabetes is set to rise from the current estimate of 194 million to 220 million in 2010, and 333 million in 2025 (Zimmet et al., Nature 414, 2001 and EASD Congress, Paris 2003). Worldwide for individuals 20-79 years of age >153-286 bio. international dollars and is predicted to rise to 213-396 in 2025 (Diabetes Atlas of International Diabetes Federation). The indirect costs, i.e. lost productivity due to disability and mortality, in the US make 40 bio. U$.

The main determinant of diabetic morbidity and mortality is due to vascular complications. The diabetic vascular damage can occur in large (macroangiopathy) and in small vessels (microangiopathy). Macrovascular disease is identical to atherosclerosis in non-diabetics and is diagnosed in about 75% of diabetic hospital admissions as well as death cases in Western countries. On the other hand, microvascular complications are present to a large extent within the kidneys, retinas and peripheral nerves of diabetic collectives: Nephropathy is a major cause of renal morbidity and mortality of diabetic patients. Up to 40 % of all diabetic patients show microalbuminuria, and, similarly, 44 % develop end stage kidney disease mellitus (Mitch, NEJM 351(19), 2004). Consequently, diabetics are the fastest growing group of renal tranplant recipients in the US, with a 5 year survival of 21% only, which in turn is worse than that for all forms of cancer combined (National Diabetes Data Group 1995). Up to 90 % of type I and around 25 % of type II diabetics suffer from diabetic retinopathy. In the U.S., diabetic retinopathy is the fourth important cause of blindness constituting 30 % of all blindness cases. Finally, up to 60% of long-term diabetic patients develop neuropathy. In sum-

mary, large proportions of diabetic patients suffer from reduced living quality for decades due to vascular complications.

The cDNA microarray or DNA-chip can be used for large scale genetic or gene expression analysis of a large number of target polynucleotides. The microarray can be used in the diagnosis of diabetic disease and in the monitoring of treatments where altered expression of genes implicated in diabetic microangiopathy cause disease. The microarray can also be used to investigate an individual's predisposition to the disease. Furthermore, the microarray can be employed to investigate cellular responses in diabetic microangiopathy. cDNA-based arrays have been used in discovery and analysis of early diabetic related retinal genes (Joussen et al. Invest Ophthalmol Vis Sci. 2001 Nov;42(12):3047-57) in rats. A first type of array was employed to characterize the expression patterns of a class of 5147 genes, of which 1691 are known genes and 3456 are expressed sequence tags (ESTs). On day 3, the expression of 27 known genes was increased by more than twofold. On days 7 and 21, the corresponding numbers were 60 and 12, respectively. A transient upregulation (>2-fold) in expression was seen in 627 of 5147 total genes. A subset of 926 genes exhibited a modest (<2-fold) decrease in expression. No genes showed a greater than twofold decrease in expression. Rat glomerular mesangial cells were tested under high glucose treatment with cDNA microarrays and found to upregulate 459, while downregulating 151 clones in this condition (Morrison et al. Physiol Genomics 2004 May 19;17(3):271-82). Another study analyzed kidneys from streptotozin-induced diabetic as well as db/db mouse models using cDNA micorarrays (Susztak et al., Diabetes 2004 Mar;53(3):784-94). Finally, another cDNA microarray experiment identified 16 induced and 65 repressed clones in diabetic kidneys of mice (Wada et al., Kidney Int 2001 Apr;59(4): 1363-73).

Current cDNA-based arrays suffer from a variety of limitations. First, it is a relative measure only that does not allow statements of absolute abundance of various RNA species. However, this would be important for selection of relevant biotargets. Also, high abundance genes are likely to be over represented and low abundance genes are likely to be under represented. Moreover, non-specific binding cannot be controlled completely. Finally, immobilization of cDNAs on surfaces is inaccurate. The present invention provides a way to overcome such limitations by using DNA chips.

DNA chips measure absolute fluorescence signals that directly correlate with the abundance of RNA levels, i.e. gene activity. This allows for easy comparison between genes and, therefore, selection of suitable targets. Moreover, DNA chips have included effective controls for non-specific hybridization signals, thereby providing better signal-to-noise ratios. On the other side, also DNA chips show some disadvantages. One is that this type of array can only detect the expression patterns of a number of genes already known in nucleotide sequence databases. However, as the human genome is fully sequenced and freely accessible, full genome DNA chips are available, which overcome this drawback.

DNA-chips were used to profile transcriptional alterations in human glomeruli from only two patients suffering from diabetic nephropathy. 96 genes were upregulated, 519 downregulated (Baelde et al. Am J Kid Dis 2004 Apr;43(4):636-50). The db/db mouse model was also analyzed for transcriptional effects of diabetes with DNA-chips. 482 genes were differentially expressed (Am J Physiol Renal Physiol 2004 May;286(5):F913-21).

An important aspect of the invention is the use of samples that were directly isolated from human patients and not brought into cell culture before DNA chip analysis. This so-called ex

vivo state has been previously proved to be the most effective method of maintaining a near- in vivo picture of the transcription profile of dermal endothelial cells.

In conclusion, the inventors combined pathomorphological experiments and pre-existing micropreparation knowledge with DNA chip data and bioinformatic analyses, in order to further investigate the molecular mechanisms of diabetic microangiopathy.

It is therefore an object of the present invention, to provide new options for the diagnosis and treatment of diabetic microangiopathy, by providing new biomarkers as respective medical and diagnostic tools, and uses thereof.

In one aspect, the present invention provides a composition comprising a nucleic acid probe for use in detecting the altered expression of genes in diabetic microangiopathy, wherein said nucleic acid probe comprises at least 12 continuous bases of a biomarker according to table 1 or a complement thereof.

During development of the present invention, the following facts and data appeared to be of major relevance:

1. The inventors have, among others, found that the cell surface protein podoplanin is expressed specifically on lymph endothelial cells (LEC), but not on endothelial cells of blood vessels (BEC) in both normal and pathological conditions. In contrast, VEGFR-3 (flt4) is predominantly, but not exclusively, expressed on the plasma membrane of LEC. Prox-1 is a transcription factor determining lymphatic endothelial differentiation, but is restricted to intracellular localizations. This makes it unusable for in vivo preparation. Thus, together with the CD44 receptor LYVE-I podoplanin constitutes the sole marker set expressed on the plasma membrane of LECs to date.

2. The inventors have generated antibodies recognizing human podoplanin protein. With these tools they have separated mixed dermal endothelial cell populations into functionally intact lymph vessel endothelial cell (LEC) and blood vessel endothelial cell (BEC) fractions by fluorescence activated cell sorting (FACS). Critically, the preparations are ex vivo, meaning they were directly lysed after FACSort, thereby avoiding any cell culture artefact.

3. The inventors have recently used the above isolation protocol in order to perform transcriptional profiling on sorted cultivated blood and lymph vessel endothelial cells by DNA- chip technology. They have also confirmed the experiments using extraction of functional data from DNA-chip experiments. They have compared the profiles of in vitro cultivated samples to those directly lysed after isolation form the patient (ex vivo) and found dramatic artefacts introduced by cell culture. Thus, they decided to perform the studies on DMA using RNA prepared from ex vivo samples.

The inventors have microprepared RNA of BECs from diabetic and non-diabetic patients in an ex vivo state and directly subjected the samples to DNA-chip analysis.

4. The inventors have optimized the bioinformatical analysis of clinical samples, i.e. low amount of starting materials and few in number. It included correction of non-uniform hybridization to DNA chips and calculation of differential gene expression between test samples by combining T-test with the Relative Variance Method (RVM). The latter identifies markers that exhibit a signal intensity of larger than first, preferably larger than second, more preferably larger than third or most preferably larger than fourth standard deviation.

The above polynucleotide probes can be selected from I) first polynucleotide probes, wherein each of said first polynucleotide probes comprises at least a portion of at least 12 continuous bases of a biomarker (gene) differentially expressed in diabetic microangiopathy; II) second polynucleotide probes, wherein each of said second polynucleotide probes comprises at least a portion of a biomarker (gene) abundantly expressed in diabetic microangiopathy; III) third polynucleotide probes, wherein each of said third polynucleotide probes comprises at least a portion of a biomarker (gene) coding for a polypeptide known to regulate diabetic microangiopathy; and IV) combinations of first, second or third polynucleotide probes.

Generally, first polynucleotide probes are selected by a) preparing at least one first target transcript profile from a first biological sample selected from the group consisting of lymphatic endothelial cells (LEC) or endothelial cells of blood vessels (BEC) in diabetic microangiopathy condition, and at least one first reference transcript profile from a nondiabetic microangiopathy or healthy biological sample; b) subtracting said first subtraction transcript profile from said first target profile to detect a plurality of genes that are differentially expressed in diabetic microangiopathy; and c) identifying one of said detected genes that are differentially expressed in diabetic microangiopathy.

In one preferred embodiment, the composition comprises a nucleic acid probe that comprises at least a portion of a sequence selected from a biomarker according to table 1 or a complement thereof. In one preferred embodiment, the composition comprises a nucleic acid probe that comprises at least 24, 30, 50 or more continuous bases. Preferably, the nucleic acid probe does not contain the complete nucleic acid sequence of the biomarker (i.e. is shorter, such as, for example, in case of segments or parts of said biomarker).

More preferably, said nucleic acid probe is a single stranded DNA, a cDNA (or parts thereof, like an EST), clone DNA and the like. In a further aspect the present invention is directed at a nucleic acid, which comprises at least one nucleic acid encoding one of the proteins of the present invention. Preferably, the nucleic acid consists of DNA, CNA, PNA, or RNA, wherein the DNA preferentially is either single or double stranded. Also comprised are DNA's, which hybridize to one of the aforementioned DNA's preferably under stringent conditions like, for example, hybridization at 6O 0 C in 2.5 x SSC buffer and several washes at 37°C at a lower buffer concentration like, for example, 0.5 x SSC buffer. Additional reagents required for carrying out stringent Northern or Southern blots like, for example, single stranded salmon sperm DNA are well known in the art. Also comprised are hybridizing nucleic acids as outlined above by the degeneration of the genetic code.

Hybridization causes a denatured polynucleotide probe and a denatured complementary target to form a stable duplex through base pairing. Hybridization methods are well known to those skilled in the art (See, for example, Laboratory Techniques in Biochemistry and Molecular Biology, Vol. 24: Hybridization With Nucleic Acid Probes, P. Tijssen, ed. Elsevier, New York, N. Y. (1993)). Conditions can be selected for hybridization where exactly complementary target and polynucleotide probe can hybridize, i.e., each base pair must interact with its complementary base pair. Alternatively, conditions can be selected where target and polynucleotide probes have mismatches but are still able to hybridize. Suitable conditions can be selected, for example, by varying the concentrations of salt or formamide in the pre- hybridization, hybridization and wash solutions, or by varying the hybridization and wash temperatures.

Hybridization specificity can be evaluated by comparing the hybridization of specificity- control polynucleotide probes to specificity-control target polynucleotides that are added to a sample in a known amount. The specificity-control target polynucleotides may have one or more sequence mismatches compared with the corresponding polynucleotide probes. In this manner, whether only complementary target polynucleotides are hybridizing to the polynucleotide probes or whether mismatched hybrid duplexes are forming is determined. Notably, a reverse hybridization variant of the technology exists in that the target is immobilized and the probe of interest is in the soluble phase of the assay. The latter variant is used for cDNA microarrays and DNA-chips.

Hybridization reactions can be performed in absolute or differential hybridization formats. In the absolute hybridization format, target polynucleotides from one sample are hybridized to the probes in a microarray format and signals detected after hybridization complex formation correlate to target polynucleotide levels in a sample. In the differential hybridization format, the differential expression of a set of genes in two biological samples is analyzed. For differential hybridization, target polynucleotides from both biological samples are prepared and labeled with different labelling moieties. A mixture of the two labelled target polynucleotides is added to a microarray. The microarray is then examined under conditions in which the emissions from the two different labels are individually detectable. Probes in the microarray that are hybridized to substantially equal numbers of target polynucleotides derived from both biological samples give a distinct combined fluorescence (Shalon et al.; WO 95/35505). In a preferred embodiment, the labels are fluorescent labels with distinguish-able emission spectra, such as a lissamine conjugated nucleotide analog and a fluorescein conjugated nu- cleotide-analog. In another embodiment Cy3/Cy5 fluorophores (Amersham Pharmacia Biotech) are employed.

After hybridization, the microarray is washed to remove nonhybridized nucleic acids and complex formation between the hybridisable array elements and the target polynucleotides is detected.

Methods for detecting complex formation are well known to those skilled in the art. In a preferred embodiment, the target polynucleotides are labelled with a fluorescent label and measurement of levels and patterns of fluorescence indicative of complex formation is accomplished by fluorescence microscopy, preferably confocal fluorescence microscopy. An argon ion laser excites the fluorescent label, emissions are directed to a photomultiplier and the amount of emitted light detected and quantitated. The detected signal should be proportional to the amount of probe/target polynucleotide complex at each position of the microarray. The fluorescence microscope can be associated with a computer-driven scanner device to generate a quantitative two-dimensional image of hybridization intensity. The scanned image is examined to determine the abundance/expression level of each hybridized target polynucleotide.

In a differential hybridization experiment, target polynucleotides from two or more different biological samples are labelled with two or more different fluorescent labels with different emission wavelengths. Fluorescent signals are detected separately with different photomulti- pliers set to detect specific wavelengths. The relative abundances/expression levels of the target polynucleotides in two or more samples is obtained.

Typically, microarray fluorescence intensities can be normalized to take into account variations in hybridization intensities when more than one microarray is used under similar test conditions. In a preferred embodiment, individual polynucleotide probe/target complex hy-

bridization intensities are normalized using the intensities derived from internal normalization controls contained on each microarray. Internal control genes can be grouped to individual sets.

In a further embodiment the nucleic acid of the present invention further comprises at least one promoter, enhancer, intron and/or polyA-sequence. Preferred promoters or enhancers have tissue specificity, such as neuronal specificity.

In some instances it might be desirable to interfere with, for example, the transcription or translation of the biomarkers of the present invention and, therefore, the present invention is also directed at a nucleic acid(s), which is/are complementary to the nucleic acid(s) of the present invention and, thus, is capable of inhibiting, for example, transcription or translation. A preferred embodiment of such a complementary nucleic acid is a so called anti-sense oligonucleotide (R. Q. Zheng and D. M. Kemeny (1995) Clin. Exp. Immunol. 100:380-2, W. Nellen and C. Lichtenstein (1993) Trends. Biochem. Sci. 18:419-423 and C. A. Stein (1992) Leukemia 6:967-74), ribozymes (M. Amarzguioui and H. Prydz (1998) Cell. MoI. Life Sci. 54:1175-1202, N. K. Vaish et al (1998) Nucleic Acids Res. 96:5237-5242, Persidis (1997) Nat. Biotechnol. 15:921-922 and L. A. Couture and D. T. Stinchcomb (1996) Trends Genet. 12:510-515) and/or so called small interfering RNA-molecules (siRNAs or RNAi 's) (S. M. Elbashir et al. (2001) Nature 411:494-498, Rondinone CM. RNAi for the Identification of New Targets for the Treatment of Metabolic Diseases. Endocrinology. 2006 Mar 23). Anti- sense oligonucleotides are able to decrease the stability of the above described nucleic acids and/or can inhibit the translation. Similarly the use of siRNA-oligonucleotides can also lead to a reduction in the amount of the translated polypeptides. Anti-sense oligonucleotides have in a preferred embodiment a length of at least 20, preferable of at least about 30, more preferably of at least about 40 and most preferably a length of at least about 50 nucleic acids.

Oligonucleotides are generally rapidly degraded by endo- or exonucleases, which are present in the cell, in particular by DNases und RNases and, therefore, it is advantageous to modify the nucleic acids which are used, for example, in anti-sense strategies, as ribozymes or siRNAs to stabilize them against degradation and thereby prolong the time over which an effective amount of the nucleic acid is maintained within the cell (L. Beigelmann et al. (1995) Nucleic acids Res. 23:3989-94, WO 95/11910, WO 98/37340 and WO 97/29116). Typically such stabilization can be obtained by the introduction of one or more internucleo- tide phosphate groups and/or by the introduction of one or more non-phosphor- internucleotides.

Suitable modified internucleotides are summarized in, for example, Uhlmann and Peimann (1990) Can. Rev. 90:544. Modified internucleotide phosphate residues and/or non-phosphate bridges which can be used in a nucleic acid of the invention comprise, for example, methyl- phosphonate, phosphorthioate, phosphoramidate, phosphordithionate, phosphate ester, non- phosphor internucleotide analogues, which can be used in nucleic acids of the invention include, for example, siloxane bridges, carbonate bridges, carboxymethylester, acetamid bridges and/or thioether bridges.

Preferred is a composition according to the invention, wherein the nucleic acid probe is immobilized on a substrate, and in particular wherein said nucleic acid probe is a hybridisable element on a microarray.

The term "microarray" refers to an ordered arrangement of hybridizable array elements. The array elements are arranged so that there are preferably at least one or more different array

elements, more preferably at least 100 array elements, and most preferably at least 1,000 array elements, on a 1 cm 2 substrate surface. The maximum number of array elements is unlimited, but is at least 100,000 array elements. Furthermore, the hybridization signal from each of the array elements is individually distinguishable. In a preferred embodiment, the array elements comprise polynucleotide probes.

The composition is particularly useful as hybridisable array elements in a microarray for monitoring the expression of a plurality of target polynucleotides (biomarkers). The microarray comprises a substrate and the hybridisable array elements. The microarray can be used, for example, in the diagnosis and the monitoring of the treatment of diabetic microangiopathy.

A preferred composition according to the present invention comprises at least 10, 15, 20, 50, 100, 125 or 560 biomarkers according to table 1 or a complement thereof.

The term "gene" or "genes" refers to the partial or complete coding sequence of a gene. The phrase "genes implicated in BEC biology" refers to genes that code for polypeptides which are differentially expressed in diabetic microangiopathy and include those listed in table 1. As used herein, the profile of transcripts which reflect gene expression in a particular tissue, at a particular time, is defined as a "transcript profile". Such profiles can be generated by naming, matching, and counting all copies of related clone inserts and arranging them in order of abundance. A "target transcript profile" refers to a profile derived from a biological sample that contains transcripts of interest along side transcripts which are not of interest. A "reference transcript profile" refers to a profile derived from a biological sample that contains predominantly transcripts that are not of interest.

Another preferred composition according to the present invention comprises all biomarkers according to table 1 or a complement thereof which exhibit a p-value in a t-test of less than 0.001, preferably of less than 0.0001, or most preferably of less than 0.00001. Another preferred composition according to the present invention comprises all biomarkers according to table 1 or a complement thereof which exhibit a signal intensity of larger than first, preferably larger than second, more preferably larger than third or most preferably larger than fourth standard deviation.

Particularly referred sets of biomarkers thus include the following, based on the t-test data:

Methyl-CpG binding domain protein 4 MBD4; 0.000007

STT3A; 0.000007 Hs.121592 Adaptor-related protein complex 1, sigma 2 subunit AP1S2; 0.000009

Hs.529408 Beta-site APP-cleaving enzyme 2 BACE2; 0.000022

Hs.544577 Glyceraldehyde-3 -phosphate dehydrogenase GAPDH; 0.000024

Adducin 3 (gamma) ADD3; 0.000033

ADP-ribosylation factor 4 ARF4; 0.000035

TLKl; 0.000052

This set includes markers according to table 1 having a p-value of less than 0.0001 (right column). Furthermore, the expression of the genes for MBD4, STT3A, AP1S2, BACE2, ADD3, ARF4, and TLKl can preferably be used as single markers for diabetic microangiopathy, or in combination with at least one of the other markers according to this set.

More preferably, this marker set can be expanded by the following markers:

Hs.374477 Ewing sarcoma breakpoint region 1 EWSRl 0.000124

Hs.469254 Lysine-rich coiled-coil 1 KRCCl 0.000133

OSBPLlA 0.000138

Leucine zipper transcription factor-like 1 LZTFLl O.OOO155

Vacuolar protein sorting 35 VPS35 0.000163

Hs.591209 DnaJ (Hsp40) homolog, subfamily C, member 3 DNAJC3 0.000177

This second set then includes markers according to table 1 having a p-value of less than 0.0002 (right column). More preferably, this second marker set can be expanded by the following markers:

Hs.519347 Splicing factor, arginine/serine-rich 12 SFRS 12 0.000202

Hs.544577 Glyceraldehyde-3 -phosphate dehydrogenase GAPDH 0.000211

RSUl 0.000222

Protease, serine, 23 PRS S23 0.000226

EPS8-like 2 EPS8L2 0.000234

Hs.438689 CDNA clone IMAGE:3897094 0.000242

Hs.603000 Acidic (leucine-rich) nuclear phosphoprotein 32 family, member E ANP32E 0.000248 GBEl 0.000276 Hs.363396 Complement factor H CFH 0.000277 Hs.159472 CDNA FLJ31718 fis, clone NT2RI2006647 0.000289 Hs.446149 Lactate dehydrogenase B LDHB 0.000299 Selenophosphate synthetase 1 SEPHSl 0.000307 Hs.210891 TBCl domain family, member 4 TBC 1D4 0.000328 Hs.480597 Ubiquitin specific peptidase 33 USP33 0.000344 STOM 0.000346 Hs.125898 GNAS 0.000350 GNAS 0.000354 Hs.374650 Interferon induced transmembrane protein 3 IFITM3 0.000372 Clone MO-30 mRNA sequence ? 0.000374 Hs.511149 Synaptosomal-associated protein, 23kDa SNAP23 0.000402 Hs.507243 Sorting nexin 4 SNX4 0.000405 Hs.511605 Annexin 2 ANXA2 0.000405 Hs.512963 Asparagine-linked glycosylation 11 homolog ALGl 1 0.000408 Hs.76152 Aquaporin 1 AQPl 0.000410 Fbxo7 0.000435 Hs.249441 WEEl homolog WEEl 0.000437 RNF 13 0.000453 NNMT 0.000461 Hs.516539 Heterogeneous nuclear ribonucleoprotein A3 HNRP A3 0.000465 Hs.532286 YTH domain family, member 2 YTHDF2 0.000519 Dual specificity phosphatase 22 DUSP22 0.000521 PRSS23 0.000530 Leucine rich repeat containing 32 LRRC32 0.000534 Tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, theta polypeptide YWHAQ 0.000538 GTP binding protein 4 GTPBP4 0.000552 Zinc finger, DHHC-type containing 17 ZDHHC 17 0.000599

Hs.222510 DAZ associated protein 1 DAZAP 1 0.000621 Mediator of RNA polymerase II transcription, subunit 4 homolog MED4 0.000621

BMX 0.000640

Splicing factor, arginine/serine-rich 6 SFRS6 0.000673 Hs.337040 ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-l,3)-N- acetylgalactosaminide alpha-2,6-sialyltransferase 3 ST6GALNAC3 0.000675

Protein phosphatase 1, regulatory (inhibitor) subunit 12A PPP1R12A 0.000680

TAF2 0.000681

Hs.446414 CD47 molecule CD47 0.000684

IFITM2 0.000689

Bromodomain containing 1 BRDl 0.000725

Hs.410817 Ribosomal protein Ll 3 RPLl 3 0.000727

Hs.544577 Glyceraldehyde-3 -phosphate dehydrogenase GAPDH 0.000766

PTPRK 0.000774

GALC 0.000781

SNX2 0.000809

GCA 0.000819

Hs.507475 Replication factor C (activator 1) 1 RFCl 0.000830

Hs.51891 Hect domain and RLD 4 HERC4 0.000861

Hs.362806 G protein-coupled receptor 116 GPRl 16 0.000874 Hs.144447 Bromodomain and WD repeat domain containing 2 BRWD2 0.000900

Hs.410817 Ribosomal protein L13 RPL13 0.000900

Hs.517148 THl-like (Drosophila) THlL 0.000913

Hs.125898 GNAS 0.000914

Hs.445403 Isoleucine-tRNA synthetase IARS 0.000920

ELF2 0.000926

ATP6V0D1 0.000933

NIMA (never in mitosis gene a)-related kinase 7 NEK7 0.000937

Hs.595822 Homeobox A5 HOXA5 0.000940

Hs.466471 Glucose phosphate isomerase GPI 0.000956

Unc-50 homolog (C. elegans) UNC50 0.000967

Hs.103183 Fragile X mental retardation 1 FMRl 0.000988

Hs.268887 Serine/threonine kinase 17a (apoptosis-inducing) STKl 7A 0.000997

This third set then includes markers according to table 1 having a p-value of less than 0.001 (right column).

Furthermore, the 559 sequences differentially regulated in diabetic compared to non-diabetic BECs as described herein can be classified in diverse (redundant) groups of discriminating significance according to several other criteria.

1. Mathematical method of detection:

Two methods were applied that identified significant differences of regulation: T-test (see also above), and the Relative Variance Method (RVM).

From table 1, sequences (group A) were identified and grouped by both T-test and RVM. Among these, 9 sequences were deregulated stronger than the 4 th standard deviation from the mean of the ratios (group Al, see table 1), while 22 sequences were deregulated to a signal level in the range bounded by the signal of the 3 rd and the 4 th standard deviation (group A2). All sequences of group A had a T-test p-value of < 0.01.

Thus, sequences of group A could additionally be ranked according to their p- values: < 0.00001 : 1 gene (group A3.1), < 0.0005: 3 additional sequences (group A3.2), < 0.001: 3 additional sequences (group A3.3), < 0.005: 11 additional sequences (group A3.4), < 0.01 : 13 additional sequences (group A3.5).

Furthermore, 478 of the 559 sequences were exclusively detected by T-test, but not by RVM (group B). All sequences of group B had a T-test p- value of < 0.01 and can additionally be ranked according to their p-values: < 0.0001 : 2 sequences (group Bl), < 0.00005: 4 additional sequences (group B2), < 0.0001 : 1 additional gene (group B3), < 0.0005: 32 additional sequences (group B4), < 0.001: 36 additional sequences (group B5), < 0.005: 226 additional sequences (group B6), < 0.01: 177 sequences (group B7).

Finally, 50 sequences were identified by RVM only (group C), with 35 sequences within the third standard deviation range (group Cl) and 15 sequences with larger values than the 4 th standard deviation (group Cl).

An additional classification can be made based on the level of fold-expression: 178 sequences were down-regulated at least twofold (group D) in diabetics versus non-diabetics. 49 sequences were up-regulated at least twofold (group E) in diabetics versus non-diabetics.

2. Multiple detections:

Due to design of the DNA chip sequences designated separate genes can belong to distant stretches within the same gene. This redundancy on the one hand side reduces the complexity of the set to 526 genes, on the other hand strengthens the validity of those genes being detected more than once. 33 genes were detected more than once (group F).

3. Annotation status :

Out of the 559 sequences 515 were annotated, i.e. assigned to a name (group G), while 44 were not annotated on protein levels (group H, 02/2007).

4. Functional groups:

All 559 sequences were functionally characterized using the software GOSurfer. GOSurfer (Zhong et al., Appl Bioinformatics 3 (4): 261-26, 2004) calculates correlation between a gene ontology (GO) term and a gene (group I). A p-value of < 0.01 was required for a functional group to be included. Moreover, at least 2 % of the 559 sequences had to be represented in a functional group. Redundancy was accepted. Note that levels of GO hierarchy were not considered and that similar groups were fused manually. The following groups were defined:

- Biosynthesis / tRNA binding / structural constituent of ribosome / cytosolic ribosome (sensu Eukaryota) / eukaryotic 48S initiation complex / ribosome / ribonuleoprotein complex (76 sequences, group II, 13.6 %)

- Hydrolase activity / acting on acid anhydrides / in phosphorus-containing anhydrides (22 sequences, group 12, 3.9 %)

- Cell adhesion / cell-cell adherence junction (17 sequences, group 13.1, 3.0 %)

- ATP binding (17 sequences, group 13.2, 3.0 %)

- Cell death (16 sequences, group 14, 2.9 %)

- GTP binding (12 sequences, group 15, 2.1 %)

In another preferred aspect thereof, the invention relates to a method for diagnosing or monitoring the treatment of diabetic microangiopathy in a sample, said method comprising the steps of: a) obtaining nucleic acids from said sample; b) contacting the nucleic acids of the sample with an array comprising a nucleic acid probe according to the present invention un-

der conditions to form one or more hybridization complexes; c) detecting said hybridization complexes; and d) comparing the levels of the hybridization complexes detected in step (c) with the level of hybridization complexes detected in a non-diseased sample, wherein the altered level of hybridization complexes detected in step (c) compared with the level of hybridization complexes of a non-diseased sample correlates with the presence of diabetic microangiopathy.

In yet another preferred aspect thereof, the invention relates to a method for identifying candidate compounds for the treatment of diabetic microangiopathy, said method comprising: a) contacting a cell with at least one candidate compound, b) obtaining nucleic acids from said cell, c) contacting the nucleic acids of said sample with an array comprising a nucleic acid probe according to the present invention under conditions to form one or more hybridization complexes; d) detecting said hybridization complexes; and e) comparing the levels of the hybridization complexes detected in step (d) with the level of hybridization complexes detected in a sample of a cell which has not been contacted with said at least one candidate compound, wherein the altered level of hybridization complexes detected in step (d) compared with the level of hybridization complexes detected in a sample of a cell which has not been contacted with said at least one candidate compound identifies candidate compounds for the treatment of diabetic microangiopathy. Preferred is a method according to the present invention, wherein said candidate compound alters the level of hybridization complexes of biomarkers according to table 1 or a complement thereof which exhibit a p-value in a t-test of less than 0.001, preferably of less than 0.0001, more preferably of less than 0.00001 or most preferably of less than 0.000001. Further preferred is a method according to the present invention, wherein said candidate compound alters the level of hybridization complexes of biomarkers according to table 1 or a complement thereof which exhibit a signal intensity of larger than first, preferably larger than second, more preferably larger than third or most preferably larger than fourth standard deviation. Further preferred is a method according to the present invention which furthermore comprises the step of formulating said identified compound into a pharmaceutical preparation.

In another aspect, the present invention provides an expression profile that can reflect the levels of a plurality of target polynucleotides (biomarkers) in a sample. The expression profile comprises a cDNA microarray or a DNA-chip and a plurality of detectable complexes. Each detectable complex is formed by hybridization of at least one of said target polynucleotides to at least one of said polynucleotide probes and further comprises a labelling moiety for detection.

In another aspect, the present invention provides biomarkers (in the following also termed "polypeptide" or" marker") comprising the same or substantially the same amino acid sequence of the polypeptides as encoded by a gene as listed in table 1 , or a splice variant thereof. A polypeptide having substantially the same amino acid sequence comprises polypeptides with at least about 95%, preferably at least about 96%, more preferably at least about 97%, more preferably with at least about 98% and most preferably with at least about 99% amino acid sequence identity. The amino acid exchanges are preferably so called conservative changes meaning substitutions of, for example, a polar amino acid residue by another polar amino acid residue, of an acidic amino acid residue by another acidic amino acid residue or of a basic amino acid residue by another basic amino acid residue.

The biomarkers as identified in the context of the present invention provide valuable tools in order to function as "targef'-genes and/or polypeptides which can be used in order to develop new and effective treatment strategies against diabetic microangiopathy. The bio-

markers may be used either as a single marker, wherein preferably markers are used as single markers that exhibit a p- value TT of less than 0.0001 or more preferably of less than 0.00001, or as a combination of markers (such as 2, 3, 4, 5, 6, and more), wherein the combination of markers provides a combined p-value TT of less than 0.00001 or more preferably of less than 0.00001. Furthermore, the biomarkers may be used either as a single marker, wherein preferably markers are used as single markers that exhibit a signal intensity of larger than first, preferably larger than second, more preferably larger than third or most preferably larger than fourth standard deviation. The biomarkers employed in the tests and assays according to the present invention can either be purified from cells or can be recombinantly expressed and purified by methods well known in the art.

In one embodiment of the present invention, the protein comprises at least one fragment of a polypeptide as encoded by a gene as listed in table 1. A fragment within the meaning of the present invention refers to one of the proteins according to a gene as listed in table 1 bearing at least one N-terminal, C-terminal and/or internal deletion. The resulting fragment has a length of at least about 50, preferably of at least about 100, more preferably of at least about 150, more preferably of at least about 200, more preferably of at least about 250, more preferably of at least about 300, and most preferably of at least about 400 amino acids.

A further aspect of the present invention is directed at a vector comprising a polypeptide according to the present invention and/or a nucleic acid according to the present invention. A vector within the meaning of the present invention is a protein or a nucleic acid or a mixture thereof which is capable of being introduced or of introducing the polypeptides and/or nucleic acid comprised into a cell. It is preferred that the polypeptides encoded by the introduced nucleic acid are expressed within the cell upon introduction of the vector.

In a preferred embodiment the vector of the present invention comprises plasmids, phagemids, phages, cosmids, artificial mammalian chromosomes, knock-out or knock-in constructs, viruses, in particular adenovirus, vaccinia virus, lentivirus (Chang, LJ. and Gay, E.E. (20001) Curr. Gene Therap. 1 :237-251), Herpes simplex virus (HSV-I, Carlezon, W.A. et al. (2000) Crit. Rev. Neurobiol.), baculovirus, retrovirus, adeno-associated-virus (AAV, Carter, P.J. and Samulski, R.J. (2000) J. MoI. Med. 6:17-27), rhinovirus, human immune deficiency virus (HIV), filovirus and engineered versions thereof (see, for example, Cobinger G. P. et al (2001) Nat. Biotechnol. 19:225-30), virosomes, "naked" DNA liposomes, and nucleic acid coated particles, in particular gold spheres. Particularly preferred are viral vectors like adenoviral vectors or retroviral vectors (Lindemann et al. (1997) MoI. Med. 3:466- 76 and Springer et al. (1998) MoI. Cell. 2:549-58). Liposomes are usually small unilamellar or multilamellar vesicles made of neutral cationic and/or anionic lipids, for example, by ultrasound treatment of liposomal suspensions. The DNA can, for example, be ionically bound to the surface of the liposomes or internally enclosed in the liposome. Suitable lipid mixtures are known in the art and comprise, for example, cholesterol, phospholipide like, for example, phosphatidylcholin (PC), phosphatidylserin (PS) and the like, DOTMA (1, 2- Dioleyloxpropyl-3-trimethylammoniumbromid) and DPOE (Dioleoylphosphatidylethanola- min) which both have been used on a variety of cell lines.

Nucleic acid coated particles are another means for the introduction of nucleic acids into cells using so called "gene guns", which allow the mechanical introduction of particles into the cells. Preferably the particles itself are inert, and therefore, are in a preferred embodiment made out of gold spheres.

In a further aspect the present invention is directed at an isolated and/or recombinant host cell comprising a polypeptide of the present invention, a nucleic acid of the present invention and/or a vector of the present invention. Cells of the present invention can be prokaryotic or eukaryotic cells. The cells preferably comprise the nucleic acids extrachromosomally or in- terchromosomally.

A further aspect of the present invention is a transgenic non-human animal generated from a cell or cells of the present invention. The animal can be a mosaic animal, which means that only part of the cells making up the body comprise cells of the present invention or the animal can be a transgenic animal which means that all cells of the animal are derived from a cell of the present invention. Mosaic or transgenic animals can be either homo- or heterozygous with respect to the nucleic acid of the present invention contained within the cell of the present invention. In a preferred embodiment the transgenic animals are either homo- or heterozygous knock-out or knock-in animals with respect to the genes which code for the polypeptides of the present invention.

In a further aspect the present invention is directed at an antibody directed, in particular specifically directed, against a polypeptide (or antigenic part thereof) of the present invention. The term "antibody" comprises monoclonal and polyclonal antibodies and binding fragments thereof, in particular Fc-fragments as well as so called "single-chain-antibodies" (Bird R. E. et al (1988) Science 242:423-6) and diabodies (Holliger P. et al (1993) Proc. Natl. Acad. Sci. U.S.A. 90:6444-8).

In a further aspect the present invention is directed at a method of producing a polypeptide of the present invention or a nucleic acid of the present invention and comprises the steps of: a) cultivating a cell of the present invention and b) isolating the polypeptide and/or the nucleic acid. If the method is used primarily to isolate nucleic acids then in a preferred embodiment the cells, which are used are prokaryotic cells, in particular E. coli cells. If the method is used primarily for the isolation of polypeptides of the invention than the cells can be either of prokaryotic or eukaryotic origin. Someone of skill in the art is aware of a variety of different cell types suitable for the production of proteins like, for example, E. coli, SfP, Hi5, P. pastoris, COS and HeLa. Eukaryotic cells are preferably chosen, if it is desired that the polypeptides produced by the cells exhibit an essentially natural pattern of glycosylation and prokaryotic cells are chosen, if, for example, glycosylation or other modifications, which are normally introduced into proteins only in eukaryotic cells, are not desired or not needed.

In a further aspect the present invention is directed at a method of isolating compounds interacting with a polypeptide (biomarker) of the present invention comprising the steps of: a) contacting one or more of the polypeptide(s) of the present invention, preferably one, with at least one potentially interacting compound, and b) measuring binding of said compound to said polypeptide. This method is suitable for the determination of compounds that can interact with the polypeptides of the present invention and to identify, for example, inhibitors, activators, competitors or modulators of polypeptides of the present invention, in particular inhibitors, activators, competitors or modulators of the enzymatic activity of the proteins of the present invention.

The potentially binding substance, whose binding to the polypeptide of the present invention is to be measured, can be any chemical substance or any mixture thereof. For example, it can be a substance of a peptide library, a combinatory library, a cell extract, in particular a plant cell extract, a "small molecular drug", a protein and/or a protein fragment.

The term "contacting" in the present invention means any interaction between the potentially binding substance(s) with the polypeptides of the invention, whereby any of the two components can be independently of each other in a liquid phase, for example in solution, or in suspension or can be bound to a solid phase, for example, in the form of an essentially planar surface or in the form of particles, pearls or the like. In a preferred embodiment a multitude of different potentially binding substances are immobilized on a solid surface like, for example, on a compound library chip and the protein of the present invention is subsequently contacted with such a chip.

The polypeptides of the present invention employed in a method of the present invention can be full length proteins or a fragments with N/C -terminal and/or internal deletions. Preferably the fragments are either N-terminal fragments comprising the enzymatic region of the polypeptide or C-terminal fragments comprising the cytoplasmic region, depending on whether potentially interacting compounds are sought that specifically interact with the N- or C- terminal fragment.

Measuring of binding of the compound to the polypeptide can be carried out either by measuring a marker that can be attached either to the protein or to the potentially interacting compound. Suitable markers are known to someone of skill in the art and comprise, for example, fluorescence or radioactive markers. The binding of the two components can, however, also be measured by the change of an electrochemical parameter of the binding compound or of the protein, e.g. a change of the redox properties of either the polypeptide or the binding compound, upon binding. Suitable methods of detecting such changes comprise, for example, potentiometric methods. Further methods for detecting and/or measuring the binding of the two components to each other are known in the art and can without limitation also be used to measure the binding of the potential interacting compound to the polypeptide or polypeptide fragments of the present invention. The effect of the binding of the compound or the activity of the polypeptide can also be measured indirectly, for example, by assaying a phosphatase activity of a polypeptide (if present) after binding, and the like.

As a further step after measuring the binding of a potentially interacting compound and after having measured at least two different potentially interacting compounds at least one compound can be selected, for example, on grounds of the measured binding activity or on grounds of the detected increase or decrease of polypeptide activity.

The thus selected binding compound is then in a preferred embodiment modified in a further step. Modification can be effected by a variety of methods known in the art, which include without limitation the introduction of novel side chains or the exchange of functional groups like, for example, introduction of halogens, in particular F, Cl or Br, the introduction of lower alkyl groups, preferably having one to five carbon atoms like, for example, methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, n-pentyl or iso-pentyl groups, lower alkenyl groups, preferably having two to five carbon atoms, lower alkynyl groups, preferably having two to five carbon atoms or through the introduction of, for example, a group selected from the group consisting of NH 2 , NO 2 , OH, SH, NH, CN, aryl, heteroaryl, COH or COOH group.

The thus modified binding substances are than individually tested with a method of the present invention, i.e. they are contacted with the polypeptide and subsequently binding of the modified compounds to the polypeptide is measured. In this step, both the binding per se can be measured and/or the effect of the function of the polypeptide like, e.g. the enzymatic activity of the polypeptide can be measured. If needed the steps of selecting the binding com-

pound, modifying the binding compound, contacting the binding compound with a polypeptide of the invention and measuring the binding of the modified compounds to the protein can be repeated a third or any given number of times as required. The above described method is also termed "directed evolution" since it involves a multitude of steps including modification and selection, whereby binding compounds are selected in an "evolutionary" process optimizing its capabilities with respect to a particular property, e.g. its binding activity, its ability to activate, inhibit or modulate the activity of the polypeptide(s) of the present invention.

In a further embodiment of the method of the present invention the interacting compound identified as outlined above, which may or may not have gone through additional rounds of modification and selection, is admixed with suitable auxiliary substances and/or additives. Such substances comprise pharmacological acceptable substances, which increase the stability, solubility, biocompatibility, or biological half-life of the interacting compound or comprise substances or materials, which have to be included for certain routs of application like, for example, intravenous solution, sprays, Band- Aids or pills.

Accordingly, a further aspect of the present invention is the use of a pharmaceutical composition of the invention for the production of a medicament for the treatment of diabetic microangiopathy and/or a related disease, such as diabetes.

A further aspect of the present invention is then a method of treatment of diabetic microangiopathy and/or a related disease or condition, such as diabetes, in a mammal, comprising administering to said mammal an effective amount of a polypeptide according to the invention as above, a nucleic acid according to the invention as above, a vector containing these nucleic acids as above, a cell according to the invention as above, an antibody according to the invention as above, a binding compound isolated by the method according to the invention as above and/or a pharmaceutical composition according to the invention as above. Preferably, an inhibiting active agent is administered in form of a pharmaceutical composition, such as an antibody, antisense nucleotide or an inhibiting binding compound.

An "effective amount" is an amount of the conpound(s) as mentioned above that a) acts on the expression and/or abundance of the biomarkers as analysed which are selected from the group of markers as given in table 1 , and which alleviates symptoms as found for diabetic microangiopathy (which might overlap with diabetic symptoms in general).

The present invention in one aspect thereof provides a composition comprising a plurality of polynucleotide probes comprising at least a portion of genes implicated in diabetic microangiopathy. Preferably, the polynucleotide probes comprise at least a portion of one or more of the sequences presented in table 1. In one preferred embodiment, the composition comprises a plurality of polynucleotide probes, wherein each polynucleotide probe comprises at least a portion of a sequence selected from the group as presented in table 1.

The composition is particularly useful when it is used as hybridisable array elements in a microarray. Such a microarray can be employed to monitor the expression of genes of unknown function, but which are differentially or abundantly expressed in diabetic microangiopathy. In addition, the microarray can be used to monitor the expression of genes with a known function in diabetes.

The microarray can be used for large scale genetic or gene expression analysis of a large number of target polynucleotides. The microarray can be used in the diagnosis of diabetic

disease and in the monitoring of treatments where altered expression of genes implicated in diabetic microangiopathy cause disease. The microarray can also be used to investigate an individual's predisposition to the disease. Furthermore, the microarray can be employed to investigate cellular responses in diabetic microangiopathy.

When the composition of the invention is employed as hybridisable array elements in a microarray, the array elements are organized in an ordered fashion so that each element is present at a specified location on the substrate. Because the array elements are at specified locations on the substrate, the hybridization patterns and intensities (which together create a unique expression profile) can be interpreted in terms of expression levels of particular genes and can be correlated with the disease or treatment.

The composition comprising a plurality of polynucleotide probes can also be used to purify a subpopulation of mRNAs, cDNAs, genomic fragments and the like, in a sample. Typically, samples will include the target polynucleotides of interest and other nucleic acids which may enhance the hybridization background in the sample. Therefore it may be advantageous to remove these nucleic acids. One method for removing the additional nucleic acids is by hybridizing the sample containing target polynucleotides with immobilized polynucleotide probes under hybridizing conditions. Those nucleic acids that do not hybridize to the polynucleotide probes are washed away. At a later point, the immobilized target polynucleotide probes can be released in the form of purified target polynucleotides.

The polynucleotide probes can be prepared by a variety of synthetic or enzymatic schemes which are well known in the art. The probes can be synthesized, in whole or in part, using chemical methods well known in the art. (Caruthers et al. (1980) Nucleic. Acids Symp. Ser. (2) 215-233). Alternatively, the probes can be generated, in whole or in part, enzymatically.

Nucleotide analogues can be incorporated into the polynucleotide probes by methods well known in the art. The only requirement is that the incorporated nucleotide analogues must serve to base pair with target polynucleotide sequences. For example, certain guanine nucleotides can be substituted with hypoxanthine which base pairs with cytosine residues. However, these base pairs are less stable than those between guanine and cytosine. Alternatively, adenine nucleotides can be substituted with 2,6-diaminopurine which can form stronger base pairs than those between adenine and-thymidine.

Additionally, the polynucleotide probes can include nucleotides that have been derivatized chemically or enzymatically. Typical chemical modifications include derivatization with acyl, alkyl, aryl or amino groups.

The polynucleotide probes can be immobilized on a substrate. Preferred substrates are any suitable rigid or semirigid 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 the polynucleotide probes are bound. Preferably, the substrates are optically transparent.

Probes can be synthesized, in whole or in part, on the surface of a substrate by using a chemical coupling procedure and a piezoelectric printing apparatus, such as that described in PCT publication WO 95/251116 (Baldeschweiler et al.). Alternatively, the probe can be synthesized using a self-addressable electronic device that controls when reagents are added

(Heller et al. U.S. Pat. No. 5,605,662) or by photolysis using imaging fibers for light delivery (Healey et al. (1995) Science 269: 1078-80).

Furthermore, the probes do not have to be directly bound to the substrate, but rather can be bound to the substrate through a linker group. The linker groups are typically about 6 to 50 atoms long to provide exposure to the attached polynucleotide probe. Preferred linker groups include ethylene glycol oligomers, diamines, diacids and the like. Reactive groups on the substrate surface react with one of the terminal portions of the linker to bind the linker to the substrate. The other terminal portion of the linker is then functionalized for binding the polynucleotide probe.

The polynucleotide probes can be attached to a substrate by dispensing reagents for probe synthesis on the substrate surface or by dispensing preformed DNA fragments or clones on the substrate surface. Typical dispensers include a micropipette delivering solution to the substrate with a robotic system to control the position of the micropipette with respect to the substrate. There can be a multiplicity of dispensers so that reagents can be delivered to the reaction regions simultaneously.

DNA or RNA can be isolated from the sample according to any of a number of methods well known to those of skill in the art. For example, methods of purification of nucleic acids are described in Laboratory Techniques in Biochemistry and Molecular Biology: Hybridization With Nucleic Acid Probes, Part I. Theory and Nucleic Acid Preparation, P. Tijssen, ed. El- sevier, New York, N. Y. (1993). In one case, total RNA is isolated using the TRIZOL total RNA isolation reagent (Life Technologies, Gaithersburg, Md.) and mRNA is isolated using oligo d(T) column chromatography or glass beads. Alternatively, when target polynucleotides are derived from an mRNA, the target polynucleotides can be a cDNA reverse transcribed from an mRNA, an RNA transcribed from that cDNA, a DNA amplified from that cDNA, an RNA transcribed from the amplified DNA, and the like. When the target polynucleotide is derived from DNA, the target polynucleotide can be DNA amplified from DNA or RNA reverse transcribed from DNA. In yet another alternative, the targets are target polynucleotides prepared by more than one method.

When target polynucleotides are amplified it is desirable to amplify the nucleic acid sample and maintain the relative abundances of the original sample, including low abundance transcripts. Total mRNA can be amplified by reverse transcription using a reverse transcriptase and a primer consisting of oligo d(T) and a sequence encoding the phage T7 promoter to provide a single stranded DNA template. The second cDNA strand is polymerized using a DNA polymerase and a RNAse which assists in breaking up the DNA/RNA hybrid. After synthesis of the double stranded cDNA, T7 RNA polymerase can be added and RNA transcribed from the second cDNA strand template (Van Gelder et al. U.S. Pat. No. 5,545,522). RNA can be amplified in vitro, in situ or in vivo (See Eberwine, U.S. Pat. No. 5,514,545).

It is also advantageous to include quantitation controls within the sample to assure that amplification and labelling procedures do not change the true distribution of target polynucleotides in a sample. For this purpose, a sample is spiked with a known amount of a control target polynucleotide and the composition of polynucleotide probes includes reference polynucleotide probes which specifically hybridize with the control target polynucleotides. After hybridization and processing, the hybridization signals obtained should reflect accurately the amounts of control target polynucleotide added to the sample.

Prior to hybridization, it may be desirable to fragment the nucleic acid target polynucleotides. Fragmentation improves hybridization by minimizing secondary structure and cross- hybridization to other nucleic acid target polynucleotides in the sample or noncomplemen- tary polynucleotide probes. Fragmentation can be performed by mechanical or chemical means.

The target polynucleotides may be labelled with one or more labelling moieties to allow for detection of hybridized probe/target polynucleotide complexes. The labelling moieties can include compositions that can be detected by spectroscopic, photochemical, biochemical, bioelectronic, immunochemical, electrical, optical or chemical means. The labelling moieties include radioisotopes, such as 32 p, 33 p or 35 S, chemiluminescent compounds, labelled binding proteins, heavy metal atoms, spectroscopic markers, such as fluorescent markers and dyes, magnetic labels, linked enzymes, mass spectrometry tags, spin labels, electron transfer donors and acceptors, and the like.

Exemplary dyes include quinoline dyes, triarylmethane dyes, phthaleins, azo dyes, cyanine dyes and the like. Preferably, fluorescent markers absorb light above about 300 nm, preferably above 400 nm, and usually emit light at wavelengths at least greater than 10 nm above the wavelength of the light absorbed. Specific preferred fluorescent markers include fluorescein, phycoerythrin, rhodamine, lissamine, and Cy3 and Cy5 available from Amersham Pharmacia Biotech (Piscataway, N.J.).

Labelling can be carried out during an amplification reaction, such as polymerase chain and in vitro transcription reactions, or by nick translation or 5' or 3 '-end-labeling reactions. In one case, labelled nucleotides are used in an in vitro transcription reaction. When the label is incorporated after or without an amplification step, the label is incorporated by using terminal transferase or by kinasing the 5' end of the target polynucleotide and then incubating overnight with a labelled oligonucleotide in the presence of T4 RNA ligase.

Alternatively, the labelling moiety can be incorporated after hybridization once a probe/target complex has formed. In one case, biotin is first incorporated during an amplification step as described above. After the hybridization reaction, unbound nucleic acids are rinsed away so that the only biotin remaining bound to the substrate is that attached to target polynucleotides that are hybridized to the polynucleotide probes. Then, an avidin-conjugated fluorophore, such as avidin-phycoerythrin, that binds with high affinity to biotin is added. In another case, the labelling moiety is incorporated by intercalation into preformed tar- get/polynucleotide probe complexes. In this case, an intercalating dye such as a psoralen- linked dye can be employed.

Under some circumstances it may be advantageous to immobilize the target polynucleotides on a substrate and have the polynucleotide probes bind to the immobilized target polynucleotides. In such cases the target polynucleotides can be attached to a substrate as described above.

The expression profile comprises the polynucleotide probes of the invention. The expression profile also includes a plurality of detectable complexes. Each complex is formed by hybridization of one or more polynucleotide probes to one or more complementary target polynucleotides. At least one of the polynucleotide probes, preferably a plurality of polynucleotide probes, is hybridized to a complementary target polynucleotide forming, at least one, preferably a plurality of complexes. A complex is detected by incorporating at least one labelling moiety in the complex. The labelling moiety has been described above. The expres-

sion profiles provide "snapshots" that can show unique expression patterns that are characteristic for diabetic microangiopathy and the different stages thereof.

In another aspect thereof the present invention relates to a composition as described above, wherein said composition comprises all biomarkers according to table 1 or a complement thereof which exhibit a signal intensity of larger than first, preferably larger than second, more preferably larger than third or most preferably larger than fourth standard deviation. Further preferred is a respective method according to the invention, where such composition is employed.

In another aspect thereof the present invention relates to a method of treating diabetic microangiopathy, comprising monitoring the diabetic microangiopathy using the methods as described herein, and selecting a further treatment based, at least in part, on said monitoring. Normally, the aim of such a further treatment would be, to regulate the expression of the biomarkers according to the invention in such a way that their expression reaches a value as found/present in non-diabetic and/or healthy samples.

Finally, the polypeptides and genes encoding the same are novel important components involved in diabetic microangiopathy. Thus the inventors provide possibly new anti-diabetic microangiopathy drug target(s).

The following examples merely serve to illustrate the invention and should not be construed to restrict the scope of the invention to the particular embodiments of the invention described in the examples. All references cited in the text are hereby incorporated in their entirety by reference.

Examples

In general, the present invention was based on a diagnostic approach for diabetic microangiopathy, wherein by means of chip-analysis the activity of 559 sequences from blood capillary endothelial cells that were directly isolated from the skin of the patient (ex vivo) were found as relevant for diagnosis and/or monitoring diabetic microangiopathy.

The inventors have compared ex vivo samples of purified BECs from 5 diabetic patoents with purified BECs from 8 non-diabetic patients. By applying technical optimization steps, the inventors identified 559 genes (see table 1, below). These genes were classified according to the p-value of t-tests, and/or deviation from average (standard deviation classes). Since some genes were present on the chip in several copies, table 1 also includes redundant genes.

Furthermore, manual checks were done by correlation of signal values (RNA values) of selected genes with clinical parameters, chromosomal location, etc.. Two genes (Aquaporin 1, AQPl and FNl) out of the listing as shown in table 1 have been exemplary confirmed on tissue sections of the patients, from which the RNA samples were derived from.

The gene Aquaporin 1 showed a p-value of 0.000410 in the T-test; and Fibronectin 1 showed p-values of 0.006306 and 0.006332 in the T-test (two tests were made).

A gene that was not present in the 559 list as shown in table 1 (CD31) was found regulated in sections as well. In addition, the inventors have performed a clinical pilot project, in which the protein for the gene SDFl was differentially abundant in sera of diabetic patients versus non-diabetic patients.

The 559 gene set as shown in table 1 includes biomarkers for: a) Diagnostic use, i.e. determining the profile of diabetic samples (for example kidney biopsies, sera, skin biopsies), as described herein, for example in the context of a diabetic treatment, b) Therapeutic targets, i.e. tools for screening of drugs, agents, and the development of medicaments against diabetic microangiopathy, such as, for example, small molecules or antibodies, and c) Pharmaceutically effective polypeptide drugs on the basis of the markers (or fragments thereof) themselves.

Table 1. List of genes associated with human diabetic microangiopathy.

As described in the main text, skin blood vascular endothelial cells from five diabetics (D) with morphologically and clinically proven diabetic microangiopathy and eight non-diabetics (ND) were analyzed for global RNA expression profiles by genome-wide DNA-chip analysis. After normalization two methods, i.e. T-test and relative variance method (RVM), were applied in order to identify those genes that were significantly differentially repressed or induced in diabetic versus non-diabetic samples. 559 genes (column 1) were found. Basic annotation (gene symbol (2) and accession number of corresponding protein (3)) was done manually. Fold-ratio of RNA expression levels for each gene (4) and its standard deviation (5). A portion of the gene set was detected by T-test only, another by RVM only, and the rest portion by both methods (TTnoOverlap, RVMnoOverlap, Overlap; 6). The corresponding significance thresholds are given in columns 7 and 8. Next, the 559 genes were subclassified according to mathematical (9 and 10), technical (11), extent of deviation, i.e. ratio, (12), annotation

(13), and functional group (14). 7-13 were done manually, 14 by GOSurfer software. Genes without current annotation are in italics.

Table 1 Biomarkers of the invention inner Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method p value TT SD RVM mathematical mathematical multiple > 2fold annotation functional group subspecified detection

1 ABIl NP_005461 1 0,584622 0,301 198 TTnoOverlap 0 002121 B6 G

2 ABLlM I NP 055760 1 1,593328 0,790633 TTnoOverlap 0 006682 B7 G

3 ACADM sp PU310 0,532034 0,312081 TTnoOverlap 0 002910 B6 G

4 ACBD3 NP_073572 2 0,4881 1 0,342935 TTnoOverlap 0 001675 B6 D G

5 ADAM 17 sp P78536 0,597569 0,278905 TTnoOverlap 0 007735 B7 G

6 ADAMTS9 NP_008919 2 2,692269 3,153053 RVMnoOverlap 3 Cl E G

7 ADD3 sp Q9UEY8 0,436167 0,202353 TTnoOverlap 0 000033 B2 D G

8 ALGU NP_067677 I 0,45039 0,19227 TTnoOverlap 0 000408 B4 D G

9 ANKRDlO NP_060134 1 0,733391 0, 174969 TTnoOverlap 0 002770 B6 G

10 ANKRD27 NP_1 15515 1 0,585753 0,285671 TTnoOverlap 0 00521 1 B7 G

1 1 ANP32E NPJ 12182 1 0,420128 0,31463 TTnoOverlap 0 000248 B4 D G

12 ANXA2 sp P07355 1 ,365312 0,305363 TTnoOverlap 0 000405 B4 F G

13 ANXA2 sp P07355 1 ,307675 0,28951 TTnoOverlap 0 001293 B6 F G

14 ANXA2 sp P07355 1,284173 0,331867 TTnoOverlap 0 005831 B7 F G

15 ANXA4 pir A42077 0,61 1786 0,338014 TTnoOverlap 0 007793 B7 G K*

16 ANXA8 sp P 13928 0,255744 0,439936 RVMnoOverlap 3 Cl D K*

G

17 AP1S2 sp P56377 0,555472 0,175214 TTnoOverlap 0 000009 Bl G

18 AP3S1 NPJ)01275 I 0,6421 14 0,303138 TTnoOverlap 0 003169 B6 G

19 APPBP2 NPJ306371 2 0,34471 0,275569 TTnoOverlap 0 002398 B6 D G 12, 13 2

20 APRIN NP_055847 1 0,485126 0,277805 TTnoOverlap 0 005170 B7 F D G

21 APRIN NP_055847 1 0,596703 0,243802 TTnoOverlap 0 001332 B6 F G 13 2

22 AQPl pir A41616 2,546389 3,22646 RVMnoOverlap 3 Cl F E G

23 AQPl pir A416I6 1,71524 0,659277 TTnoOverlap 0 000410 B4 F G

24 AQP3 sp Q92482 0,263151 0,349338 RVMnoOverlap 3 Cl D G

25 ARF4 pir B38622 1,594536 0,397344 TTnoOverlap 0 000035 B2 G 12, 15

26 ARHGEF3 NP_062455 1 0,803872 0,184568 TTnoOverlap 0 006237 B7 G

27 ARID4A NP_002883 2 0,428782 0,297903 TTnoOverlap 0 001381 B6 D G

28 ARL3 pir A54869 0,598321 0,326498 TTnoOverlap 0 002874 B6 G 15

29 ARL6IP2 NP_071769 1 1,547533 0,65881 TTnoOverlap 0 004843 B6 G

30 ASB9 pir T12477 0,591 195 0,18383 TTnoOverlap 0 00151 1 B6 G

31 ATFl pir S 12560 0,378147 0,435574 TTnoOverlap 0 003001 B6 D G

32 ATF2 pir SO538O 0,392332 0,284757 TTnoOverlap 0 006403 B7 D G

33 ATPl B3 sp P54709 1,770005 0,804062 TTnoOverlap 0 001033 B6 G 12. 13 2

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T 1T 1 S SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

34 ATP5B pir A33370 1,292428 0,347491 TTnoOverlap 0 007105 B7 G 12, 13 2

35 ATP6V0D1 pir JN0908 2,002379 1,023683 TTnoOverlap 0 000933 B5 E G 12, 13 2

36 ATRX sp P46100 0,456371 0,363531 TTnoOverlap 0 004789 B6 D G 12, 13 2

37 BACE2 sp Q9Y5Z0 1,859479 0,605561 TTnoOverlap 0 000022 B2 G

38 BAGl sp Q99933 0,661981 0,299473 TTnoOverlap 0 005964 B7 G 14

39 BAZ2B NP_038478 1 0,467937 0,400639 TTnoOverlap 0 005976 B7 D G

40 BIRC6 NP_057336 1 0,458674 0,366391 TTnoOverlap 0 009055 B7 D G

41 BMIl pir 154339 0,3834 0,36481 1 TTnoOverlap 0 003333 B6 D G

42 BMX sp P51813 2,54759 1,71 Overlap 0 000640 3 A2 A33 E G

43 BRDI NPJJ55392 1 0,54636 0,275919 TTnoOverlap 0 000725 B5 G

44 BRMSlL NP_056214 1 0,553647 0,35263 TTnoOverlap 0 007466 B7 G

45 BRP44L NP_057182 1 0,59466 0,313807 TTnoOverlap 0 003951 B6 G

46 BRWD2 sp Q9BZH6 0,569404 0,230362 TTnoOverlap 0 000900 B5 G

47 BTF3 pir JC1235 1,307835 0,316766 TTnoOverlap 0 002208 B6 F G

48 BTF3 pir JC1235 1,407674 0,415825 TTnoOverlap 0 001679 B6 F G

49 Cl Iorf67 sp P39 I93 0,617384 0,203854 TTnoOverlap 0 002907 B6 H

50 C16orβ NP_037531 1 1,818437 0,928199 TTnoOverlap 0 002646 B6 H

51 C17orf49 H*. 511 Ml 1 ,40273 0,514617 TTnoOverlap 0 006862 B7 H κ>

W

52 C17orf85 NP_061O23 1 0,636332 0,230465 TTnoOverlap 0 004070 B6 H

53 Cl orflOδ NP_078871 1 0,406437 0,583671 RVMnoOverlap 3 Cl D H

54 Cloιf77 pir T08660 0,5861 15 0,340939 TTnoOverlap 0 008663 B7 H

55 CI S sp P09871 2,861654 3,123524 Overlap 0 008007 3 A2 A35 E H

56 C20orfl 9 Hs !H7λiS 0,532443 0,288549 TTnoOverlap 0 004927 B6 H

57 C21orf59 sp P57076 0,633526 0,253596 TTnoOverlap 0 003497 B6 H

58 C2orf33 NP_064579 1 1,541245 0,604015 TTnoOverlap 0 002079 B6 H

59 C5orQ6 NP_443726 1 1,604247 0,782059 TTnoOverlap 0 005925 B7 H

60 C6orfl l l NP_1 16259 1 0,3521 18 0,349084 TTnoOverlap 0 002867 B6 D H

61 C7 sp P 10643 2,520922 4,071 108 RVMnoOverlap 3 Cl E G

62 CALM2 sp P02593 0,21 1479 0,292561 RVMnoOverlap 3 Cl D G

63 CAMSAPlLl pir T14744 0,38569 0,366373 TTnoOverlap 0 004657 B6 F D G

64 CAMSAPlLl pir T 14744 0,462657 0,382375 TTnoOverlap 0 004622 B6 F D G

65 CANX NPJX) 1737 1 0,785748 0,216537 TTnoOverlap 0007173 B7 G

66 CAPN2 NPJX) 1739 1 1,391307 0,45593 TTnoOverlap 0 004204 B6 G

67 CBXl sp P23197 0,754536 0,233672 TTnoOverlap 0 005500 B7 G

68 CBX3 NP_0092072 0,609416 0,297873 TTnoOverlap 0 004295 B6 G

69 CCDC 14 pir T34561 0,503316 0,328031 TTnoOverlap 0 001665 B6 G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee TTTT SSD RVM mathematical mathematical multiple detection > 2fold annotation functional group

70 CCDC3 NPJ 13643 1 1,997422 1,508225 TTnoOverlap 0 007032 B7 G

71 CCNC pir A40268 0,666839 0,267308 TTnoOverlap 0 008422 B7 G

72 CD47 sp Q08722 0,368086 0,327833 TTnoOverlap 0 000684 B5 G

73 CD93 NP_036204 1 1,425784 0,487541 TTnoOverlap 0 004480 B6 G

74 CD99 sp P 14209 2,288404 1 ,7433 TTnoOverlap 0 001622 B6 G

75 CDC42SE2 NP_064625 1 0,661744 0,223353 TTnoOverlap 0 002218 B6 G

76 CDH I pir IJHUCE 1,627424 0,684332 TTnoOverlap 0 001628 B6 G

77 CENTB2 NP_036419 1 0,559897 0,348008 TTnoOverlap 0 007652 B7 G

78 CEP 170 NP_055627 1 0,6641 14 0,262791 TTnoOverlap 0 003686 B6 G

79 CFH sp P08603 2,502988 1,739617 Overlap 0 000277 3 A2 A3 2 G

80 CFHRl sp Q92496 4,576801 5,509064 Overlap 0 003672 4 Al A3 5 G

81 CFLl pir S 12632 1,50344 0,613686 TTnoOverlap 0 004941 B6 G

82 CHSYl pιrT46919 0,700327 0,188551 TTnoOverlap 0 001374 B6 G

83 CLCN3 pir 137240 0,63172 0,304945 TTnoOverlap 0 006588 B7 G

84 CLEC 14A NP_065137 1 1 ,462326 0,591728 TTnoOverlap 0 006103 B7 G

85 CLIC2 NP_001280 2 0,647378 0,297775 TTnoOverlap 0 003559 B6 G

86 CLK.4 NP_065717 1 0,730159 0,207521 TTnoOverlap 0 002049 B6 G

87 CLU sp P 10909 0,507023 0,334947 TTnoOverlap 0 003938 B6 G

88 CMAH Ih 4X49 1 M 3,330327 5,990238 RVMnoOverlap 4 C2 G

89 CMPK NP_057392 1 0,521 175 0,402949 TTnoOverlap 0 007650 B7 G 11, 13 2

90 CMTM6 NP_060271 1 0,504212 0,326105 TTnoOverlap 0 002619 B6 G

91 CNN3 pir JC4501 0,274041 0,371021 RVMnoOverlap 3 Cl D G

92 CNTN AP3 NP_006826 1 0,455055 0,414271 TTnoOverlap 0 005736 B7 D G 13 1

93 COMAl sp P02462 3,957273 5,563786 RVMnoOverlap 4 C2 E G

94 COL4A2 NP_001837 1 2,572352 2,803818 RVMnoOverlap 3 Cl E G

95 COL5AI NP_000084 2 1,685829 0,973302 TTnoOverlap 0 007950 B7 G

96 CPNE8 sp Q9HCH3 0,488527 0,378486 TTnoOverlap 0 004517 B6 G

97 CPVL pir A31589 0,517009 0,313427 TTnoOverlap 0 006341 B7 G

98 CREBl pir A35769 0,381 149 0,305984 TTnoOverlap 0 008276 B7 D G

99 CREBBP sp Q92793 0,43486 0,302613 TTnoOverlap 0 002393 B6 D G

100 CRIl NP_055150 1 0,490784 0,38775 TTnoOverlap 0 003094 B6 D G

101 CRLF3 sp P39194 0,538962 0,281882 TTnoOverlap 0 001225 B6 G

102 CROP NP_006098 1 0,502449 0,29483 TTnoOverlap 0 003004 B6 G

103 CROP NP_006098 1 0,521994 0,388317 TTnoOverlap 0 005063 B7 G

104 CSEl L pir 139166 0,515265 0,22222 TTnoOverlap 0 001730 B6 G

105 CSF2RB sp P32927 0,687451 0,312769 TTnoOverlap 0 009917 B7 G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee TTTT S SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

106 CSNKlAl pir A57011 0,655344 0,333908 TTnoOverlap 0 008095 B7 G

107 CSPG2 sp P1361 1 3,106385 3,12284 RVMnoOverlap 4 C2 E G

108 CSPG2 sp P1361 1 3,528393 3,512293 RVMnoOverlap 4 C2 E G 13 1

109 CSRP2 sp Q 16527 0,539381 0,27723 TTnoOverlap 0 002221 B6 G

1 10 CSRP2 sp Q 16527 0,723049 0,267168 TTnoOverlap 0 008268 B7 G

1 11 CSTF2T NP_056050 1 0,519971 0,385724 TTnoOverlap 0 006732 B7 G

1 12 CTBP2 sp P56545 0,608904 0,218427 TTnoOverlap 0 006424 B7 G

1 13 CTSZ sp Q9UBR2 2,577124 2,586303 Overlap 0 007729 3 A2 A35 E G

1 14 CTTNBP2NL NP_219499 1 2,009727 1,123026 TTnoOverlap 0 001297 B6 E G

1 15 CUGBP2 NPJM6552 1 0,532174 0,356293 TTnoOverlap 0 002934 B6 G

1 16 CUUA NP_OO358O 1 0,387297 0,3143 TTnoOverlap 0 004248 B6 D G 14

1 17 CUL5 sp Q93034 0,49066 0,32831 TTnoOverlap 0 003366 B6 D G

1 18 CXCL 12 NP_000600 1 2,256658 1 ,980934 Overlap 0 009788 3 A2 A35 E G 13 I

1 19 CXCL 14 sp O95715 0,132809 0,326973 RVMnoOverlap 4 C2 D G

120 CYCS NP_061820 1 0,531662 0,409419 TTnoOverlap 0 008499 B7 G 14

121 CYR61 sp 000622 2,153798 1 ,814667 TTnoOverlap 0 005081 B7 E G

122 DAZAPl NP_002433 1 0,679592 0,216378 TTnoOverlap 0 000621 B5 G

123 DAZAP2 NP_055579 1 0,735263 0,232151 TTnoOverlap 0 003031 B6 G

K>

124 DBI NP_065438 1 0,603533 0,228597 TTnoOverlap 0 002184 B6 G Ul

125 DBI NP_065438 1 0,547652 0,244468 TTnoOverlap 0 008931 B7 G

126 DBI NP_065438 1 0,540331 0,234227 TTnoOverlap 0 002280 B6 G

127 DCUNlDl NP_060655 1 0,578219 0,305516 TTnoOverlap 0 009569 B7 G

128 DHX 15 NP_001349 1 0,69921 1 0,251533 TTnoOverlap 0 004923 B6 G 12, 13 2

129 DLGl pir 138756 0,70379 0,228386 TTnoOverlap 0 003678 B6 G

130 DMKN sp P23490 0,215219 0,515319 RVMnoOverlap 3 Cl D G

131 DNAJC3 pir JC4775 0,575823 0,227177 TTnoOverlap 0 000177 B4 G

132 DOCK4 pir TO 1357 0,441953 0,370215 TTnoOverlap 0 006857 B7 D G

133 DRl pir A43320 0,46857 0,395192 TTnoOverlap 0 002939 B6 D G

134 DSC3 NPJ)01932 1 0,223195 0,380801 RVMnoOverlap 3 Cl D G 13 1

135 DSP sp P 15924 0,423508 0,340717 TTnoOverlap 0 001510 B6 D G 13 I

136 DUSP22 NP_064570 1 1,550296 0,503135 TTnoOverlap 0 000521 B5 G 14

137 EBAG9 NP_004206 1 0,47312 0,376612 TTnoOverlap 0 001327 B6 D G

138 EBF l sp Q9H4W6 0,285313 0,392407 Overlap 0 006917 3 A2 A34 D G

139 EED sp P53621 0,58097 0,280597 TTnoOverlap 0 001204 B6 G 13 1

140 EEFlG pir S22655 1,445377 0,614018 TTnoOverlap 0 009975 B7 G

141 EHBPl NP 055447 1 0,630725 0,312788 TTnoOverlap 0 008376 B7 G

iNummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T TTT S SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

142 EIFl pdb 2IFl 1,205338 0,249377 TTnoOverlap 0 008413 B7 G I l

143 EIFl AX sp P47813 0,554759 0,289357 TTnoOverlap 0 003134 B6 G I l

144 EIFlAY sp P47813 0,468267 0,410533 TTnoOverlap 0 002325 B6 D G

145 EIF4A2 sp Q 14240 1,362291 0,447549 TTnoOverlap 0 007198 B7 G 11, 12, 13 2

146 EIF4G2 NP_067034 1 0,614755 0,354982 TTnoOverlap 0 006795 B7 G 11, 14

147 ELF2 NP_006865 1 0,42551 1 0,212754 TTnoOverlap 0 000926 B5 D G

148 EMPl sp P54849 0,71 1964 0,250656 TTnoOverlap 0 006481 B7 G 14

149 ENPP2 pir A55 I44 0,655486 0,195584 TTnoOverlap 0 001517 B6 G 12

150 EPHA4 sp P54764 2,191748 1,8151 16 TTnoOverlap 0 004770 B6 E G

151 EPS 15 NPJ)01972 1 0,621895 0,367665 TTnoOverlap 0 008806 B7 G

152 EPS8L2 sp Q 12929 0,565722 0,168185 TTnoOverlap 0 000234 B4 G

153 ERBB2IP NP_061 165 1 0,553559 0,298179 TTnoOverlap 0 002724 B6 G

154 EROlL NP_055399 1 1,653232 0,690179 TTnoOverlap 0 001172 B6 G

155 EWSRl pir A49358 0,654885 0,190749 TTnoOverlap 0 000124 B4 G

156 EXOC6 pir T46262 0,492121 0,264686 TTnoOverlap 0 003704 B6 D G

157 FAM105A NP 061891 1 0,282366 0,307851 RVMnoOverlap 3 Cl D G

158 FAM35A NPJ)61927 1 0,584425 0,151477 TTnoOverlap 0 002304 B6 G

159 FBNl pir A47221 2,564846 4,069578 RVMnoOverlap 3 Cl E G K*

160 FBXO3 NP_036307 2 0,380752 0,220783 TTnoOverlap 0 001453 B6 D G

161 Fbxo7 NP_03631 1 2 1,388071 0,310961 TTnoOverlap 0 000435 B4 G

162 FER 1L3 NP_038479 1 1 ,793965 1,023688 TTnoOverlap 0 003741 B6 G

163 FGFBPl NP 005121 1 0,277005 0,400423 RVMnoOverlap 3 Cl D G

164 FGFR3 sp P22607 0,300865 0,5051 18 RVMnoOverlap 3 Cl D G

165 FGL2 sp Q14314 0,322824 0,432052 TTnoOverlap 0 006942 B7 D G

166 FLJ10154 NPJ160481 1 0,365818 0,546198 RVMnoOverlap 3 Cl D H

167 FMRl pir A40724 0,440927 0,356435 TTnoOverlap 0 000988 B5 D G

168 FN l NP_002017 1 1 1,897555 15,356095 Overlap 0 006332 4 Al A3 5 E G

169 FN l NPJKGOl 7 1 13,089084 16,027773 Overlap 0 006306 4 Al A3 5 E G 13 1

170 FNDC3A pιr T46917 0,46015 0,2861 TTnoOverlap 0 002574 B6 D G

171 FRMD4B sp Q9Y2L6 0,633363 0,258147 TTnoOverlap 0 004287 B6 G

172 FZD4 sp Q9ULV1 4, 180317 4,464036 Overlap 0 001547 4 Al A3 5 E G

173 G3BP sp Ql 3283 0,418051 0,322872 TTnoOverlap 0 003568 B6 D G 12, 13 2

174 GABPB2 pir 138744 0,537429 0,26605 TTnoOverlap 0 003677 B6 G

175 GALC sp P54803 0,470315 0,252458 TTnoOverlap 0 000781 B5 D G

176 GAPD+HMGI 247X94 2,421266 2,20259 Overlap 0 006416 3 A2 A3 4 E G

177 GAPDH sp P04406 1,835388 0,889021 TTnoOverlap 0 000766 B5 G

Nummcr Gene symbol Ace no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee TTTT S SDD R RVVMM mmaathematical mathematical multiple detection > 2fold annotation functional group

178 GAPDH sp P04406 1 ,948059 0,886835 TTnoOverlap 0 00021 1 B4 F G

179 GAPDH sp P04406 1,952373 0,649045 TTnoOverlap 0 000024 B2 F G

180 GAPVDl pir T125O6 0,592328 0,298335 TTnoOverlap 0 006703 B7 G

181 GBEI pir A46075 0,30535 0,231475 TTnoOverlap 0 000276 B4 D G

182- GCA sp P28676 0,420484 0,356406 TTnoOverlap 0 000819 B5 D G

183 GDI2 sp P5O395 1,507161 0,591 177 TTnoOverlap 0 006485 B7 F G

184 GDI2 sp P5O395 2,005189 1,198491 TTnoOverlap 0 001602 B6 F E G

185 GLS sp 094925 0,519813 0,413361 TTnoOverlap 0 005767 B7 G

186 GMFB sp P 17774 0,51921 1 0,360087 TTnoOverlap 0 004122 B6 G

187 GNAS NP_000507 I 1,687749 0,61312 TTnoOverlap 0 000350 B4 F G

188 GNAS NP_000507 1 1 ,714261 0,723719 TTnoOverlap 0 000914 B5 F G

189 GNAS NP_057676 1 ,61229 0,531 198 TTnoOverlap 0 000354 B4 F G

190 GNAS NP_000507 1 2,382232 1 ,845762 TTnoOverlap 0 001072 B6 F E G

191 GNAS NP_000507 1 1 ,725766 0,80501 TTnoOverlap 0 00181 1 B6 F G

192 GNB2L1 pir B33928 1 ,710229 0,766384 TTnoOverlap 0 001302 B6 G

193 GNGIO sp P5O151 0,492167 0,408816 TTnoOverlap 0 004565 B6 D G 12, 15

194 GOLGA5 pir 138153 0,595832 0,291364 TTnoOverlap 0 004753 B6 G

K*

195 GOLGA8E pir JH0821 0,592819 0,280186 TTnoOverlap 0 003549 B6 G

196 GPI sp P06744 0,472436 0,333994 TTnoOverlap 0 000956 B5 D G

197 GPNMB pir 138065 0,174603 0,364975 RVMnoOverlap 4 C2 D G

198 GPRI 16 pir T08685 0,433553 0,316614 TTnoOverlap 0 000874 B5 D G

199 GTF2H1 pir S27958 0,557467 0,407088 TTnoOverlap 0 007152 B7 G

200 GTPBP4 NP_036473 1 0,662588 0,221575 TTnoOverlap 0 000552 B5 G

201 GYG 1/2 sp P46976/NP_003909 1 1,39809 0,413658 TTnoOverlap 0 002114 B6 G

202 H2AFY NP_004884 I 0,655973 0,31297 TTnoOverlap 0 006642 B7 G

203 HCG 12 NP_078915 1 0,6091 17 0,3721 19 TTnoOverlap 0 008471 B7 G

204 HERC4 pir B38919 0,461886 0,311596 TTnoOverlap 0 000861 B5 D G

205 HIATLl NPJ l 5947 1 0,455032 0,357859 TTnoOverlap 0 004371 B6 D G

206 HLA-DRB4 sp P 13762 1 ,529645 0,578501 TTnoOverlap 0 002715 B6 G

207 HMGN3 sp P052O4 0,685636 0,240688 TTnoOverlap 0 005072 B7 G

208 HMGN4 NP_006344 1 0,566057 0,321362 TTnoOverlap 0 004504 B6 G

209 HNRPAI NP_002127 I 0,665517 0,241 141 TTnoOverlap 0 008164 B7 G

210 HNRP A3 sp P51991 0,446043 0,334172 TTnoOverlap 0 001268 B6 F D G

21 1 HNRP A3 sp P51991 0,6001 0,225317 TTnoOverlap 0 002178 B6 F G

212 HNRP A3 sp P51991 0,617322 0,186452 TTnoOverlap 0 000465 B4 F G

213 HNRP A3 sp P51991 0,661476 0,214785 TTnoOverlap 0 001 138 B6 F G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T TT SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

214 HNRPR sp 043390 0,689964 0,315981 TTnoOverlap 0 008988 B7 G

215 HOXA5 sp QOOO56 0,418433 0,393697 TTnoOverlap 0 000940 B5 D G

216 HSP90AB1 sp PO8238 1 ,706092 0,950166 TTnoOverlap 0 006595 B7 G 13 2

217 HTLF sp P32314 0,333066 0,540452 TTnoOverlap 0 009160 B7 D G

218 HYPK NP_060312 1 0,620642 0,308627 TTnoOverlap 0 008512 B7 G

219 IARS pir 159314 0,492044 0,26822 TTnoOverlap 0 000920 B5 D G

220 IER3 sp P46695 1,392508 0,529841 TTnoOverlap 0 009925 B7 G

221 IER3IP1 NP_057181 1 0,522575 0,435529 TTnoOverlap 0 009365 B7 G

222 IFITMl pir A31454 1,531 19 0,634554 TTnoOverlap 0 003665 B6 G

223 IFITMl pir A31454 1,535051 0,708712 TTnoOverlap 0 006394 B7 G

224 IF1TM2 NP_006426 1 1,551605 0,51 1531 TTnoOverlap 0 000689 B5 G

225 IF1TM3 NP_066362 I 1,450922 0,362683 TTnoOverlap 0 000372 B4 G

226 IGF2 sp PO 1344 0,4231 19 0,262749 TTnoOverlap 0 007592 B7 D G in IRF6 sp O 14896 0,304917 0,408079 RVMnoOverlap Cl D G

228 ITGA9 NP_002198 I 0,345066 0,213642 TTnoOverlap 0 006796 B7 D G

229 ITGB3BP pir A57277 0,596224 0,245636 TTnoOverlap 0 009742 B7 G 13 1

230 ITM2A NP_004858 0,7031 12 0,237166 TTnoOverlap 0 003903 B6 G

231 ITM2B NP_068839 0,698009 0,242459 TTnoOverlap 0 008155 B7 G

232 JAGl NP_000205 0,51556 0,266139 TTnoOverlap 0 007155 B7 K*

G 90

233 JAGl NP_000205 0,504101 0,242303 TTnoOverlap 0 007160 B7 G

234 KALRN NP_003938 1,838053 1,292021 TTnoOverlap 0 008108 B7 G

235 KARS NP_00S539 1,421266 0,547593 TTnoOverlap 0 007716 B7 G

236 KDR NP_002244 0,633566 0,336074 TTnoOverlap 0 009898 B7 G

237 KIAA0323 NP_064580 0,660975 0,287717 TTnoOverlap 0 009614 B7 H

238 KIAA0368 Ws 3M255 0,750612 0,139883 TTnoOverlap 0 002571 B6 H

239 KIAA0528 pir T00072 0,534875 0,31 1 179 TTnoOverlap 0 004628 B6 H

240 KIAA1O33 12144 0,539803 0,233156 TTnoOverlap 0 002312 B6 H

241 KlAA 1 109 pir T46438 0,458255 0,385981 TTnoOverlap 0 007229 B7 D H

242 KIDINS220 pir T43458 0,458144 0,361697 TTnoOverlap 0 001414 B6 D G

243 KIF5B sp P33176 0,44742 0,305524 TTnoOverlap 0 001521 B6 D G 12, 13 2

244 KIFAP3 NP_055785 2 1,335977 0,345536 TTnoOverlap 0 002225 B6 G

245 KLF6 sp Q99612 2,890602 2,354147 Overlap 0 002026 Al A3 5 E G

246 KXF7 NP_003700 1 1,773544 1,057263 TTnoOverlap 0 005505 B7 G

247 KLHL9 sp Q9P2J3 0,526855 0,34045 TTnoOverlap 0 005802 B7 G

248 KRCCl NP_057702 1 0,496532 0,213891 TTnoOverlap 0 000133 B4 D G

249 KRTl NP 0061 12 2 0,362182 0,664436 RVMnoOverlap Cl D G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T TTT S SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

250 KRT 17 pir A37343 0,199797 0,396361 RVMnoOverlap 4 C2 F D G

251 KRTl 7 pir A37343 0,230105 0,505097 RVMnoOverlap 3 Cl D G

252 KRT5 NP_258259 1 0,224914 0,481534 RVMnoOverlap 4 C2 F D G

253 KRT77 NP_OO61 I2 2 0,238798 0,369288 RVMnoOverlap 3 Cl D G

254 KTN l pir S32763 0,735523 0,233073 TTnoOverlap 0 004862 B6 G

255 KTNl pir S32763 0,72166 0,20857 TTnoOverlap 0 001760 B6 G

256 LAMP2 sp P 13473 0,522598 0,323899 TTnoOverlap 0 001541 B6 G

257 LBR NP_002287 1 0,503248 0,383758 TTnoOverlap 0 007239 B7 G

258 LDHA NP_002292 1 1,328373 0,350566 TTnoOverlap 0 003531 B6 G

259 LDHB pir DEHULH 0,568536 0,232067 TTnoOverlap 0 000299 B4 F G

260 LDHB pir DEHULH 0,584362 0,278124 TTnoOverlap 0 001 143 B6 F G

261 LEPR sp P48357 0,472663 0,410737 TTnoOverlap 0 006681 B7 F D G

262 LEPR sp P48357 0,229064 0,279708 Overlap 0 001768 3 A2 A34 F D G

263 LEREPO4 NP_060941 1 0,628814 0,352577 TTnoOverlap 0 007602 B7 G

264 LETMDl pir T08763 0,627334 0,282033 TTnoOverlap 0 004209 B6 G

265 LGALS l sp P09382 2,507894 4,451305 RVMnoOverlap 3 Cl EE GG 14

266 LGALS7 sp P47929 0,177319 0,388027 RVMnoOverlap 4 C2 DD GG 131

267 LIMAl NP_057441 1 0,74451 0,247243 TTnoOverlap 0 00581 1 B7 G

K*

268 LMCDl NP_055398 1 2,848582 2,355051 Overlap 0 007484 3 A2 A34 E G

269 LOC375010 NP_ 1 15626 1 0,320624 0,24453 TTnoOverlap 0 003901 B6 D H

270 LOC441050 NP_036294 1 0,705869 0,276896 TTnoOverlap 0 007022 B7 H

271 LRRC32 sp Q 14392 2,081414 1,212091 TTnoOverlap 0 000534 B5 E G

272 LRRC40 pir T47176 0,431397 0,383132 TTnoOverlap 0 003417 B6 D G

273 LSMI4A pir Tl 7274 0,650624 0,287001 TTnoOverlap 0 008259 B7 G

274 LZTFLl NP_065080 1 0,435518 0,219673 TTnoOverlap 0 000155 B4 D G

275 MAK NP_005897 1 0,139989 0,242331 RVMnoOverlap 4 C2 D G

276 MAP4 NP_002366 1 3,063072 2,79178 Overlap 0 001457 4 Al A35 E G

277 MARCH7 NP_073737 1 0,415651 0,410975 TTnoOverlap 0 004888 B6 D G

278 MATR3 sp P43243 0,505628 0,400405 TTnoOverlap 0 004330 B6 G

279 MBD4 NPJJ03916 I 0,554296 0,14002 TTnoOverlap 0 000007 Bl G

280 MBNL2 NP_005748 1 0,496385 0,412497 TTnoOverlap 0 003857 B6 D G

281 MED4 NP_054885 1 0,46839 0,280502 TTnoOverlap 0 000621 B5 D G

282 MINA NP_078920 1 0,451342 0,250885 TTnoOverlap 0 003273 B6 F D G

283 MINA sp Q9Y4K1 0,587794 0,30256 TTnoOverlap 0 001482 B6 F G

284 MKRN l sp Q9UHC7 0,686057 0,312737 TTnoOverlap 0 00821 1 B7 G

285 MRPL39 sp Q9NYK5 0,606348 0,347381 TTnoOverlap 0 007716 B7 G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T TT SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

286 MYL6 sp P 16475 1,255325 0,277876 TTnoOverlap 0 003644 B6 G

287 MYOl B sp Q9UBC5 0,432228 0,30323 TTnoOverlap 0005685 B7 D G

288 MYST4/HBOA NP_036462 I 1 ,688338 0,991646 TTnoOverlap 0 007415 B7 G

289 NABl sp Q 13506 0,45641 1 0,420632 TTnoOverlap 0 003144 B6 D G

290 NARGl L NP_079361 1 0,598391 0,278293 TTnoOverlap 0 009843 B7 G

291 NARS sp 043776 0,666385 0,232129 TTnoOverlap 0 001826 B6 G Il

292 NBN pir T00393 0,518971 0,288697 TTnoOverlap 0 001455 B6 G

293 NCOA6 NP_003473 1 0,569505 0,248776 TTnoOverlap 0 009613 B7 G

294 NCORl sp 075376 0,697524 0,217677 TTnoOverlap 0 009056 B7 G

295 NDFIPl NP_085048 1 0,564999 0,400008 TTnoOverlap 0 008261 B7 G

296 NDUFA5 sp Q16718 0,435098 0,39598 TTnoOverlap 0 001424 B6 D G

297 NEK.7 sp P51957 0,550491 0,31 1061 TTnoOverlap 0 000937 B5 G

298 NFAT5 NP_006590 1 0,485504 0,384713 TTnoOverlap 0 005180 B7 D G

299 NFlA sp Q12857 0,554109 0,295701 TTnoOverlap 0 005488 B7 G

300 NGDN pir T08694 0,730323 0,206888 TTnoOverlap 0 005380 B7 G

301 NIN prf 22U333A 0,42244 0,356957 TTnoOverlap 0 006848 B7 D G

302 NNMT pir A54060 2,093201 1,140718 TTnoOverlap 0 000461 B4 E G

303 NOP5/NOP58 sp Q9Y2X3 0,431063 0,382722 TTnoOverlap 0 002468 B6 D G O

304 N0S3 sp P39188 0,425236 0,44543 TTnoOverlap 0 009872 B7 D G

305 NPTN NP_036560 1 0,570979 0,360931 TTnoOverlap 0 007817 B7 G

306 NTN4 NP_067052 1 0,447853 0,345951 TTnoOverlap 0 009744 B7 D G

307 NUMBL NP_004747 1 0,547168 0,34447 TTnoOverlap 0 003978 B6 G

308 OASL NP_003724 1 2,297938 1,806393 Overlap 0 006415 A2 A34 E G

309 OAZl (2,3) pir 138591 1,234145 0,27333 TTnoOverlap 0006245 B7 G Il

310 OPTN NP_003630 1 0,65388 0,2861 13 TTnoOverlap 0 007079 B7 G 14

31 1 OSBPLlO NP_065892 1 2,464363 1,829894 Overlap 0 001703 A2 A33 E G

312 OSBPLlA NP_055650 1 0,434317 0,29177 TTnoOverlap 0 000138 B4 D G

313 OSMR NP_003990 1 0,56877 0,276363 TTnoOverlap 0 001754 B6 G

314 P4HB pir ISHUSS 1,938984 1,055365 TTnoOverlap 0 004065 B6 G

315 PABPCl NP_002559 1 1,432164 0,439541 TTnoOverlap 0 003454 B6 G

316 PACS l pιr T00262 0,618068 0,275212 TTnoOverlap 0 001027 B6 G

317 PAKl sp QI 3153 1,936432 1,228821 TTnoOverlap 0 003857 B6 G

318 PCAF pir S71788 0,448212 0,382152 TTnoOverlap 0 004359 B6 D G

319 PCMTD2 NPJJ60727 1 0,513423 0,226123 TTnoOverlap 0 001 134 B6 G

320 PCNP NP_065090 1 0,451789 0,51 1 148 TTnoOverlap 0 009887 B7 D G

321 PECAMl sp P16284 1,391606 0,497456 TTnoOverlap 0007104 B7 G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T 1T I S SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

322 PECAMl sp P 16284 1,468757 0,529271 TTnoOverlap 0 004201 B6 G 131

323 PECAMl sp P16284 1 ,874238 1 ,05952 TTnoOverlap 0 002864 B6 G

324 PER2 NP_OO3885 2 0,339824 0,309478 TTnoOverlap 0 006236 B7 D G

325 PER3 NP_O585 I 5 1 0,41 1 139 0,29766 TTnoOverlap 0 001656 B6 D G

326 PGRMC2 NP_00631 1 1 0,537253 0,362537 TTnoOverlap 0 009553 B7 G

327 PHFU NP_057203 1 0,631715 0,320024 TTnoOverlap 0 008096 B7 G

328 PHF2 pir T00369 0,457309 0,289626 TTnoOverlap 0 002659 B6 G

329 PHGDH NP_OO1319 1 1 ,678536 0,828045 TTnoOverlap 0 002844 B6 G

330 PHLDB2 pir A57013 0,263224 0,407902 RVMnoOverlap 3 Cl D G

331 PIK.3R3 ref NP_003620 1 2,394271 2,589136 RVMnoOverlap 3 Cl E G

332 PKN2 pιf 2104208B 0,51755 0,410623 TTnoOverlap 0 004852 B6 G

333 PLAGLl sp Q9UM63 0,439071 0,392367 TTnoOverlap 0 007718 B7 G

334 POGZ pir T00075 0,636834 0,31 1264 TTnoOverlap 0 009714 B7 G

335 POSTN pir S36110 2,522072 2,917981 RVMnoOverlap 3 Cl G 13 I

336 PPAP2A NP_003702 1 1 ,975455 1 ,374717 TTnoOverlap 0 005331 B7 G

337 PPAP2A2 NP_003702 1 1 ,758396 0,916969 TTnoOverlap 0 003960 B6 G

338 PPMl D sp 015297 0,583508 0,295451 TTnoOverlap 0 008020 B7 G

339 PPPlCB NP_002700 1 0,319265 0,392389 Overlap 0 007646 3 A2 A35 D G W

340 PPPlCB NP_002700 1 0,386711 0,44085 TTnoOverlap 0 002822 B6 D G

341 PPPlCC pdb 1JK.7 0,597345 0,270363 TTnoOverlap 0 002627 B6 G

342 PPPl Rl 2A NP_002471 I 0,421048 0,246263 TTnoOverlap 0 000680 B5 G

343 PRDXl pir A4671 1 1 ,589534 0,610303 TTnoOverlap 0 001222 B6 G

344 PREI3 pir T12466 0,624733 0,302172 TTnoOverlap 0 002589 B6 G

345 PREI3 pir Tl 2466 0,56232 0,337303 TTnoOverlap 0 002278 B6 G

346 PRGl sp P10124 2,800619 2,31645 Overlap 0 001044 4 Al A35 G

347 PRKD3 sp 094806 0,607402 0,31 1 166 TTnoOverlap 0 003834 B6 G

348 PRPF4B NP_003904 2 0,572651 0,300273 TTnoOverlap 0 009836 B7 G

349 PRSS23 NP_009104 1 3,479282 2,95003 Overlap 0 000226 4 Al A35 E G

350 PRSS23 NP_009104 1 2,284676 1,334407 Overlap 0 000530 3 A2 A32 E G

351 PSIPI NP_066967 2 0,433328 0,3272 TTnoOverlap 0 002113 B6 D G

352 PSMA2 sp P25787 0,59417 0,25073 TTnoOverlap 0 002726 B6 G

353 PSMA3 sp P25788 0,642338 0,292399 TTnoOverlap 0 002965 B6 G

354 PSMB4 pir S50147 0,274517 0,37387 RVMnoOverlap 3 Cl G

355 PSPCl NP_060752 1 0,58558 0,328826 TTnoOverlap 0 007054 B7 G

356 PTK9 pir A55922 0,50302 0,357541 TTnoOverlap 0 001825 B6 G

357 PTPLB NP 055056 2 0,658004 0,329034 TTnoOverlap 0 007749 B7 G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T TT SD RVM mathematical mathematical multiple detection >> Z2ffoolldd annotation functional group

358 PTPRK sp Q 15262 0,4841 0,258494 TTnoOverlap 00 000000777744 B5 DD G

359 PURA sp Q00577 0,437325 0,370796 TTnoOverlap 0 0 000044007711 B6 DD G

360 PUS7 NP_061915 1 0,63551 0,309827 TTnoOverlap 0 0 000055990099 B7 G

361 QKI pir A38219 0,363459 0,413908 TTnoOverlap 00 000033441100 B6 DD G

362 R3HDM1 sp Q 15032 0,706627 0,185332 TTnoOverlap 00 000077778844 B7 G

363 R3HDM2 sp Q 15032 0,701734 0,299555 TTnoOverlap 00 000088773333 B7 G

364 RAB21 sp Q9UL25 0,45256 0,503692 TTnoOverlap 00 000099116600 B7 DD G 12, 15

365 RAB4A pir E34323 0,574826 0,362504 TTnoOverlap 00 000077664488 B7 G 12, 15

366 RAD21 NPJJ06256 1 0,570198 0,406358 TTnoOverlap 00 000099444444 B7 G

367 RAMP3 sp 060896 1,776869 1,096073 TTnoOverlap 00 000077225588 B7 G

368 RAP2C NP_066361 1 0,382469 0,441 107 TTnoOverlap 00 000055332233 B7 F DD G 12, 15

369 RAP2C NP_066361 1 0,401833 0,448528 TTnoOverlap 00 000044558844 B6 F DD G

370 RAPHl NP_004481 1 0,44052 0,285085 TTnoOverlap 00 000033335599 B6 DD G

371 RB l NP_000312 1 0,485465 0,389043 TTnoOverlap 00 000033222288 B6 DD G

372 RBL2 prf 2002263 A 0,644589 0,337127 TTnoOverlap 00 000077227755 B7 G

373 RBM26 NP_008921 1 0,541387 0,264021 TTnoOverlap 00 000022665500 B6 G

374 RDHI l NP 065956 1 0,452037 0,449093 TTnoOverlap 00 000044777700 B6 DD G

375 REVI L NP_057400 1 0,472108 0,239723 TTnoOverlap 00 000011663300 B6 DD G K*

376 RFCl pιr A49651 0,421047 0,254238 TTnoOverlap 00 000000883300 BS DD G 12, 15

377 RHBDD2 NP 065735 1 1,579577 0,79963 TTnoOverlap 00 000077772277 B7 G

378 RHOJ NP_065714 1 2,372707 1,577067 Overlap 00 000022339944 3 A2 A3 4 F EE G 12, 15

379 RHOJ NP_065714 1 1,827355 0,915636 TTnoOverlap 00 000011009922 B6 F G

380 RHOU NP_067028 1 0,434392 0,31172 TTnoOverlap 00 000099446644 B7 DD G 12, 15

381 RKHD2 NP_057710 I 0,427142 0,356024 TTnoOverlap 00 000033338888 B6 DD G

382 RND3 sp P52199 0,268526 0,445922 RVMnoOverlap 3 Cl DD G 12, 13 1, 15

383 RNFI03 NP_005658 1 1,26908 0,310437 TTnoOverlap 00 000055667788 B7 G

384 RNF 13 NP 009213 1 0,587782 0,233407 TTnoOverlap 00 000000445533 B4 G

385 RNF6 sp Q9Y252 0,423455 0,409542 TTnoOverlap 00 000011558855 B6 DD G

386 ROBOl NP_002932 1 0,398543 0,343873 TTnoOverlap 00 000077774488 B7 DD G 13 I

387 RPlA /λ 4M264 0,566671 0,347781 TTnoOverlap 00 000099220000 B7 G

388 RPIB9 NP_006686 1 0,28267 0,343861 Overlap 00 000055221166 3 A2 A3 4 DD G

389 RPLlO sp P27635 1,603087 0,626084 TTnoOverlap 00000011 113333 B6 G Il

390 RPL13 NPJ 50254 1 1,307439 0,269931 TTnoOverlap 00 000000772277 B5 F G II

391 RPLl 3 NPJ 50254 I 1,363696 0,474302 TTnoOverlap 00 000099552200 B7 F G Il

392 RPL 13 NPJ 50254 1 1,428827 0,402949 TTnoOverlap 00000000990000 B5 F G Il

393 RPL 13A pir S29539 1,404404 0,434935 TTnoOverlap 00 000022335555 B6 F G Il

Nummcr Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T TTT S SD RVM mathematical mathematical multiple detection > 2 fold annotation functional group

394 RPL13A pir S29539 1,404524 0,4132 TTnoOverlap 0 001921 B6 G I l

395 RPLl 3 A pir S29539 1,443509 0,594739 TTnoOverlap 0 008557 B7 G I l

396 RPL23A sp P29316 1 ,632775 0,913456 TTnoOverlap 0 008535 B7 G I l

397 RPL23A sp P29316 1 ,926676 1,249278 TTnoOverlap 0 00401 1 B6 G I I

398 RPL3 pir S34195 1,557371 0,79663 TTnoOverlap 0 009347 B7 G I I

399 RPL3 pir S34195 1,655435 0,850435 TTnoOverlap 0 004332 B6 G I I

400 RPL3I sp P 12947 0,410365 0,294979 TTnoOverlap 0 005562 B7 D G

401 RPL38 sp P2341 I 0,240822 0,284745 RVMnoOverlap 3 Cl D G I I

402 RPL4 NP_000959 2 1,364322 0,429832 TTnoOverlap 0 004832 B6 G I l

403 RPLPO sp P05388 1 ,503821 0,531064 TTnoOverlap 0 002058 B6 G I l

404 RPLPO sp P05388 1 ,582922 0,644491 TTnoOverlap 0 002031 B6 G I l

405 RPLPO sp P05388 1,634392 0,886263 TTnoOverlap 0 008555 B7 G I l

406 RPLPO sp P05388 1,657312 0,806935 TTnoOverlap 0 003475 B6 G I l

407 RPS 12 NPJ)01007 2 1,655892 0,943776 TTnoOverlap 0 008540 B7 G

408 RPS 12 NPJ)01007 2 0,68847 0,212469 TTnoOverlap 0 004276 B6 G

409 RPS 14 sp P06366 1 ,4691 1 0,522764 TTnoOverlap 0 007830 B7 G

410 RPS 15 sp Pl 1 174 1,426386 0,524274 TTnoOverlap 0 005173 B7 G H

41 1 RPS 2 NP_002943 2 1,357602 0,433124 TTnoOverlap 0 006289 B7 G I l

412 RPS20 sp P 17075 0,320462 0,453728 RVMnoOverlap 3 Cl D G I l

413 RREBI sp Q92766 0,245614 0,232602 RVMnoOverlap 3 Cl D G

414 RRS l pir CGHU7L 0,645651 0,2861 14 TTnoOverlap 0 009541 B7 G

415 RSUl pir 160122 0,362465 0,382815 TTnoOverlap 0 006817 B7 D G

416 RSUl pir 160122 0,475405 0,250427 TTnoOverlap 0000222 B4 D G

417 SART3 NP_055521 1 0,594959 0,28296 TTnoOverlap 0 003236 B6 G

418 SDC4 sp P31431 0,297396 0,39077 RVMnoOverlap 3 Cl D G

419 SDFl NP_000600 1 2,402453 2,143343 Overlap 0 006703 3 A2 A3 4 E G

420 SEC22B NP_004883 1 0,52246 0,333788 TTnoOverlap 0 002439 B6 G

421 SEC23A sp Ql 5436 0,434601 0,446734 TTnoOverlap 0 003119 B6 G

422 SELlL sp Q9UBV2 0,63125 0,291926 TTnoOverlap 0 008659 B7 G

423 SEP 15 sp 060613 0,565971 0,275587 TTnoOverlap 0 001249 B6 G

424 SEPHS l sp Q9961 1 0,632923 0, 199216 TTnoOverlap 0 000307 B4 G 13 2, 15

425 SEPHS2 sp Q9961 1 1,362894 0,422002 TTnoOverlap 0 00451 1 B6 G

426 SEPPl sp P49908 0,599358 0,2796 TTnoOverlap 0 002178 B6 G

427 SEPTlO NP_060713 1 0,548629 0,394304 TTnoOverlap 0 007720 B7 G

428 SEPT7 sp Q 16181 0,667225 0,302224 TTnoOverlap 0008451 B7 G

429 SERINC5 pir T46332 0,546288 0,300081 TTnoOverlap 0005562 B7 G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method p value TT SD RVM mathemati leal mathematical multiple detection > 2fold annotation functional group

430 SERP1NB2 pir A32853 0,1 15283 0,321787 RVMnoOverlap 4 C2 D G

431 SERP1NB5 pir A36898 0,186554 0,457196 RVMnoOverlap 4 C2 D G

432 SFRSlO NP_004584 1 0,741666 0,181558 TTπoOverlap 0 001243 B6 G

433 SFRS12 pir A40988 0,493883 0,260336 TTnoOverlap 0 000202 B4 D G

434 SFRS3 sp P23152 0,326763 0,29691 1 TTnoOverlap 0 002510 B6 D G

435 SFRS6 pir S59043 0,647264 0,221437 TTnoOverlap 0 000673 B5 G

436 SH3D5 Hs 3X62 i 0,2481 1 0,351694 Overlap 0 005355 3 A2 A3 4 D G 13 1

437 SH3PXD2B pir T00056 2,080552 1,681876 TTnoOverlap 0 006043 B7 E G

438 SHQl NP_060600 1 0,563151 0,26315 TTnoOverlap 0 003606 B6 G

439 SIAHl NP_003022 1 0,519794 0,319318 TTnoOverlap 0 005763 B7 G

440 SLC25A3 NP_002626 1 1,636781 0,788813 TTnoOverlap 0 003474 B6 G

441 SLC2A3P1 sp Pl 1 169 0,475832 0,421239 TTnoOverlap 0 005575 B7 D G

442 SLC44A1 NP_536856 2 0,559558 0,3479 TTnoOverlap 0 002543 B6 G

443 SLCO2B 1 NP_009187 1 0,256299 0,229236 Overlap 0 002390 3 A2 A3 4 D G

444 SLK NP_055535 1 0,617761 0,325622 TTnoOverlap 0 006736 B7 G

445 SMADl sp Q 15797 0,417199 0,327902 TTnoOverlap 0 001810 B6 D G

446 SMARCAl sp P28370 0,588896 0,307253 TTnoOverlap 0 006784 B7 G 12, 13 2

447 SMARCA5 sp P28370 0,482723 0,369796 TTnoOverlap 0 007020 B7 D G

448 SMGl NP_055907 2 0,594925 0,318607 TTnoOverlap 0 009390 B7 G

449 SMURF2 NP_073576 1 0,2097 0,28286 RVMnoOverlap 4 C2 D G

450 SNAP23 NP_003816 2 0,552031 0,265875 TTnoOverlap 0 000402 B4 G

451 SNAP25 NP_003072 2 1,658907 0,838178 TTnoOverlap 0 005377 B7 G

452 SNX2 sp 060749 0,422568 0,319473 TTnoOverlap 0 000809 B5 D G

453 SNX4 sp 095219 0,51256 0,243441 TTnoOverlap 0000405 B4 G

454 SOD2 NP_000627 1 0,305083 0,413456 RVMnoOverlap 3 Cl D G

455 SORBS l NP_006425 1 0,512197 0,415401 TTnoOverlap 0 008315 B7 G

456 SP3 pir B44489 0,412279 0,44183 TTnoOverlap 0 003601 B6 D G

457 SPARC sp P09486 1,53452 0,660658 TTnoOverlap 0 005677 B7 G

458 SPRYl sp 043597 1,468492 0,560075 TTnoOverlap 0 004215 B6 G

459 SPTLCl NP_006406 1 0,595101 0,365131 TTnoOverlap 0 007483 B7 G

460 SPTLC2 NP_004854 1 1,406583 0,5321 19 TTnoOverlap 0 007838 B7 G

461 SQHl Hs 52X650 0,46778 0,234999 TTnoOverlap 0 007747 B7 D G

462 SRRMl NP_005830 1 0,48412 0,338946 TTnoOverlap 0 001741 B6 D G

463 SSB NP_003133 1 0,530295 0,418906 TTnoOverlap 0 005191 B7 G

464 ST6GALNAC3 NP_1 12227 1 2,450188 1,624553 Overlap 0 000675 3 A2 A3 3 E G

465 STAG2 NP 005853 1 0,49529 0,343277 TTnoOverlap 0 001830 B6 D G

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee T 1T SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

466 STATl sp P42224 0,573163 0,370935 1 I noOverlap 0 008159 B7 G 14

467 STCl sp P52823 0,187437 0,268528 RVMnoOverlap C2 G

468 STKl 7 A sp Q9UEE5 1 ,684927 0,693411 TTnoOverlap 0 000997 B5 G

469 STOM sp P27105 1,369989 0,280342 TTnoOverlap 0 000346 B4 G

470 STT3A pir S70029 2,33535 0,990125 Overlap 0 000007 A2 A31 G

471 SUCLG2 NP_003841 1 0,632528 0,250966 TTnoOverlap 0 001816 B6 G

472 SUCLG2 NP_003841 1 0,659785 0,2891 17 TTnoOverlap 0 003823 B6 G

473 SUMO2 pir JC4760 0,669988 0,272967 TTnoOverlap 0 002583 B6 G

474 SYNCRlP sp 043390 0,688916 0,249386 TTnoOverlap 0 003988 B6 G

475 TAF2 NP_003175 1 0,473108 0,363192 TTnoOverlap 0 006673 B7 D G

476 TAF2 NP_003175 1 0,4171 12 0,2933 TTnoOverlap 0 000681 B5 D G

477 TBC 1D4 pir T00261 0,420681 0,203343 TTnoOverlap 0 000328 B4 D G

478 TBCA NP_004598 1 0,508479 0,272503 TTnoOverlap 0 002380 B6 G

479 TCEALl pir 153785 0,666937 0,268748 TTnoOverlap 0 003567 B6 G

480 TFDPl sp Q14186 0,529009 0,323755 TTnoOverlap 0 003736 B6 G

481 THl L NP_057481 1 1 ,345818 0,30869 TTnoOverlap 0 000913 B5 G

482 THOC7 NP_079351 1 0,619589 0,275179 TTnoOverlap 0 001 187 B6 G

483 THUMPDl NP_060206 1 0,477229 0,335454 TTnoOverlap 0 002803 B6 G Ul

484 TlAl pir A39293 0,556501 0,283904 TTnoOverlap 0 002407 B6 G

485 TJP2 sp Q9UDY2 0,665741 0,166279 TTnoOverlap 0 004265 B6 G

486 TLKl NP_006843 1 0,394069 0,24402 TTnoOverlap 0 000052 B3 D G

487 TM4SF18 pir A42926 0,431229 0,285919 TTnoOverlap 0 001749 B6 D G

488 TM9SF3 sp Q9HD45 0,657049 0,319357 TTnoOverlap 0 009011 B7 G

489 TMEM 14C NPJ57546 1 0,539738 0,306045 TTnoOverlap 0 005476 B7 G

490 TMEM57 pir T 17272 0,409893 0,420816 TTnoOverlap 0 002682 B6 G

491 TMEM70 sp P 17075 0,641568 0,284908 TTnoOverlap 0 005353 B7 G

492 TncRNA pir B34087 0,379373 0,560751 RVMnoOverlap Cl G

493 TNFAIPl pir A41784 1,408896 0,512561 TTnoOverlap 0 006041 B7 G

494 TNFAIP3 pir A35797 1,400149 0,432532 TTnoOverlap 0 003906 B6 G

495 TOP2B pir A39242 0,470231 0,205324 TTnoOverlap 0 002480 B6 D G 132

496 TSPAN 12 sp 095859 0,418364 0,385356 TTnoOverlap 0 005941 B7 D G

497 TSPYL4 NP_071400 1 0,501455 0,321 136 TTnoOverlap 0 003237 B6 G

498 TTC28 pir T 12496 0,645293 0,285592 TTnoOverlap 0 008363 B7 G

499 TUBAl sp P05215 1,389453 0,467546 TTnoOverlap 0 005452 B7 G

500 TUBAl sp P05215 1,417402 0,424679 TTnoOverlap 0 003083 B6 G

501 TUBA3 pir 177403 1 ,404697 0,42607 TTnoOverlap 0 002677 B6 G

Nummer Gene symbol λcc. no. protein Ratio D/ND SD of D/ND Detection method pp vvaalluuee 1 TT SD RVM mathematical mathematical multiple detection > 2fold annotation functional group

502 TXNDC9 NP_005774 2 0,47992 0,328846 TTnoOverlap 0 002524 B6 D G

503 TXNDC9 NP_005774 2 0,498653 0,293542 TTnoOverlap 0 001000 B6 D G

504 TYMS sp P04818 2,82938 4,032007 RVMnoOverlap Cl E G

505 UBElC pir T17306 0,575957 0,306841 TTnoOverlap 0 001205 B6 G

506 UBE2B pir B41222 0,493348 0,385373 TTnoOverlap 0 002887 B6 D G

507 UBE2N pdb 1J7D 0,585909 0,347268 TTnoOverlap 0 009796 B7 G

508 UBE4A sp Q14139 0,585265 0,332865 TTnoOverlap 0 005557 B7 G

509 UBL5 NP_077268 1 0,550313 0,280277 TTnoOverlap 0 001065 B6 G

510 UBPl pir B56205 0,610508 0,208795 TTnoOverlap 0 001609 B6 G

51 1 UGDH NP_003350 1 0,314902 0,4483 Overlap 0 002713 A2 A3 4 D G

512 UNC50 pir Tl 2451 0,592229 0,265935 TTnoOverlap 0 000967 B5 G

513 UNC84A pιr T00371 0,622122 0,296973 TTnoOverlap 0 005106 B7 G

514 unknown sp P39191 0,30423 0,482701 RVMnoOverlap Cl D H

515 unknown sp P39194 0,542223 0,315216 TTnoOverlap 0 001816 B6 H

516 unknown Ih 60257 2,567823 2,55103 RVMnoOverlap Cl E H

517 unknown Ih 17202ft 0,418318 0,286182 TTnoOverlap 0 000374 B4 D H

518 unknown sp P39188 0,392944 0,31451 1 TTnoOverlap 0 001513 B6 D H

519 unknown Hs 149367 0,387272 0,438716 TTnoOverlap 0 002628 B6 D H

9\

520 unknown sp P39191 2,406157 1,44691 1 Overlap 0 000289 A2 A3 2 E H

521 unknown sp P39191 2,046554 1,54878 TTnoOverlap 0 004548 B6 E H

522 unknown pir B34087 0,44056 0,360617 TTnoOverlap 0 009585 B7 D H

523 unknown pir A54661 0,529268 0,39259 TTnoOverlap 0 007877 B7 H

524 unknown Hs 438689 1 ,81968 0,745284 TTnoOverlap 0 000242 B4 H

525 unknown Hs 407674 0,640919 0,315683 TTnoOverlap 0 009332 B7 H

526 unknown sp P39192 0,480452 0,31 1281 TTnoOverlap 0 0031 1 1 B6 D H

527 unknown pir A35363 0,644802 0,369292 TTnoOverlap 0 009882 B7 H

528 unknown sp P39189 0,620736 0,229151 TTnoOverlap 0 003309 B6 H

529 unknown Hs 633432 0,341 156 0,286068 TTnoOverlap 0 002493 B6 D H

530 unknown NP_055707 1 0,52395 0,308828 TTnoOverlap 0 002359 B6 H

531 unknown Hs 14376 1,500134 0,679025 TTnoOverlap 0 007977 B7 H

532 unknown Hs 198891 0,476636 0,384667 TTnoOverlap 0 004130 B6 D H

533 unknown Hs 327729 0,494462 0,272661 TTnoOverlap 0 001845 B6 D H 12, 13 2

534 unknown Hs 302108 0,505561 0,21081 TTnoOverlap 0 001884 B6 H

535 unknown /Is 306084 0,536887 0,223974 TTnoOverlap 0 001 177 B6 H

536 unknown gb hM_03 ( F93 1 0,618664 0,239201 TTnoOverlap 0 004621 B6 H

537 unknown vb BC005S5S I 19,797519 27,528793 Overlap 0 002954 Al A3 5 E H

Nummer Gene symbol Ace. no. protein Ratio D/ND SD of D/ND Detection method p value TT SD RVM mmaathematical mathematical multiple detection > 2fold annotation functional group

538 USP33 sp Q9Y2K6 0,396316 0,236882 TTnoOverlap 0 000344 B4 D G

539 USP34 pir T00338 0,548809 0,363876 TTnoOverlap 0 009097 B7 G

540 UXSl NP_079352 1 0,509839 0,384694 TTnoOverlap 0 006449 B7 G

541 VCL NP_003364 1 1 ,462088 0,556669 TTnoOverlap 0 004222 B6 G

542 VCP NP_009057 1 1 ,532855 0,664872 TTnoOverlap 0 004726 B6 G 12, 13 2

543 VPS 13C NP_060550 1 0,514261 0,370863 TTnoOverlap 0 003252 B6 G

544 VPS35 NP_056132 1 0,496103 0,270696 TTnoOverlap 0 000163 B4 D G

545 WDR3 sp Q9UNX4 0,426084 0,225438 TTnoOverlap 0 004706 B6 D G

546 WDR47 sp 094967 0,545704 0,280428 TTnoOverlap 0 004059 B6 G

547 WEEl pir S55048 0,386239 0,284579 TTnoOverlap 0 000437 B4 G

548 XPOl NP_003391 1 0,693014 0,313152 TTnoOverlap 0 009959 B7 G

549 XPOT NP_009166 2 0,643722 0,296673 TTnoOverlap 0 005469 B7 G

550 YTHDF2 NPJJ57342 1 0,588197 0,215356 TTnoOverlap 0 000519 B5 G

551 YWHAQ pir S 15076 1,373487 0,321958 TTnoOverlap 0 000538 B5 G

552 YY l sp P25490 0,597668 0,307821 TTnoOverlap 0 002752 B6 G

553 ZDHHC 17 NP_061901 1 0,477556 0,235875 TTnoOverlap 0 000599 B5 G

554 ZFAND6 NP_005998 1 0,542785 0,35856 TTnoOverlap 0 007475 B7 G

555 ZMPSTE24 sp 075844 0,616139 0,250954 TTnoOverlap 0 001059 B6 G

556 ZNF540 sp Q99676 0,669981 0,236287 TTnoOverlap 0 006154 B7 G

557 ZNF71 1 NP 068838 2 0,234768 0,369613 RVMnoOverlap 4 C2 D G

558 ZRANBl sp Q9UGI0 0,492893 0,248976 TTnoOverlap 0 003649 B6 D G

559 ZZZ3 pir Tl 2463 0,610636 0,215302 TTnoOverlap 0 002935 B6 G