# Patent

## Title
Melanoma gene signature

## Abstract

Methods and compositions for evaluating gene expression in melanoma samples are provided herein.

## Background
RELATED APPLICATIONS
This application claims the benefit of U.S. Provisional Application No. 60/824,849, filed Sep. 7, 2006, which is incorporated herein by reference in its entirety.


GOVERNMENT SUPPORT
The methods and compositions described herein were made with government support awarded by the ARMY Medical Research and Material Command (MRMC) under Grant No. DAMD17-02-2-0051. The government has certain rights in the invention.


TECHNICAL FIELD
Methods and compositions for evaluating tissues, e.g., tumors, are provided herein.
BACKGROUND
In the United States, the overall incidence of melanoma is increasing at a rate faster than any other cancer, with recent estimates for lifetime risk of developing invasive melanoma at 1/49 (Jemal et al., C. A. Cancer J. Clin. 57:43-66, 2007). The development of melanoma begins with the malignant transformation of normal human epithelial melanocytes (NHEM) located within the basement membrane of the skin, but the genetic changes associated with the progression of NHEM to melanoma are not well characterized (Bittner et al., Nature. 406:536-540, 2000; DeRisi et al., Nat. Genet. 14:457-460, 1996; Golub et al., Science. 286:531-37, 1999; Hanahan et al., Cell. 100-57-70, 2000; Seykora et al., Am. J. Dermatopathol. 25:6-11, 2003; Su et al., Nature. 406:536-540, 2000; Trent et al., Science. 247:568-571, 1990; Weyers et al., Cancer. 86:288-299, 1999). Similarly, the molecular mechanisms underlying further progression from a primary tumor to a metastatic melanoma are also inadequately defined.
There is a correlation between the thickness of the primary melanoma and its capacity to metastasize to the draining lymph node basin(s) and hematogenously (Haddad et al., Ann. Surg. Oncol. 6:144-149, 1999; Cascinelli et al., Ann. Surg. Oncol. 7:469-474, 2000). Once melanoma has metastasized by either route, the overall survival for patients greatly diminishes (Balch et al., Cancer. 88:3635-3648; 2001; Balch et al., J. Clin. Oncol. 19:3622-3634, 2001). Whereas patients with thin primary tumors are cured by surgery, patients diagnosed with metastatic melanoma (AJCC stage IV) have an overall poor prognosis, with 6 out of every 7 skin cancer deaths due to metastatic melanoma (Balch et al., Cancer. 88:1484-1491, 2000; Eton et al., J. Clin. Oncol. 16:1103-1111, 1998; Jemal et al., C. A. Cancer J. Clin. 57:43-66, 2007).
SUMMARY
The compositions and related methods provided herein are based, in part, on the discovery of unique gene expression profiles characteristic of primary basal cell, squamous cell, non-metastatic, and metastatic melanoma skin cancer samples. A consistent “transition zone” of gene expression change within primary melanoma samples was observed and has allowed identification of gene expression profiles capable of distinguishing a primary tumor from metastatic melanoma. This transition in gene expression involves both increased expression levels of genes such as MAGE genes, GPR19, BCL2A1, SOX5, BUB1, and RGS20, and an even greater reduction in the expression of genes such as SPRR1A/B, KRT16/17, CD24, LOR, GATA3, MUC15, and TMPRSS4. The transition in gene expression also involves other genes described herein. For example, the transition involves a reduction in expression of a plurality of (including all of) the following genes: GJB6, SPRR1A, SERPINB5, CALML5 (CLSP), DSC1, PKP1, CLCA2, DSG1, CDSN, LY6D, LCE2B, FLG; RP1-14N1.3, KRT16, SBSN, SERPINB3, SERPINB7, KRT17, KLK7, LOR, SLURP1, LOC63928, KRT15, LGALS7, CST6, SPRR1B, CNFN, TRIM29, EPPK1, SFN, KRT6B, DSG3, SPRR2B, DMKN, ASAH3, SERPINB13, KLK11, AADACL2, DAPL1, ABCA12, DSC3, POF1B, GATA3, LYPD3, KRT6A, EHF, PCDH21, CBLC, FGFR2, SCEL, and FGFR3. For example, the transition involves an increase in expression of a plurality of (including all of) the following genes: MAGEA3, MAGEA6, CSAG2 (TRAG3), MAGEA12, MAGEA2, TRIM51, NRP2, MAGEA1, MSI2, GYPC, SPP1, SOX5, KIFC1, HILS1, RGS20, BUB1, IGF2BP3, FRMD5, C1orf90, EYA4, BCL2A1, SLC16A4, AKT3, CDC45L, SEC22L3, PEG10, POPDC3, MAGEA5, GLUD2, ST6GALNAC3, SEZ6L2, DUSP4, ABCB5, RASGRF1, DUSP4, FLJ40142, BRRN1, PHLDA1, MMP14, DUSP6, DPY19L1, GLUD1, LOC346615, CALU, RNF157, PRDM13, PBK, KIAA1618, NEDD4L, BICD1, and RRM2. The transition may further involve an increase in expression of one or more of the foregoing genes in conjunction with a decrease in expression of one or more of the previous set of genes. Additionally, a correlation between primary melanoma tumor thickness, as measured by Breslow's depth, and the accumulation of individual gene expression changes has also been discovered. The genes identified as changing expression in primary cutaneous melanoma along the spectrum of increasing Breslow's thickness, are useful markers for the existence of cells characteristic of metastatic melanoma. As further described herein, expression of the genes (e.g., five or more of the genes listed above, and/or five or more of the genes described in Tables. A-D, herein) can be examined in various combinations.
Accordingly, in one aspect, the technology herein features a method of evaluating a melanoma from a patient. The method includes determining expression of five or more genes in a test sample from a melanoma, relative to a control, wherein the five or more genes are selected from the genes listed in Table A and Table B, thereby evaluating the melanoma.
In various embodiments, expression of at least 10 genes from Tables A and B is determined, e.g., expression of at least 25, 50, 100, 250, 500, 750, 1000, 1250, or 1500 genes is determined. In various embodiments, expression of no more than 1500, 1250, 1000, 750, 500, 250, 100, 50, or 25 genes is determined. The at least 10 genes may be chosen in any combination from Tables A and B. Thus, in some embodiments, the at least 10 genes includes five genes from Table A and five genes from Table B. Other combinations may be examined, such as one gene from Table A and nine genes from Table B, and so forth. In some embodiments, expression of genes from Table A or Table B is determined (e.g., expression of at least 10 genes from Table A is determined to the exclusion of genes from Table B, or, alternatively, expression of at least 10 genes from Table B is determined, to the exclusion of genes from Table A).
In various embodiments, expression of the five or more genes is determined relative to expression of the five or more genes in a reference set of non-metastatic cutaneous tissue samples, wherein a decrease in expression of one or more of a gene of Table A, and an increase in expression of one or more of a gene of Table B, relative to expression of the five or more genes in the reference set, indicates an increased likelihood that the test sample is from a metastatic melanoma and/or indicates a poor prognosis. The method can further include determining that the patient should undergo a treatment protocol. For example, patients for which the melanoma sample expression is indicative of a metastatic melanoma may elect to undergo a more aggressive treatment, e.g., with interferon alpha 2b, or interleukin2, surgery to remove additional tissue (e.g., addition melanoma tissue at the site from which the original sample was obtained, or at another site, e.g., in a lymph node), or an experimental treatment. Patients in which expression is not indicative of a metastatic melanoma may elect to forgo a treatment.
The non-metastatic cutaneous tissue samples (e.g., the reference samples to which expression in the test sample is compared) can include one or more of the following: normal human epithelial melanocytes, primary cutaneous melanoma, basal cell carcinoma, squamous cell carcinoma, melanoma in situ, and/or thin melanoma (<1.5 mm Breslow's thickness).
In various embodiments, expression of the five or more genes is compared to: (a) expression in a first reference set of non-metastatic cutaneous tissue samples, and (b) expression in a second reference set of metastatic melanoma tissue samples; wherein a greater similarity in expression of the five or more genes in the test sample to the second reference set than to the first reference set indicates an increased likelihood that the test sample is a metastatic melanoma.
The determining expression of five or more genes in the test sample can include isolating RNA from the test sample, and detecting expression of the RNA. RNA expression can be detected directly or indirectly, e.g., using microarray or PCR analysis. The sample can be a fixed, paraffin-embedded biopsy sample, or a frozen sample.
In various embodiments, the determining expression of five or more genes in the test sample includes reverse transcriptase polymerase chain reaction (RT-PCR), e.g., quantitative PCR, e.g., real time quantitative PCR.
In various embodiments, the determining expression of five or more genes in the test sample includes microarray analysis.
In other embodiments, the determining expression of five or more genes in the test sample includes analysis of protein expression, e.g., immunohistochemical analysis of proteins encoded by on or more of the genes, or proteomic analysis.
The test sample can be a test sample from a melanoma having an intermediate thickness (e.g., a Breslow's thickness of 1-4 mm). The test sample can be from a thin or thick melanoma.
In another aspect, the technology features a method of evaluating a melanoma from a patient, which method includes, for example, determining expression of five or more genes in a test sample from the melanoma, relative to a control, wherein the five or more genes are selected from the genes listed in Table C and Table D, thereby evaluating the melanoma. The method can include other features described herein. For example, expression of at least 10, 25, 50, 75, or 100 genes from Tables C and D can determined. Expression of no more than 100, 75, 50, 25, or 10 genes can be determined. The at least 5 genes from Table C and Table D may be examined in any combination, such as one gene from Table C and four genes from Table D; or four genes from Table C and one gene from Table D. In some embodiments, expression of genes solely from just one of Table C or Table D is determined (e.g., expression of at least five genes from Table C is determined, or expression of at least five genes from Table D is determined).
Expression of the five or more genes can be determined relative to expression of the five or more genes in a reference set of non-metastatic cutaneous tissue samples, wherein a decrease in expression of one or more of a gene of Table C, and an increase in expression of one or more of a gene of Table D, relative to expression of the five or more genes in the reference set, indicates an increased likelihood that the test sample is a metastatic melanoma and/or indicates a poor prognosis. The method can further include determining that the patient should undergo a treatment protocol, based on the determination of gene expression.
In some embodiments expression of the five or more genes is compared to: (a) expression in a first reference set of non-metastatic cutaneous tissue samples, and (b) expression in a second reference set of metastatic melanoma tissue samples; wherein a greater similarity in expression of the five or more genes in the test sample to the second reference set than to the first reference set indicates an increased likelihood that the test sample is a metastatic melanoma.
The determining expression of five or more genes in the test sample can include isolating RNA from the test sample, and detecting expression of the RNA, or detecting protein expression.
In another aspect, the technology also features kits for evaluating a melanoma sample. The kits include polynucleotides (e.g., primers or probes) for analysis of at least 5, 10, 25, 50, 75, or 100 genes from Tables C and D, wherein each oligonucleotide specifically hybridizes to one of the genes from Tables C and D. The kits can include polynucleotides for analysis of up to 25, 50, 75, or 100 genes from Tables C and D.
For example, a kit includes pairs of polynucleotides for amplification of the genes from Tables C and D by PCR.
The technology also features kits for evaluating a melanoma sample that include polynucleotides (e.g., primers or probes) for analysis of at least 250, 500, 750, 1000, 1250, or 1500 genes from Tables A and B, wherein each oligonucleotide specifically hybridizes to one of the genes from Tables A and B. The kits can include polynucleotides for analysis of up to 250, 500, 270, 1000, 1250, or 1500 genes from Tables A and B. In some embodiments, the polynucleotides are immobilized on a solid support, e.g., as in a microarray.
The technology also features kits for evaluating protein expression in a melanoma sample. The kit includes, for example, reagents (e.g., antibodies) for detection of proteins encoded by at least 5, 10, 25, or 50 genes from Tables C and D.
A “sample” is any biological material obtained from an individual. A “melanoma sample” or “melanoma tissue sample” is a sample that includes primarily melanoma cells.
“Gene” refers to a polynucleotide sequence that comprises sequences that are expressed in a cell as RNA and control sequences necessary for the production of a transcript or precursor. A gene expression product analyzed according to a method described herein can be encoded by a full length coding sequence or by any portion of the coding sequence.
“Polynucleotide” refers to a polymeric form of nucleotides of any length, either ribonucleotides or deoxyribonucleotides. Thus, the term includes, but is not limited to, single-, double-, or multi-stranded DNA or RNA, genomic DNA, cDNA, DNA-RNA hybrids, or a polymer comprising purine and pyrimidine bases or other natural, chemically or biochemically modified, non-natural, or derivatized nucleotide bases, as well as polynucleotides that have been modified in order to introduce a means for attachment (e.g., to a support for use as a microarray).
The descriptions herein are phrased in terms of “five or more” or “ten or more” genes, but the choices of five and ten would be understood to be for the purposes of illustration and are non-limiting. One may also examine expression of other numbers such as 3, 4, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, and 30 genes, and so forth. In some embodiments, the combination of genes from Tables A, B, C, and/or D which is examined includes one or more genes implicated in one or more (e.g., 2, 3, 4, 5, 6, 7, 8, or 9) of the following biological processes, as understood by one skilled in the art: keratinocyte differentiation, epidermis development, melanocyte differentiation, cell differentiation, morphogenesis, muscle development, nervous system development, cell adhesion, the Wnt receptor signaling pathway, cell-cell signaling, cytoskeleton organization and biogenesis, inflammatory or immune response, cell motility and chemotaxis, electron transport, carbohydrate metabolism, lipid metabolism, proteolysis, signal transduction, protein transport, protein biosynthesis, transcription, DNA repair, cell cycle regulation or proliferation, or apoptosis. In some embodiments, at least one gene implicated in each of the above processes is examined.
The details of one or more embodiments of the technology are set forth in the accompanying drawings and the description below. Other features, objects, and advantages of the technology will be apparent from the description and drawings, and from the claims. All cited patents, and patent applications and references (including references to public sequence database entries) are incorporated by reference in their entireties for all purposes.



DESCRIPTION OF DRAWINGS
FIG. 1A is a graph depicting the number and functional classifications of genes, lower expression (upper bar for each classification) and higher expression (lower bar for each classification) of which is associated with metastatic melanoma.
FIG. 1B is a heatmap depicting the relative gene expression of the full spectrum of genes described herein in the non-metastatic (primary) tumors relative to the metastatic tumors (MM). The dark grey shading (appearing primarily in the upper left and lower right quadrants) corresponds to higher than average gene expression, black depicts average gene expression, and the light shading (appearing primarily in lower left and upper right quadrants) depicts lower than average gene expression. Average is set as the average across all the samples used in the figure. Individual rows represent individual tumor samples and individual columns depict individual genes identified in the experiments described herein.
FIG. 1C is a set of graphs depicting relative expression levels of a subset of genes described herein in samples of normal skin, basal cell carcinoma (BCC), squamous cell carcinoma (SCC), melanoma in situ (MIS), thin melanoma, melanoma of intermediate thickness (I.M.), thick primary, metastatic melanoma (subcutaneous, lymph node and distant; MM), and melanoma cell lines derived from patients with stage IV melanoma. Genes more highly expressed in metastatic melanoma are depicted in the upper graph and genes whose expression is decreased in the metastatic melanoma cells are depicted in the lower graph. In both cases the transition from a non-metastatic tissue expression level to the metastatic tissue expression level occurs in the I.M. thickness sample set. This figure illustrates the distinct differences between the non-metastatic and metastatic melanoma tumors and also illustrates the transitional tumor class that would most benefit from assays to detect the metastatic cell type.
FIG. 2A is a graph depicting comparative quantitative PCR (qPCR) gene expression analysis data of putative tumor suppressor genes (CST6, DSC3, PITX1, POU2F3) and oncogenes (GDF15, SPP-1) in PCM (n=7) and MM (n=13) samples. Relative quantitation of target gene expression for each sample was, determined using the equation 2-ΔΔCt, where GAPDH was used as the internal reference and normal skin as the calibrator. Values were Log base 10 transformed (y-axis) so that all values below zero represent a down-regulation in gene expression and values above zero represent an up-regulation in gene expression, compared to normal skin.
FIG. 2B is a graph depicting results of correlative microarray analysis of gene expression levels in primary and metastatic melanoma samples compared with normal skin. The statistical differences of gene expression between primary (PCM) and metastatic melanoma (MM) samples were analyzed by Wilcoxon's signed rank test; two-tailed significance level was set at α=0.05. Compared to PCM samples (n=7), the expression levels of 4 putative tumor suppressor genes (CST6, p<0.0001; DSC3, p<0.0001; PITX1, p=0.0043, POU2F3, p<0.0001) were significantly decreased in MM samples (n=40), while the expression of putative oncogenes (GDF15, p=0.0027; SPP1, p<0.0001) were significantly increased in MM samples.
FIG. 3A is a table listing results of semi-quantitative. RT-PCR analysis of oncogene and tumor suppressor gene (TSG) mRNA expression in normal human skin, NHEM, PCM and MM cell lines. A panel of 12 putative oncogenes and 6 TSG were analyzed, with the relative levels of mRNA expression as follows: negative band (−), faintly visible band (+/−), visible band (+), strongly visible band (++), N=Not Done. β-actin served as the internal comparative control. The grey values of PCR products of each gene were analyzed by the AlphaEase 3 software and standardized according to β-actin in every sample.
FIG. 3B is a set of western blots in which expression of SPP1 (FIG. 3B, panels a and b), DSC3, CLCA2, PDGFRL, and TUBULIN (FIG. 3B, panels c, d, e, and f, respectively) was examined in metastatic melanoma (MM) and primary cutaneous melanoma (PCM) daughter cell lines. The blot depicted in FIG. 3B, panels a and b, was probed with anti-SPP1 antibody. Panels c, d, e, and f, were probed with antibodies to DSC-3, CLCA2, PDGFRL, and α-tubulin (as an internal control), respectively. Lanes 1-3 of each blot contained PCM samples. Lanes 4-6 of each blot contained MM cell lines.



DETAILED DESCRIPTION
Methods and compositions for evaluating tissue samples (e.g., cutaneous tissue samples, e.g., samples from primary melanomas) are provided herein to determine whether the samples exhibit a gene expression profile characteristic of aggressive, metastatic melanomas, or a profile characteristic of non-metastatic melanomas. The ability to classify samples with a high degree of accuracy and sensitivity facilitates prognosis and subsequent clinical decisions (e.g., whether or not to undergo further surgery or other treatment modalities). Accordingly, the technology provides, inter alia, sets of genes whose expression can be examined to determine whether a cutaneous tissue sample is non-metastatic, or metastatic, as well as methods of analyzing expression of the gene sets, and compositions for performing the analysis.
The technology herein features combinations of genes, e.g., combinations of genes listed in Tables A and B below, combinations of genes listed in Tables C and D below. Analysis of the expression of these genes can be performed to identify metastatic melanoma tumors (e.g., in primary cutaneous melanoma samples, or in samples from compound nevi). The technology also features methods of analyzing the expression of combinations of genes. Various techniques are suitable for analyzing gene expression, including those that measure RNA or protein expression. For example, a sample from a melanoma (e.g., a primary cutaneous melanoma) is collected and processed to obtain RNA, protein, or tissue sections, to produce a test sample for analysis. The relative expression of several, dozens, 50, 100, or hundreds of genes in the test sample is determined. The gene expression values are compared to a reference set of values derived from selected non-metastatic melanoma samples and metastatic melanoma samples measured by the same assay as used to determine expression in the test sample. The values obtained for the test sample characterize the sample as metastatic or non-metastatic.
In some methods, a small number of genes (e.g., a subset of genes from Tables C and D, e.g., 5, 10, 15, 25 genes) is selected for analysis, and expression levels are determined by a quantitative or semi-quantitative PCR method or by immunohistochemistry. The combination of measured values for the respective genes are compared to control values to determine the degree to which the test sample contains gene expression values indicative of a metastatic tumor sample. The test samples are, for example, surgically collected tumors collected in a manner that preserves RNA, or alternatively fixed (e.g., formalin fixed) and embedded in paraffin prior to analysis, preserved by flash freezing or fixation, and/or treated with an RNA Stabilization Reagent.
In some methods, expression of a larger number of genes is analyzed, e.g., using microarrays. Nucleic acids from the test sample are hybridized to arrays under appropriate conditions, arrays are scanned, and the data processed by standard methods for feature extraction and normalization in order to obtain individual gene expression values. In these methods, a few hundred to more than a thousand genes can be used to determine the character of the test sample. One of several methods might be employed to identify the metastatic potential of the sample under investigation, based on the microarray-determined gene expression values. Typically, reference samples for metastatic melanoma and non-metastatic melanoma are analyzed in advance. The test sample is compared to the reference samples by classification schemes such as clustering, weighted voting, principle components analysis, self organizing maps, and/or neural networks. Each of these schemes is essentially a mathematical system for maximizing the geometric separation of classes (metastatic and non-metastatic) in multidimensional space using the individual gene expression values as coordinates to plot an individual sample relative to reference samples in multidimensional space.
Whether a method suitable for analysis of smaller or larger numbers of genes is employed, the reference samples define the combination of measures that identify a metastatic sample and a non-metastatic sample. The specific mathematical process depends on the method used for measuring gene expression, the number of genes, and the nature of the genes chosen to participate in the assay. Based on this unique combination and the reference sample values a threshold value will be determined (or mathematical formula) that will identify the unknown sample as more like the metastatic samples or more like the non-metastatic samples. One of skill would understand that genes that are not differentially expressed can be examined in methods described herein, e.g., as a control.
Tables A-D set forth sets of genes, the expression of which has been shown to correlate with metastatic melanoma. Tables A and C list genes whose expression is decreased in metastatic melanoma samples, relative to non-metastatic samples. Tables B and D list genes whose expression is increased in metastatic melanoma samples, relative to non-metastatic samples. Thus, the genes provided in these tables, and subsets thereof, are useful markers for metastatic melanoma.
In various embodiments, the technology provides a subset of genes from Tables A and B for evaluating a cutaneous tissue sample, sets of oligonucleotides (e.g., for use as probes and primers) for analyzing expression of the subsets, and methods for analyzing their expression, as described in more detail below. The set includes, for example, at least 5, 10, 50, 100, 250, 500, 750, or 1000 genes from Tables A and B, in any proportion (e.g., 800 genes from Table A and 200 genes from Table B).
For example, the subset includes the genes listed in Tables C and D. The genes in Tables C and D, and subsets thereof, are useful for evaluating a cutaneous-tissue sample, and in methods for analyzing expression of the subsets, as described in more detail below. An exemplary set includes, for example, at least 5, 10, 25, 35, or 51 genes from each of Tables C and D.
The lists shown in Tables C and D were generated from the lists shown in Tables A and B by selecting the genes that exhibit the greatest difference in gene expression between the metastatic samples and the non-metastatic samples based on microarray analysis. The genes on these lists also represent genes, the expression or expression products of which have been the subject of biological investigations.
Tables A-D include full length gene names (Gene description), gene symbols, GenBank accession numbers (GenBank ID), Entrez gene accession numbers (Entrez Gene ID), and UniGene accession numbers (UniGene ID). GenBank, Entrez, and UniGene records can be accessed on the World Wide Web at the following address: ncbi.nlm.nih.gov. These records provide sequences and additional information for each gene.
The genes listed in Tables A-D are generally referred to elsewhere herein by gene symbol. Gene symbols shown in parentheses are aliases or former designations.







TABLE A







Genes differentially expressed in metastatic melanoma. Expression


of the genes listed in this table is decreased relative to non-metastatic samples.














Gene

Entrez




Gene description
Symbol
GenBank ID
Gene ID
UniGene ID
















1.
24-dehydrocholesterol reductase
DHCR24
NM_014762.2
1718
Hs.498727


2.
26 serine protease
P11
NM_006025.2
8909
Hs.997


3.
abhydrolase domain containing 9
ABHD9
NM_024794.1
79852
Hs.156457


4.
ABI gene family, member 3 (NESH)
ABI3BP
NM_015429.2
25890
Hs.477015



binding protein


5.
absent in melanoma 1
AIM1
NM_001624.1
202
Hs.486074


6.
absent in melanoma 1-like
AIM1L
NM_017977
55057
Hs.128738


7.
acid phosphatase, prostate
ACPP
NM_001099.2
55
Hs.433060


8.
Acrg embryonic lethality (mouse)
AK000009
AA425275
170622
Hs.356605



minimal region ortholog


9.
actin binding LIM protein 1
ABLIM1
NM_001003407.1
3983
Hs.438236


10.
activin A receptor, type IIA
ACVR2A
NM_001616.3
92
Hs.470174


11.
adaptor-related protein complex 1, mu
AP1M2
NM_005498.3
10053
Hs.18894



2 subunit


12.
adenosine kinase
ADK
NM_001123.2
132
Hs.500118


13.
ADMP
ADMP
NM_145035
165679
Hs.369104


14.
AFG3 ATPase family gene 3-like 2
AFG3L2
NM_006796
10939
Hs.436683



(yeast)


15.
AHNAK nucleoprotein (desmoyokin)
AHNAK
NM_024060
79026
Hs.378738


16.
aldehyde dehydrogenase 2 family
ALDH2
NM_000690.2
217
Hs.436437



(mitochondrial)


17.
aldehyde dehydrogenase 3 family,
ALDH3A2
NM_000382.2
224
Hs.499886



member A2


18.
aldehyde dehydrogenase 3 family,
ALDH3B2
NM_000695.3
222
Hs.87539



member B2


19.
aldehyde dehydrogenase 3 family,
ALDH3A1
NM_000691.3
218
Hs.531682



memberA1


20.
aldo-keto reductase family 1, member
AKR1B10
NM_020299.3
57016
Hs.116724



B10 (aldose reductase)


21.
aldo-keto reductase family 1, member
AKR1C1
NM_001353
1645
Hs.295131



C1 (dihydrodiol dehydrogenase 1; 20-



alpha (3-alpha)-hydroxysteroid



dehydrogenase)


22.
aldo-keto reductase family 1, member
AKR1C2
NM_001354.4
1646
Hs.558319



C2 (dihydrodiol dehydrogenase 2; bile



acid binding protein; 3-alpha



hydroxysteroid dehydrogenase, type



III)


23.
alkaline ceramidase
ACER1
NM_133492
125981
Hs.352609


24.
alpha-2-glycoprotein 1, zinc
AZGP1
NM_001185
563
Hs.407861


25.
alpha-2-macroglobulin-like 1
A2ML1
AK057908.1
144568
Hs.334306


26.
ALS2 C-terminal like
ALS2CL
NM_147129.2
259173
Hs.517937


27.
androgen receptor (dihydrotestosterone
AR
NM_001011645.1
367
Hs.496240



receptor; testicular feminization; spinal



and bulbar muscular atrophy; Kennedy



disease)


28.
ankyrin 3, node of Ranvier (ankyrin G)
ANK3
NM_001149.2
288
Hs.499725


29.
ankyrin repeat domain 22
ANKRD22
NM_144590.1
118932
Hs.217484


30.
ankyrin repeat domain 35
ANKRD35
NM_144698.2
148741
Hs.133081


31.
annexin A3
ANXA3
NM_005139
306
Hs.480042


32.
annexin A8
ANXA8
NM_001630
244
Hs.87268


33.
annexin A9
ANXA9
NM_003568.1
8416
Hs.430324


34.
aquaporin 3
AQP3
NM_004925
360
Hs.234642


35.
arachidonate 12-lipoxygenase
ALOX12
NM_000697.1
239
Hs.422967


36.
arachidonate 12-lipoxygenase, 12R
ALOX12B
NM_001139.1
242
Hs.136574



type


37.
arachidonate lipoxygenase 3
ALOXE3
NM_021628.1
59344
Hs.232770


38.
arginase, liver
ARG1
NM_000045.2
383
Hs.440934


39.
argininosuccinate synthetase
ASS
NM_054012.2
445
Hs.558301


40.
arrestin domain containing 4
ARRDC4
NM_183376.1
91947
Hs.6093


41.
aryl hydrocarbon receptor nuclear
ARNTL2
NM_020183
56938
Hs.434269



translocator-like 2


42.
arylacetamide deacetylase(esterase)
AADAC
NM_001086.2
13
Hs.506908


43.
arylacetamide deacetylase-like 2
AADACL2
NM_207365.1
344752
Hs.100206


44.
ataxin 3
ATXN3
NM_001024631.1
4287
Hs.526425


45.
ATPase type 13A4
ATP13A4
NM_032279.2
84239
Hs.561100


46.
ATPase type 13A5
ATP13A5
AY358667.1
344905
Hs.531335


47.
ATPase, Ca++ transporting, type 2C,
ATP2C2
NM_014861.1
9914
Hs.6168



member 2


48.
ATPase, Class 1, type 8B, member 1
ATP8B1
NM_005603
5205
Hs.418426


49.
ATPase, H+ transporting, lysosomal
ATP6V1C2
NM_001039362.1
245973
Hs.372429



42 kDa, V1 subunit C isoform 2


50.
ATPase, H+/K+ transporting,
ATP12A
NM_001676.4
479
Hs.147111



nongastric, alpha polypeptide


51.
ATP-binding cassette, sub-family A
ABCA12
NM_173076.2
26154
Hs.134585



(ABC1), member 12


52.
autism susceptibility candidate 2
AUTS2
NM_015570.1
26053
Hs.21631


53.
bactericidal/permeability-increasing
BPIL2
NM_174932
254240
Hs.372939



protein-like 2


54.
basonuclin 1
BNC1
NM_001717.2
646
Hs.459153


55.
B-box and SPRY domain containing
BSPRY
NM_017688.1
54836
Hs.494870


56.
B-cell CLL/lymphoma 11A (zinc
BCL11A
NM_138559.1
53335
Hs.370549



finger protein)


57.
B-cell CLL/lymphoma 11B (zinc finger
BCL11B
NM_022898.1
64919
Hs.510396



protein)


58.
BCL2/adenovirus E1B 19 kD
BNIPL
AY033000.1
149428
Hs.553613



interacting protein like


59.
BCL2-associated athanogene
BAG1
NM_004323.3
573
Hs.377484


60.
BCL2-like 10 (apoptosis facilitator)
BCL2L10
NM_020396.2
10017
Hs.283672


61.
betacellulin
BTC
NM_001729.1
685
Hs.558302


62.
bleomycin hydrolase
BLMH
NM_000386.2
642
Hs.371914


63.
Boc homolog (mouse)
BOC
NM_033254.2
91653
Hs.556004


64.
bradykinin receptor B2
BDKRB2
NM_000623.2
624
Hs.525572


65.
BRG1-binding protein ELD/OSA1
ELD/OSA1
NM_020732
57492
Hs.436008


66.
BTB (POZ) domain containing 11
BTBD11
NM_001017523.1
121551
Hs.271272


67.
BTG family, member 3
BTG3
NM_006806
10950
Hs.473420


68.
butyrobetaine (gamma), 2-oxoglutarate
BBOX1
NM_003986
8424
Hs.144845



dioxygenase (gamma-butyrobetaine



hydroxylase) 1


69.
cadherin-like 22
CDH22
NM_021248
64405
Hs.382126


70.
cadherin-like 26
CDH26
NM_021810.3
60437
Hs.54973


71.
calcium channel, voltage-dependent,
CACNA2D3
NM_018398.2
55799
Hs.128594



alpha 2/delta 3 subunit


72.
calcium channel, voltage-dependent,
CACNB4
NM_001005746.1
785
Hs.284800



beta 4 subunit


73.
calcium/calmodulin-dependent protein
CAMK1D
NM_020397.2
57118
Hs.156723



kinase ID


74.
calmodulin-like 3
CALML3
NM_005185
810
Hs.239600


75.
calmodulin-like 5
CALML5
NM_017422.3
51806
Hs.180142


76.
calpain small subunit 2
CAPNS2
NM_032330
84290
Hs.13359


77.
carbonic anhydrase II
CA2
NM_000067.1
760
Hs.155097


78.
carbonic anhydrase XII
CA12
NM_001218.3
771
Hs.210995


79.
carbonic anhydrase XIII
CA13
NM_198584.1
377677
Hs.127189


80.
carboxypeptidase A4
CPA4
NM_016352
51200
Hs.93764


81.
carboxypeptidase Z
CPZ
NM_001014447.1
8532
Hs.78068


82.
carcinoembryonic antigen-related cell
CEACAM19
BC083499.1
56971
Hs.416925



adhesion molecule 19


83.
carcinoembryonic antigen-related cell
CEACAM6
NM_002483.3
4680
Hs.466814



adhesion molecule 6 (non-specific



cross reacting antigen)


84.
Cas-Br-M (murine) ecotropic retroviral
CBLC
NM_012116.2
23624
Hs.466907



transforming sequence c


85.
casein kinase 1, alpha 1
CSNK1A1
NM_001892
1452
Hs.442592


86.
caspase 14, apoptosis-related cysteine
CASP14
NM_012114
23581
Hs.248226



protease


87.
caspase recruitment domain family,
CARD14
NM_024110
79092
Hs.550529



member 14


88.
castor homolog 1, zinc finger
CASZ1
NM_017766.2
54897
Hs.439894



(Drosophila)


89.
catenin, beta interacting protein 1
CTNNBIP1
NM_020248.2
56998
Hs.463759


90.
cathepsin L2
CTSL2
NM_001333.2
1515
Hs.87417


91.
CCAAT/enhancer binding protein
CEBPA
NM_004364.2
1050
Hs.76171



(C/EBP), alpha


92.
CD1a antigen
CD1A
NM_001763.1
909
Hs.1309


93.
CD1E antigen, e polypeptide
CD1E
NM_030893.1
913
Hs.249217


94.
CD207 antigen, langerin
CD207
NM_015717.2
50489
Hs.199731


95.
CD24 antigen (small cell lung
CD24
NM_013230.2
934
Hs.375108



carcinoma cluster 4 antigen)


96.
CDC-like kinase 4
CLK4
NM_020666
57396
Hs.406557


97.
CDP-diacylglycerol synthase
CDS1
NM_001263.2
1040
Hs.444924



(phosphatidate cytidylyltransferase) 1


98.
cellular retinoic acid binding protein 2
CRABP2
NM_001878.2
1382
Hs.405662


99.
centaurin, delta 1
CENTD1
NM_015230
116984
Hs.427719


100.
checkpoint suppressor 1
CHES1
NM_005197
1112
Hs.434286


101.
chemokine (C-C motif) ligand 22
CCL22
NM_002990.3
6367
Hs.534347


102.
chemokine (C-X3-C motif) receptor 1
CX3CR1
NM_001337
1524
Hs.78913


103.
chemokine (C-X-C motif) ligand 14
CXCL14
NM_004887.3
9547
Hs.483444


104.
chitinase 3-like 2
CHI3L2
NM_001025197.1
1117
Hs.514840


105.
chloride channel, calcium activated,
CLCA2
NM_006536
9635
Hs.241551



family member 2


106.
chloride channel, calcium activated,
CLCA4
NM_012128.2
22802
Hs.555012



family member 4


107.
chloride intracellular channel 3
CLIC3
NM_004669.2
9022
Hs.64746


108.
cholinergic receptor, nicotinic, alpha
CHRNA9
NM_017581.2
55584
Hs.272278



polypeptide 9


109.
chromatin modifying protein 4C
CHMP4C
NM_152284.3
92421
Hs.183861


110.
chromosome 1 open reading frame 106
C1orf106
NM_018265.1
55765
Hs.518997


111.
chromosome 1 open reading frame 116
C1orf116
NM_023938.4
79098
Hs.32417


112.
chromosome 1 open reading frame 161
C1orf161
NM_152367.1
126868
Hs.376194


113.
chromosome 1 open reading frame 172
C1orf172
NM_152365.1
126695
Hs.188881


114.
Chromosome 1 open reading frame 21
C1orf21
NM_030806.3
81563
Hs.497159


115.
chromosome 1 open reading frame 210
C1orf210
NM_182517.1
149466
Hs.158963


116.
chromosome 1 open reading frame 42
C1orf42
NM_019060.1
54544
Hs.110196


117.
chromosome 1 open reading frame 46
C1orf46
AF005082
388699
Hs.516420


118.
chromosome 1 open reading frame 68
C1orf68
AF005081.1
553168
Hs.547272


119.
chromosome 10 open reading frame
C10orf118
NM_018017.2
55088
Hs.159066



118


120.
chromosome 10 open reading frame 57
C10orf57
NM_025125.2
80195
Hs.169982


121.
chromosome 10 open reading frame 72
C10orf72
NM_144984.1
196740
Hs.522928


122.
chromosome 10 open reading frame 99
C10orf99
NM_207373.1
387695
Hs.298713


123.
chromosome 11 open reading frame 52
C11orf52
NM_080659.1
91894
Hs.97013


124.
chromosome 14 open reading frame
C14orf116
NM_018589
55453
Hs.60548



116


125.
chromosome 14 open reading frame 29
C14orf29
NM_181533
145447
Hs.271896


126.
chromosome 14 open reading frame 47
C14orf47
NM_152332
123036
Hs.57787


127.
chromosome 14 open reading frame 78
C14orf78
AK094143.1
113146
Hs.441783


128.
chromosome 19 open reading frame 33
C19orf33
NM_033520.1
64073
Hs.348553




(IMUP)


129.
chromosome 2 open reading frame 54
C2orf54
NM_024861.1
79919
Hs.193745


130.
chromosome 2 open reading frame 55
C2orf55
NM_207362.1
343990
Hs.469398


131.
chromosome 20 open reading frame
C20orf128
NM_178468.2
128876
Hs.554917



128


132.
chromosome 20 open reading frame 38
C20orf38
NM_018327.1
55304
Hs.272242


133.
chromosome 20 open reading frame 42
C20orf42
NM_017671.3
55612
Hs.472054


134.
chromosome 20 open reading frame 55
C20orf55
NM_031424
83541
Hs.534072


135.
chromosome 20 open reading frame 74
C20orf74
AK002211.1
57186
Hs.472285


136.
chromosome 21 open reading frame 34
C21orf34
NM_001005733.1
388815
Hs.473394


137.
chromosome 4 open reading frame 32
C4orf32
NM_152400.1
132720
Hs.23439


138.
chromosome 5 open reading frame 27
C5orf27
NM_175616.2
202299
Hs.8373


139.
Chromosome 5 open reading frame 4
C5orf4
NM_016348.1
10826
Hs.519694


140.
chromosome 6 open reading 132
C6orf132
XM_371820
647024
Hs.444277


141.
chromosome 6 open reading frame 143
C6orf143
NM_001010872.1
222584
Hs.258095


142.
chromosome 6 open reading frame 162
C6orf162
NM_020425
57150
Hs.70769


143.
chromosome 8 open reading frame 47
C8orf47
NM_173549.1
203111
Hs.171455


144.
chromosome 8 open reading frame 61
C8orf61
NM_001034061.1
619435
Hs.127675


145.
chromosome 9 open reading frame 111
C9orf111
NM_152286.2
375775
Hs.294147


146.
chromosome 9 open reading frame 3
C9orf3
NM_032823.3
84909
Hs.434253


147.
clathrin, light polypeptide (Lcb)
CLTB
NM_007097.2
1212
Hs.484241


148.
claudin 1
CLDN1
NM_021101.3
9076
Hs.439060


149.
claudin 4
CLDN4
NM_001305.3
1364
Hs.520942


150.
claudin 8
CLDN8
NM_199328.1
9073
Hs.162209


151.
coagulation factor II (thrombin)
F2RL1
NM_005242.3
2150
Hs.154299



receptor-like 1


152.
coagulation factor III (thromboplastin,
F3
NM_001993.2
2152
Hs.62192



tissue factor)


153.
COBL-like 1
COBLL1
NM_014900.3
22837
Hs.470457


154.
coiled-coil domain containing 3
CCDC3
NM_031455.2
83643
Hs.498720


155.
collagen, type VII, alpha 1
COL7A1
NM_000094.2
1294
Hs.476218



(epidermolysis bullosa, dystrophic,



dominant and recessive)


156.
collagen, type XVII, alpha 1
COL17A1
NM_130778.1
1308
Hs.117938


157.
collagen, type XXI, alpha 1
COL21A1
NM_030820.3
81578
Hs.47629


158.
contactin 1
CNTN1
NM_001843
1272
Hs.143434


159.
cordon-bleu homolog (mouse)
COBL
NM_015198.2
23242
Hs.99141


160.
corneodesmosin
CDSN
NM_001264.3
1041
Hs.310958


161.
cornifelin
CNFN
NM_032488.2
84518
Hs.148590


162.
coxsackie virus and adenovirus
CXADR
NM_001338.3
1525
Hs.473417



receptor


163.
creatine kinase, mitochondrial 1A
CKMT1A
NM_001015001.1
548596
Hs.425633


164.
crumbs homolog 3 (Drosophila)
CRB3
NM_174881.2
92359
Hs.150319


165.
cryptochrome 2 (photolyase-like)
CRY2
NM_021117.1
1408
Hs.532491


166.
C type lectin domain family 2, member B
CLEC2B
NM_005127.2
9976
Hs.85201


167.
cyclic nucleotide gated channel beta 1
CNGB1
NM_001297.1
1258
Hs.147062


168.
cylindromatosis (turban tumor
CYLD
NM_015247
1540
Hs.432993



syndrome)


169.
cystatin A (stefin A)
CSTA
NM_005213.3
1475
Hs.518198


170.
cystatin E/M
CST6
NM_001323.2
1474
Hs.139389


171.
cysteine rich transmembrane BMP
CRIM1
NM_016441.1
51232
Hs.332847



regulator 1 (chordin-like)


172.
cysteine/tyrosine-rich 1
CYYR1
NM_052954.2
116159
Hs.37445


173.
cysteine-rich protein 1 (intestinal)
CRIP1
NM_001311.3
1396
Hs.70327


174.
cysteine-rich secretory protein 3
CRISP3
NM_006061.1
10321
Hs.404466


175.
cytidine deaminase
CDA
NM_001785.2
978
Hs.466910


176.
cytochrome b5 type A (microsomal)
CYB5A
NM_001914.2
1528
Hs.465413


177.
cytochrome P450, family 2, subfamily
CYP2C18
NM_000772.1
1562
Hs.511872



C, polypeptide 18


178.
cytochrome P450, family 2, subfamily
CYP2E1
NM_000773.3
1571
Hs.12907



E, polypeptide 1


179.
cytochrome P450, family 26, subfamily
CYP26B1
NM_019885.2
56603
Hs.91546



B, polypeptide 1


180.
cytochrome P450, family 3, subfamily
CYP3A5
NM_000777.2
1577
Hs.150276



A, polypeptide 5


181.
cytochrome P450, family 3, subfamily
CYP3A7
NM_000765.2
1551
Hs.111944



A, polypeptide 7


182.
cytochrome P450, family 39, subfamily
CYP39A1
NM_016593.3
51302
Hs.387367



A, polypeptide 1


183.
cytochrome P450, family 4, subfamily
CYP4F12
NM_023944.1
66002
Hs.131459



F, polypeptide 12


184.
cytochrome P450, family 4, subfamily
CYP4F2
NM_001082.3
8529
Hs.558423



F, polypeptide 2


185.
cytochrome P450, family 4, subfamily
CYP4F22
NM_173483.1
126410
Hs.156452



F, polypeptide 22


186.
cytochrome P450, family 4, subfamily
CYP4F3
NM_000896.1
4051
Hs.106242



F, polypeptide 3


187.
cytochrome P450, family 4, subfamily
CYP4X1
NM_178033.1
260293
Hs.439760



X, polypeptide 1


188.
cytokine receptor-like factor 1
CRLF1
NM_004750.2
9244
Hs.114948


189.
cytoplasmic polyadenylation element
CPEB3
NM_014912.3
22849
Hs.131683



binding protein 3


190.
death associated protein-like 1
DAPL1
NM_001017920.1
92196
Hs.59761


191.
death-associated protein kinase 2
DAPK2
NM_014326.3
23604
Hs.237886


192.
decorin
DCN
NM_133505.2
1634
Hs.156316


193.
dedicator of cytokinesis 9
DOCK9
NM_015296.1
23348
Hs.314413


194.
defensin, beta 1
DEFB1
NM_005218.3
1672
Hs.32949


195.
defensin, beta 103A
DEFB103A
NM_018661.2
55894
Hs.283082


196.
deiodinase, iodothyronine, type II
DIO2
NM_001007023.1
1734
Hs.202354


197.
DENN/MADD domain containing 2C
DENND2C
NM_198459.2
163259
Hs.127350


198.
dermcidin
DCD
NM_053283.2
117159
Hs.350570


199.
dermokine
DMKN
NM_033317.2
93099
Hs.417795


200.
desmocollin 1
DSC1
NM_004948
1823
Hs.348436


201.
desmocollin 2
DSC2
NM_004949.2
1824
Hs.95612


202.
desmocollin 3
DSC3
NM_001941
1825
Hs.41690


203.
desmoglein 1
DSG1
NM_001942.1
1828
Hs.2633


204.
desmoglein 3 (pemphigus vulgaris
DSG3
NM_001944.1
1830
Hs.1925



antigen)


205.
desmoplakin
DSP
NM_001008844.1
1832
Hs.519873


206.
DIRAS family, GTP-binding RAS-like 3
DIRAS3
NM_004675.2
9077
Hs.194695


207.
Discs, large homolog 2, chapsyn-110
DLG2
NM_001364.2
1740
Hs.503453



(Drosophila)


208.
distal-less homeo box 3
DLX3
NM_005220.2
1747
Hs.134194


209.
DKFZP564O0823 protein
DKFZP564O0823
NM_015393.2
25849
Hs.105460


210.
dual adaptor of phosphotyrosine and 3-
DAPP1
NM_014395.1
27071
Hs.436271



phosphoinositides


211.
dual oxidase 1
DUOX1
NM_017434
53905
Hs.272813


212.
dual oxidase 2
DUOX2
NM_014080.3
50506
Hs.71377


213.
dual oxidase maturation factor 1
DUOXA1
NM_144565
90527
Hs.356664


214.
dynein, light chain, roadblock-type 2
DYNLRB2
NM_130897.1
83657
Hs.98849


215.
dystonin
DST
NM_020388.2
667
Hs.485616


216.
E74-like factor 5 (ets domain
ELF5
NM_001422.2
2001
Hs.11713



transcription factor)


217.
Early endosome antigen 1, 162 kD
EEA1
NM_003566
8411
Hs.403150


218.
echinoderm microtubule associated
EML1
NM_001008707.1
2009
Hs.12451



protein like 1


219.
ectonucleoside triphosphate
ENTPD3
NM_001248
956
Hs.441145



diphosphohydrolase 3


220.
EF-hand calcium binding domain 6
EFCAB6
NM_198856.1
64800
Hs.368507


221.
EGF-like-domain, multiple 3
EGFL3
AL134303
1953
Hs.56186


222.
egl nine homolog 3 (C. elegans)
EGLN3
NM_022073.2
112399
Hs.135507


223.
EH-domain containing 2
EHD2
NM_014601.2
30846
Hs.325650


224.
electron-transferring-flavoprotein
ETFDH
NM_004453.1
2110
Hs.155729



dehydrogenase


225.
ELL-related RNA polymerase II,
ELL2
NM_012081
22936
Hs.192221



elongation factor


226.
ELMO domain containing 1
ELMOD1
NM_018712.2
55531
Hs.495779


227.
elongation factor RNA polymerase II-
ELL3
NM_025165.2
80237
Hs.424126



like 3


228.
elongation of very long chain fatty
ELOVL4
NM_022726.2
6785
Hs.101915



acids (FEN1/Elo2, SUR4/Elo3, yeast)-



like 4


229.
ELOVL family member 7, elongation
ELOVL7
NM_024930.1
79993
Hs.274256



of long chain fatty acids (yeast)


230.
embryonal Fyn-associated substrate
EFS
NM_005864.2
10278
Hs.24587


231.
empty spiracles homolog 2
EMX2
NM_004098.2
2018
Hs.202095



(Drosophila)


232.
endothelial differentiation, sphingolipid
EDG8
NM_030760.3
53637
Hs.501561



G-protein-coupled receptor, 8


233.
endothelin 1
EDN1
NM_001955
1906
Hs.511899


234.
engulfment and cell motility 3 (ced-12
ELMO3
NM_024712.3
79767
Hs.377416



homolog, C. elegans)


235.
enoyl Coenzyme A hydratase domain
ECHDC2
NM_018281.1
55268
Hs.476319



containing 2


236.
envoplakin
EVPL
NM_001988.1
2125
Hs.500635


237.
EPH receptor B6
EPHB6
NM_004445.2
2051
Hs.380089


238.
ephrin-A3
EFNA3
NM_004952.3
1944
Hs.516656


239.
epidermal growth factor receptor
EGFR
NM_201282.1
1956
Hs.488293



(erythroblastic leukemia viral (v-erb-b)



oncogene homolog, avian)


240.
epidermal retinal dehydrogenase 2
RDHE2
NM_138969.2
195814
Hs.170673


241.
epiplakin 1
EPPK1
NM_031308.1
83481
Hs.200412


242.
epiregulin
EREG
NM_001432
2069
Hs.115263


243.
epithelial membrane protein 2
EMP2
NM_001424.3
2013
Hs.531561


244.
epithelial V-like antigen 1
EVA1
NM_005797.2
10205
Hs.116651


245.
EPS8-like 1
EPS8L1
NM_133180.1
54869
Hs.438862


246.
EPS8-like 2
EPS8L2
NM_022772.2
64787
Hs.55016


247.
epsin 3
EPN3
NM_017957.1
55040
Hs.165904


248.
erythrocyte membrane protein band 4.1
EPB41L4A
NM_022140
64097
Hs.553542



like 4A


249.
erythrocyte membrane protein band 4.1
EPB41L4B
NM_018424.1
54566
Hs.269180



like 4B


250.
erythrocyte membrane protein band 4.1
EPB41L5
NM_020909.2
57669
Hs.369232



like 5


251.
ets homologous factor
EHF
NM_012153.3
26298
Hs.502306


252.
ets variant gene 7 (TEL2 oncogene)
ETV7
NM_016135.2
51513
Hs.272398


253.
eukaryotic elongation factor-2 kinase
EEF2K
NM_013302.3
29904
Hs.498892


254.
exophilin 5
EXPH5
NM_015065.1
23086
Hs.269591


255.
family with sequence similarity 107,
FAM107A
NM_007177.1
11170
Hs.8022



member A


256.
family with sequence similarity 13,
FAM13C1
NM_001001971.1
220965
Hs.499704



member C1


257.
family with sequence similarity 46,
FAM46B
NM_052943.2
115572
Hs.59771



member B


258.
family with sequence similarity 62 (C2
FAM62C
BC037292.1
83850
Hs.477711



domain containing), member C


259.
family with sequence similarity 79,
FAM79B
NM_198485.1
285386
Hs.338851



member B


260.
family with sequence similarity 83,
FAM83A
NM_032899.4
84985
Hs.379821



member A


261.
family with sequence similarity 83,
FAM83F
NM_138435.1
113828
Hs.197680



member F


262.
FAT tumor suppressor homolog 2
FAT2
NM_001447.1
2196
Hs.132158



(Drosophila)


263.
fatty acid amide hydrolase 2
FAAH2
NM_174912.2
158584
Hs.496205


264.
fatty acid binding protein 5 (psoriasis-
FABP5
NM_001444.1
2171
Hs.558327



associated)


265.
F-box and WD-40 domain protein 7
FBXW7
NM_001013415.1
55294
Hs.519029



(archipelago homolog, Drosophila)


266.
F-box protein 42
FBXO42
NM_018994.1
54455
Hs.522384


267.
Fc fragment of IgE, high affinity I,
FCER1A
NM_002001
2205
Hs.897



receptor for; alpha polypeptide


268.
Fc fragment of IgG binding protein
FCGBP
NM_003890.1
8857
Hs.111732


269.
fer-1-like 3, myoferlin (C. elegans)
FER1L3
NM_013451.2
26509
Hs.500572


270.
FERM and PDZ domain containing 1
FRMPD1
NM_014907.1
22844
Hs.163990


271.
fetuin B
FETUB
NM_014375.2
26998
Hs.81073


272.
fibroblast growth factor binding protein 1
FGFBP1
NM_005130.3
9982
Hs.1690


273.
fibroblast growth factor receptor 2
FGFR2
NM_022972.1
2263
Hs.533683



(bacteria-expressed kinase,



keratinocyte growth factor receptor,



craniofacial dysostosis 1, Crouzon



syndrome, Pfeiffer syndrome, Jackson-



Weiss syndrome)


274.
fibroblast growth factor receptor 3
FGFR3
NM_000142.2
2261
Hs.1420



(achondroplasia, thanatophoric



dwarfism)


275.
fibronectin type III domain containing 6
FNDC6
NM_144717.2
152028
Hs.61232


276.
fibulin 2
FBLN2
NM_001998.2
2199
Hs.198862


277.
filaggrin
FLG
NM_002016.1
2312
Hs.23783


278.
filaggrin 2
RP1-14N1.3
NM_001014342.1
388698
Hs.156124


279.
FLJ41603 protein
FLJ41603
NM_001001669.2
389337
Hs.256206


280.
forkhead box N1
FOXN1
NM_003593.2
8456
Hs.198313


281.
forkhead box Q1
FOXQ1
NM_033260.2
94234
Hs.297452


282.
frizzled homolog 10 (Drosophila)
FZD10
NM_007197.2
11211
Hs.31664


283.
furry homolog (Drosophila)
FRY
NM_023037
10129
Hs.390874


284.
FYVE, RhoGEF and PH domain
FGD6
BC013319.1
55785
Hs.506381



containing 6


285.
G protein-coupled receptor 1
GPR1
NM_005279.2
2825
Hs.184907


286.
G protein-coupled receptor 115
GPR115
NM_153838.2
221393
Hs.150131


287.
G protein-coupled receptor 172B
GPR172B
NM_017986.2
55065
Hs.110128


288.
G protein-coupled receptor 87
GPR87
NM_023915.2
53836
Hs.58561


289.
G protein-coupled receptor, family C,
GPRC5C
NM_022036.2
55890
Hs.446438



group 5, member C


290.
galectin-related protein
HSPC159
NM_014181.1
29094
Hs.372208


291.
gamma-aminobutyric acid (GABA) A
GABRE
NM_021984.2
2564
Hs.22785



receptor, epsilon


292.
gamma-glutamyltransferase 6 homolog
GGT6
NM_153338.1
124975
Hs.130749



(rat)


293.
gap junction protein, alpha 1, 43 kDa
GJA1
NM_000165.2
2697
Hs.74471



(connexin 43)


294.
gap junction protein, beta 2, 26 kDa
GJB2
NM_004004.3
2706
Hs.524894



(connexin 26)


295.
gap junction protein, beta 3, 31 kDa
GJB3
NM_024009.2
2707
Hs.522561



(connexin 31)


296.
gap junction protein, beta 5 (connexin
GJB5
NM_005268.2
2709
Hs.198249



31.1)


297.
gap junction protein, beta 6 (connexin
GJB6
NM_006783.2
10804
Hs.511757



30)


298.
GATA binding protein 3
GATA3
NM_001002295.1
2625
Hs.524134


299.
giant axonal neuropathy (gigaxonin)
GAN
NM_022041.2
8139
Hs.112569


300.
GIPC PDZ domain containing family,
GIPC2
NM_017655.4
54810
Hs.13852



member 2


301.
gliomedin
GLDN
BX538105.1
342035
Hs.526441


302.
GLIS family zinc finger 1
GLIS1
NM_147193.1
148979
Hs.306691


303.
glutamic pyruvate transaminase
GPT2
NM_133443.1
84706
Hs.460693



(alanine aminotransferase) 2


304.
glutathione peroxidase 2
GPX2
NM_002083.2
2877
Hs.2704



(gastrointestinal)


305.
glutathione peroxidase 3 (plasma)
GPX3
NM_002084.3
2878
Hs.386793


306.
glutathione S-transferase A3
GSTA3
NM_000847.3
2940
Hs.102484


307.
glutathione S-transferase A4
GSTA4
NM_001512.2
2941
Hs.485557


308.
glutathione S-transferase omega 2
GSTO2
NM_183239.1
119391
Hs.203634


309.
glycerophosphodiester
GDPD2
NM_017711.2
54857
Hs.438712



phosphodiesterase domain containing 2


310.
glycerophosphodiester
GDPD3
NM_001031718.1
79153
Hs.289015



phosphodiesterase domain containing 3


311.
glycolipid transfer protein
GLTP
NM_016433.3
51228
Hs.381256


312.
glycoprotein Ib (platelet), beta
GP1BB
NM_000407.4
2812
Hs.517410



polypeptide


313.
glycosylphosphatidylinositol specific
GPLD1
NM_001503.2
2822
Hs.512001



phospholipase D1


314.
GM2 ganglioside activator
GM2A
NM_000405.3
2760
Hs.483873


315.
GPI-gamma 4
GPIG4
NM_152545
153020
Hs.352552


316.
grainyhead-like 1 (Drosophila)
GRHL1
NM_198182.1
29841
Hs.418493


317.
grainyhead-like 2 (Drosophila)
GRHL2
NM_024915.1
79977
Hs.161160


318.
grainyhead-like 3 (Drosophila)
GRHL3
NM_021180.2
57822
Hs.369825


319.
GRAM domain containing 1C
GRAMD1C
NM_017577.2
54762
Hs.24583


320.
GRINL1A combined protein
Gcom1
NM_001018090.1
145781
Hs.50841


321.
growth arrest-specific 6
GAS6
NM_000820.1
2621
Hs.369201


322.
growth hormone regulated TBC protein 1
GRTP1
NM_024719.1
79774
Hs.170904


323.
guanine deaminase
GDA
NM_004293
9615
Hs.494163


324.
guanylate binding protein family,
GBP6
AL703282
163351
Hs.254338



member 6


325.
H3 histone, family 3B (H3.3B)
H3F3B
NM_005324.3
3021
Hs.180877


326.
hairless homolog (mouse)
HR
NM_005144.3
55806
Hs.272367


327.
heparan sulfate (glucosamine) 3-O-
HS3ST6
NM_001009606.1
64711
Hs.200735



sulfotransferase 6


328.
hepatic leukemia factor
HLF
NM_002126.4
3131
Hs.196952


329.
hepatocellular carcinoma antigen gene
LOC63928
NM_022097.1
63928
Hs.178589



520


330.
hephaestin
HEPH
NM_014799
9843
Hs.31720


331.
histidine ammonia-lyase
HAL
NM_002108.2
3034
Hs.190783


332.
homeo box A9
HOXA9
NM_152739.3
3205
Hs.127428


333.
homeodomain-only protein
HOP
NM_032495
84525
Hs.13775


334.
homer homolog 2 (Drosophila)
HOMER2
NM_004839.2
9455
Hs.93564


335.
hook homolog 1 (Drosophila)
HOOK1
NM_015888.4
51361
Hs.378836


336.
HtrA serine peptidase 1
HTRA1
NM_002775.3
5654
Hs.501280


337.
huntingtin interacting protein 1 related
HIP1R
NM_003959.1
9026
Hs.524815


338.
hyaluronan synthase 3
HAS3
NM_138612.1
3038
Hs.85962


339.
hyaluronoglucosaminidase 1
HYAL1
NM_153282.1
3373
Hs.75619


340.
hyaluronoglucosaminidase 4
HYAL4
NM_012269.1
23553
Hs.28673


341.
hydatidiform mole associated and
HYMAI
NR_002768.1
57061
Hs.698009



imprinted


342.
hydroxysteroid (11-beta)
HSD11B2
NM_000196.2
3291
Hs.1376



dehydrogenase 2


343.
hypothetical gene supported by
LOC441461
XM_499157.2
441461
Hs.163155



BC030123


344.
hypothetical LOC653602
LOC653602
XM_939526.1
653602
Hs.433956


345.
hypothetical protein DJ667H12.2
DJ667H12.2
NM_019605
56256
Hs.445835


346.
hypothetical protein DKFZP761M1511
DKFZP761M1511
AK096661.1
54492
Hs.91521


347.
hypothetical protein FLJ10156
FLJ10156
NM_019013
54478
Hs.404323


348.
hypothetical protein FLJ10634
FLJ10634
XM_938980.1
643338
Hs.334475


349.
hypothetical protein FLJ10706
FLJ10706
NM_018186
55732
Hs.443551


350.
hypothetical protein FLJ11183
FLJ11183
AK026881
55785
Hs.170623


351.
hypothetical protein FLJ11235
FLJ11235
NM_019033
54508
Hs.555952


352.
hypothetical protein FLJ20003
FLJ20003
NM_017615
54780
Hs.258798


353.
hypothetical protein FLJ21511
FLJ21511
NM_025087.1
80157
Hs.479703


354.
hypothetical protein FLJ22757
FLJ22757
NM_024898
79958
Hs.236449


355.
hypothetical protein FLJ23306
FLJ23306
NM_024530
79579
Hs.5890


356.
hypothetical protein FLJ25217
FLJ25217
XM_939893.1
650803
Hs.153450


357.
hypothetical protein FLJ30532
FLJ30532
NM_144724
153562
Hs.390601


358.
hypothetical protein FLJ32798
FLJ32798
NM_173496
143098
Hs.350684


359.
hypothetical protein FLJ33868
FLJ33868
NM_152574
158219
Hs.49605


360.
hypothetical protein FLJ35880
FLJ35880
NM_153264.2
256076
Hs.205403


361.
hypothetical protein FLJ37464
FLJ37464
NM_173815.3
283848
Hs.346947


362.
hypothetical protein FLJ39005
FLJ39005
NM_178521
284313
Hs.130286


363.
hypothetical protein FLJ90492
FLJ90492
NM_181783
160418
Hs.331268


364.
hypothetical protein from clone 643
LOC57228
NM_020467
57228
Hs.206501


365.
hypothetical protein LOC126917
LOC126917
XM_928886.1
126917
Hs.466625


366.
hypothetical protein LOC130576
LOC130576
NM_177964.3
130576
Hs.357567


367.
hypothetical protein LOC131873
LOC131873
XM_940071.1
131873
Hs.477571


368.
hypothetical protein LOC144501
LOC144501
NM_182507
144501
Hs.140978


369.
hypothetical protein LOC147645
LOC147645
XM_085831.10
147645
Hs.293236


370.
hypothetical protein LOC151878
LOC151878
BC014063.1
151878
Hs.680377


371.
hypothetical protein LOC196264
LOC196264
BG037101
196264
Hs.15396


372.
hypothetical protein LOC283070
LOC283070
AK097377.1
283070
Hs.376041


373.
hypothetical protein LOC283404
LOC283404
BC039104.1
283404
Hs.556299


374.
hypothetical protein LOC283666
LOC283666
BC035094.2
283666
Hs.560343


375.
hypothetical protein LOC283874
LOC283874
AK097909.1
283874
Hs.459699


376.
hypothetical protein LOC284023
LOC284023
XM_933997.1
284023
Hs.354493


377.
hypothetical protein LOC285535
LOC285535
AK021540.1
285535
Hs.400256


378.
hypothetical protein LOC286440
LOC286440
AK123807.1
286440
Hs.348844


379.
hypothetical protein LOC338667
LOC338667
BC043578.1
338667
Hs.558217


380.
hypothetical protein LOC348938
LOC348938
XM_371777.4
348938
Hs.4285


381.
hypothetical protein LOC646014
LOC646014
XM_928978.1
646014
Hs.117853


382.
hypothetical protein MGC14128
MGC14128
NM_032899
84985
Hs.290881


383.
hypothetical protein MGC14376
MGC14376
NM_001001870.1
84981
Hs.417157


384.
hypothetical protein MGC2655
MGC2655
XM_085463.6
146439
Hs.513285


385.
hypothetical protein MGC4248
MGC4248
NM_032333
84293
Hs.301519


386.
ICEBERG caspase-1 inhibitor
ICEBERG
NM_021571
59082
Hs.56279


387.
IGF-like family member 1
IGFL1
NM_198541.1
374918
Hs.546554


388.
IGF-like family member 2
IGFL2
NM_001002915.1
147920
Hs.99376


389.
InaD-like (Drosophila)
INADL
NM_170605.2
10207
Hs.478125


390.
inhibitor of DNA binding 1, dominant
ID1
NM_002165.2
3397
Hs.504609



negative helix-loop-helix protein


391.
inositol 1,3,4,5,6-pentakisphosphate 2-
IPPK
NM_022755.4
64768
Hs.459896



kinase


392.
inositol(myo)-1(or 4)-
IMPA2
NM_014214.1
3613
Hs.367992



monophosphatase 2


393.
insulin-degrading enzyme
IDE
NM_004969
3416
Hs.500546


394.
integrin, beta 4
ITGB4
NM_000213.3
3691
Hs.370255


395.
integrin, beta 6
ITGB6
NM_000888.3
3694
Hs.470399


396.
interferon regulatory factor 6
IRF6
NM_006147.2
3664
Hs.355827


397.
interleukin 1 family, member 10 (theta)
IL1F10
NM_173161.1
84639
Hs.306974


398.
interleukin 1 family, member 5 (delta)
IL1F5
NM_012275.2
26525
Hs.516301


399.
interleukin 1 family, member 7 (zeta)
IL1F7
NM_014439.3
27178
Hs.166371


400.
interleukin 1 family, member 8 (eta)
IL1F8
NM_014438.3
27177
Hs.278909


401.
interleukin 1 family, member 9
IL1F9
NM_019618.2
56300
Hs.211238


402.
interleukin 1 receptor antagonist
IL1RN
NM_173843.1
3557
Hs.81134


403.
interleukin 1 receptor, type I
IL1R1
NM_000877.2
3554
Hs.557403


404.
interleukin 18 (interferon-gamma-
IL18
NM_001562.2
3606
Hs.83077



inducing factor)


405.
interleukin 20 receptor, alpha
IL20RA
NM_014432.2
53832
Hs.445868


406.
interleukin 22 receptor, alpha 1
IL22RA1
NM_021258.2
58985
Hs.110915


407.
involucrin
IVL
NM_005547
3713
Hs.157091


408.
iroquois homeobox protein 1
IRX1
NM_024337.3
79192
Hs.424156


409.
iroquois homeobox protein 3
IRX3
NM_024336.1
79191
Hs.499205


410.
iroquois homeobox protein 4
IRX4
NM_016358.1
50805
Hs.196927


411.
iroquois homeobox protein 5
IRX5
NM_005853.4
10265
Hs.435730


412.
jagged 1 (Alagille syndrome)
JAG1
NM_000214.1
182
Hs.224012


413.
junction plakoglobin
JUP
NM_002230.1
3728
Hs.514174


414.
kallikrein 10
KLK10
NM_002776.3
5655
Hs.275464


415.
kallikrein 11
KLK11
NM_006853.2
11012
Hs.57771


416.
kallikrein 12
KLK12
NM_019598.2
43849
Hs.411572


417.
kallikrein 13
KLK13
NM_015596.1
26085
Hs.165296


418.
kallikrein 5
KLK5
NM_012427.3
25818
Hs.50915


419.
kallikrein 6 (neurosin, zyme)
KLK6
NM_001012964.1
5653
Hs.79361


420.
kallikrein 7 (chymotryptic, stratum
KLK7
NM_005046.2
5650
Hs.151254



corneum)


421.
kallikrein 8 (neuropsin/ovasin)
KLK8
NM_007196.2
11202
Hs.104570


422.
kallikrein 9
KLK9
NM_012315.1
284366
Hs.448942


423.
keratin 1 (epidermolytic
KRT1
NM_006121
3848
Hs.80828



hyperkeratosis)


424.
keratin 10 (epidermolytic
KRT10
NM_000421.2
3858
Hs.99936



hyperkeratosis; keratosis palmaris et



plantaris)


425.
keratin 14 (epidermolysis bullosa
KRT14
NM_000526.3
3861
Hs.355214



simplex, Dowling-Meara, Koebner)


426.
keratin 15
KRT15
NM_002275.2
3866
Hs.80342


427.
keratin 16 (focal non-epidermolytic
KRT16
NM_005557.2
3868
Hs.432448



palmoplantar keratoderma)


428.
keratin 17
KRT17
NM_000422.1
3872
Hs.2785


429.
keratin 1B
KRT1B
BC033366.1
374454
Hs.334989


430.
keratin 23 (histone deacetylase
KRT23
NM_015515.3
25984
Hs.9029



inducible)


431.
keratin 2A (epidermal ichthyosis
KRT2A
NM_000423.2
3849
Hs.707



bullosa of Siemens)


432.
keratin 5 (epidermolysis bullosa
KRT5
NM_000424.2
3852
Hs.433845



simplex, Dowling-



Meara/Kobner/Weber-Cockayne types)


433.
keratin 5b
K5B
NM_173352
196374
Hs.121824


434.
keratin 6A
KRT6A
NM_005554
3853
Hs.367762


435.
keratin 6B
KRT6B
NM_005555.2
3854
Hs.524438


436.
keratin 7
KRT7
NM_005556
3855
Hs.411501


437.
keratin 74
KRT74
NM_175053.2
121391
Hs.56255


438.
keratin, hair, acidic, 1
KRTHA1
NM_002277.2
3881
Hs.41696


439.
keratin, hair, acidic, 2
KRTHA2
NM_002278.2
3882
Hs.41752


440.
keratinocyte differentiation-associated
KRTDAP
NM_207392.1
388533
Hs.112457



protein


441.
KIAA0513
KIAA0513
NM_014732
9764
Hs.301658


442.
KIAA0514
KIAA0514
NM_014696.2
9721
Hs.523375


443.
KIAA0874 protein
KIAA0874
NM_015208
23253
Hs.388877


444.
KIAA1117
KIAA1117
AK094766.1
23033
Hs.520246


445.
KIAA1145 protein
KIAA1145
NM_020698
57458
Hs.173392


446.
KIAA1217
KIAA1217
BX648451.1
56243
Hs.445885


447.
KIAA1411
KIAA1411
NM_020819
57579
Hs.211700


448.
KIAA1543
KIAA1543
BC020431
57662
Hs.17686


449.
KIAA1671 protein
KIAA1671
AL832019.1
85379
Hs.419171


450.
KIAA1912 protein
KIAA1912
XM_055636.4
114800
Hs.117136


451.
KIAA2022
KIAA2022
NM_001008537.1
340533
Hs.124128


452.
kinesin family member 1C
KIF1C
NM_006612.3
10749
Hs.435120


453.
kinesin light chain 3
KLC3
BC025318.1
147700
Hs.298079


454.
KIT ligand
KITLG
NM_000899.3
4254
Hs.1048


455.
kringle containing transmembrane
KREMEN1
NM_001039571.1
83999
Hs.229335



protein 1


456.
Kruppel-like factor 4 (gut)
KLF4
NM_004235.3
9314
Hs.376206


457.
Kruppel-like factor 5 (intestinal)
KLF5
NM_001730.3
688
Hs.508234


458.
Kruppel-like factor 8
KLF8
NM_007250
11279
Hs.411296


459.
ladinin 1
LAD1
NM_005558.3
3898
Hs.519035


460.
LAG1 longevity assurance homolog 3
LASS3
NM_178842.2
204219
Hs.416099



(S. cerevisiae)


461.
LAG1 longevity assurance homolog 4
LASS4
NM_024552.1
79603
Hs.515111



(S. cerevisiae)


462.
laminin, alpha 2 (merosin, congenital
LAMA2
NM_000426.2
3908
Hs.200841



muscular dystrophy)


463.
laminin, alpha 3
LAMA3
NM_198129.1
3909
Hs.436367


464.
laminin, beta 3
LAMB3
NM_000228
3914
Hs.497636


465.
laminin, beta 4
LAMB4
NM_007356.1
22798
Hs.62022


466.
laminin, gamma 2
LAMC2
NM_005562.1
3918
Hs.530509


467.
late cornified envelope 1B
LCE1B
NM_178349.1
353132
Hs.375103


468.
late cornified envelope 2B
LCE2B
NM_014357.3
26239
Hs.234766


469.
late cornified envelope 3D
LCE3D
NM_032563.1
84648
Hs.244349


470.
latrophilin 3
LPHN3
NM_015236.3
23284
Hs.28391


471.
lectin, galactoside-binding, soluble, 7
LGALS7
NM_002307.1
3963
Hs.558355



(galectin 7)


472.
leucine rich repeat containing 8 family,
LRRC8E
NM_025061.3
80131
Hs.501511



member E


473.
leucine rich repeat neuronal 1
LRRN1
NM_020873.3
57633
Hs.163244


474.
leucine-rich repeat-containing G
LGR4
NM_018490.1
55366
Hs.502176



protein-coupled receptor 4


475.
leucine-rich repeat-containing G
LGR6
NM_021636.2
59352
Hs.497402



protein-coupled receptor 6


476.
leucine-rich repeats and
LRIG3
NM_153377.3
121227
Hs.253736



immunoglobulin-like domains 3


477.
leukotriene B4 receptor
LTB4R
NM_181657.1
1241
Hs.525256


478.
leukotriene C4 synthase
LTC4S
NM_145867.1
4056
Hs.456


479.
ligand of numb-protein X 1
LNX1
NM_032622.1
84708
Hs.407755


480.
likely ortholog of mouse Sh3 domain
SH3YL1
NM_015677
26751
Hs.147365



YSC-like 1


481.
LIM domain kinase 2
LIMK2
NM_005569.3
3985
Hs.474596


482.
lines homolog 1 (Drosophila)
LINS1
BC010363.1
55180
Hs.105633


483.
lipocalin 2 (oncogene 24p3)
LCN2
NM_005564
3934
Hs.204238


484.
LOC153470
LOC153470
BC021680.1
389336
Hs.173059


485.
LOC284752
LOC284752
AI056877
284752
Hs.38207


486.
LOC340813
LOC340813
AL117475
340813
Hs.306344


487.
LOC345926
LOC345926
XM_933651.1
644241
Hs.62929


488.
LOC346876
LOC346876
AI224578
346876
Hs.147678


489.
LOC349496
LOC349496
BF064181
349496
Hs.147964


490.
LOC349889
LOC349889
AW589793
349889
Hs.224713


491.
loricrin
LOR
NM_000427
4014
Hs.251680


492.
lunatic fringe homolog (Drosophila)
LFNG
NM_001040168.1
3955
Hs.159142


493.
Ly-6 neurotoxin-like protein 1
LYNX1
NM_023946
66004
Hs.158665


494.
LY6/PLAUR domain containing 3
LYPD3
NM_014400.2
27076
Hs.377028


495.
LY6/PLAUR domain containing 5
LYPD5
NM_182573.1
284348
Hs.44289


496.
lymphocyte antigen 6 complex, locus D
LY6D (E48)
NM_003695.2
8581
Hs.415762


497.
lymphocyte antigen 6 complex, locus
LY6G6C
NM_025261.1
80740
Hs.241586



G6C


498.
lymphocyte antigen 75
LY75
NM_002349.1
4065
Hs.153563


499.
lysosomal-associated membrane
LAMP3
NM_014398.2
27074
Hs.518448



protein 3


500.
macrophage stimulating 1 receptor (c-
MST1R
NM_002447.1
4486
Hs.517973



met-related tyrosine kinase)


501.
major histocompatibility complex,
HLA-DQB2
NM_182549.1
3120
Hs.554753



class II, DQ beta 2


502.
mal, T-cell differentiation protein 2
MAL2
NM_052886
114569
Hs.201083


503.
mal, T-cell differentiation protein-like
MALL
NM_005434.3
7851
Hs.185055


504.
malic enzyme 1, NADP(+)-dependent,
ME1
NM_002395
4199
Hs.14732



cytosolic


505.
MAM domain containing 2
MAMDC2
NM_153267.3
256691
Hs.127386


506.
mannan-binding lectin serine peptidase
MASP1
NM_001879.4
5648
Hs.89983



1 (C4/C2 activating component of Ra-



reactive factor)


507.
MAS-related GPR, member F
MRGPRF
NM_145015.2
219928
Hs.118513


508.
matrix metallopeptidase 28
MMP28
NM_024302.3
79148
Hs.380710


509.
melanoma-derived leucine zipper,
MLZE
NM_031415.2
56169
Hs.133244



extra-nuclear factor


510.
membrane associated guanylate kinase,
MAGI1
NM_004742.2
9223
Hs.651939



WW and PDZ domain containing 1


511.
membrane protein, palmitoylated 7
MPP7
NM_173496.2
143098
Hs.499159



(MAGUK p55 subfamily member 7)


512.
membrane-associated ring finger
MAR3
NM_178450.2
115123
Hs.132441



(C3HC4) 3


513.
membrane-spanning 4-domains,
MS4A2
NM_000139.2
2206
Hs.386748



subfamily A, member 2 (Fc fragment



of IgE, high affinity 1, receptor for;



beta polypeptide)


514.
meningioma (disrupted in balanced
MN1
NM_002430.2
4330
Hs.268515



translocation) 1


515.
metallo phosphoesterase
MPPE1
NM_023075
65258
Hs.154145


516.
metastasis associated lung
MALAT1
AK130345.1
378938
Hs.187199



adenocarcinoma transcript 1 (non-



coding RNA)


517.
methyltransferase like 7A
METTL7A
NM_014033.3
25840
Hs.288771


518.
MICAL C-terminal like
MICALCL
NM_032867.1
84953
Hs.128196


519.
microfibrillar-associated protein 3-like
MFAP3L
AB014526.1
9848
Hs.178121


520.
microseminoprotein, beta-
MSMB
NM_002443.2
4477
Hs.255462


521.
microsomal glutathione S-transferase 1
MGST1
NM_020300.3
4257
Hs.389700


522.
microtubule associated serine/threonine
MAST4
NM_198828.1
375449
Hs.482329



kinase family member 4


523.
microtubule-associated protein 7
MAP7
NM_003980.3
9053
Hs.486548


524.
mitogen-activated protein kinase kinase
MAP3K9
NM_033141.2
4293
Hs.437214



kinase 9


525.
monoamine oxidase A
MAOA
NM_000240.2
4128
Hs.183109


526.
MRS2-like, magnesium homeostasis
MRS2L
NM_020662.2
57380
Hs.533291



factor (S. cerevisiae)


527.
mucin 15
MUC15
NM_145650.2
143662
Hs.407152


528.
muscleblind-like (Drosophila)
MBNL1
NM_021038.3
4154
Hs.478000


529.
myosin VB
MYO5B
XM_371116.4
4645
Hs.550481


530.
myosin VI
MYO6
NM_004999.3
4646
Hs.149387


531.
NACHT, leucine rich repeat and PYD
NALP1
AK057464.1
22861
Hs.104305



(pyrin domain) containing 1


532.
NAD(P) dependent steroid
HSPC105
NM_145168
93517
Hs.87779



dehydrogenase-like


533.
NADH dehydrogenase (ubiquinone) 1
NDUFA4L2
NM_020142.3
56901
Hs.221447



alpha subcomplex, 4-like 2


534.
Nance-Horan syndrome (congenital
NHS
NM_198270.2
4810
Hs.201623



cataracts and dental anomalies)


535.
Nanog homeobox
NANOG
NM_024865.1
79923
Hs.329296


536.
NDRG family member 4
NDRG4
NM_020465.2
65009
Hs.322430


537.
nebulette
NEBL
NM_006393
10529
Hs.5025


538.
nephronectin
NPNT
NM_001033047.1
255743
Hs.518921


539.
netrin 4
NTN4
NM_021229.3
59277
Hs.201034


540.
neuroepithelial cell transforming gene 1
NET1
NM_005863.2
10276
Hs.25155


541.
neuromedin U
NMU
NM_006681.1
10874
Hs.418367


542.
neuronal guanine nucleotide exchange
NGEF
NM_019850.1
25791
Hs.97316



factor


543.
neurotrophin 5 (neurotrophin 4/5)
NTF5
NM_006179
4909
Hs.266902


544.
NGNL6975
UNQ6975
AK095550.1
400952
Hs.468368


545.
nicotinamide nucleotide
NMNAT3
NM_178177.2
349565
Hs.208673



adenylyltransferase 3


546.
NIPA-like domain containing 1
NPAL1
CR749484.1
152519
Hs.134190


547.
NIPA-like domain containing 2
NPAL2
NM_024759.1
79815
Hs.309489


548.
NSE1
NSE1
NM_145175
151354
Hs.260855


549.
NUAK family, SNF1-like kinase, 1
NUAK1
NM_014840.2
9891
Hs.524692


550.
nuclear factor I/B
NFIB
NM_005596.2
4781
Hs.370359


551.
nuclear factor of activated T-cells,
NFATC3
NM_004555.2
4775
Hs.341716



cytoplasmic, calcineurin-dependent 3


552.
nucleosome assembly protein 1-like 2
NAP1L2
NM_021963.2
4674
Hs.66180


553.
O-acyltransferase (membrane bound)
OACT2
NM_138799.2
129642
Hs.467634



domain containing 2


554.
odz, odd Oz/ten-m homolog 2
ODZ2
AB032953
57451
Hs.155915



(Drosophila)


555.
odz, odd Oz/ten-m homolog 4
ODZ4
BF112171
26011
Hs.213087



(Drosophila)


556.
olfactomedin-like 2A
OLFML2A
NM_182487.1
169611
Hs.357004


557.
orphan short-chain dehydrogenase/
SDR-O
NM_148897.1
121214
Hs.380178



reductase


558.
OTU domain, ubiquitin aldehyde
OTUB2
BC009615.1
78990
Hs.278815



binding 2


559.
ovo-like 1 (Drosophila)
OVOL1
NM_004561.2
5017
Hs.134434


560.
oxoglutarate (alpha-ketoglutarate)
OXGR1
NM_080818.3
27199
Hs.352218



receptor 1


561.
p21(CDKN1A)-activated kinase 6
PAK6
NM_020168.3
56924
Hs.513645


562.
p53-regulated apoptosis-inducing
P53AIP1
NM_022112.1
63970
Hs.160953



protein 1


563.
paired-like homeodomain transcription
PITX1
NM_002653
5307
Hs.84136



factor 1


564.
palladin, cytoskeletal associated protein
PALLD
NM_016081
23022
Hs.194431


565.
palmdelphin
PALMD
NM_017734.2
54873
Hs.483993


566.
par-6 partitioning defective 6 homolog
PARD6G
NM_032510
84552
Hs.223584



gamma (C. elegans)


567.
patatin-like phospholipase domain
PNPLA1
NM_173676.1
285848
Hs.407002



containing 1


568.
PDZ domain containing 3
PDZK3
NM_178140.2
23037
Hs.481819


569.
PDZK1 interacting protein 1
PDZK1IP1
NM_005764.3
10158
Hs.431099


570.
peptidase inhibitor 3, skin-derived
PI3
NM_002638.2
5266
Hs.112341



(SKALP)


571.
peptidyl arginine deiminase, type 1
PADI1
NM_013358.1
29943
Hs.412941


572.
peptidylprolyl isomerase C (cyclophilin
PPIC
NM_000943.4
5480
Hs.110364



C)


573.
peptidylprolyl isomerase D
PPID
NM_005038.2
5481
Hs.183958



(cyclophilin D)


574.
periplakin
PPL
NM_002705.3
5493
Hs.192233


575.
peroxisomal biogenesis factor 3
PEX3
AK023593.1
153914
Hs.7277


576.
PERP, TP53 apoptosis effector
PERP
NM_022121.2
64065
Hs.520421


577.
PET112-like (yeast)
PET112L
NM_004564.1
5188
Hs.119316


578.
Phosphatidylinositol glycan anchor
PIGL
NM_004278
9487
Hs.433422



biosynthesis, class L


579.
phosphoinositide-3-kinase, class 2,
PIK3C2G
NM_004570.2
5288
Hs.22500



gamma polypeptide


580.
phospholipase A2 receptor 1, 180 kDa
PLA2R1
NM_001007267.1
22925
Hs.410477


581.
phospholipase A2, group III
PLA2G3
NM_015715.2
50487
Hs.149623


582.
phospholipase A2, group IVB
PLA2G4B
NM_005090.2
8681
Hs.567254



(cytosolic)


583.
phosphorylase kinase, alpha 1 (muscle)
PHKA1
NM_002637.1
5255
Hs.201379


584.
phosphotyrosine interaction domain
PID1
NM_017933.3
55022
Hs.409352



containing 1


585.
phytanoyl-CoA dioxygenase domain
PHYHD1
NM_174933.2
254295
Hs.326391



containing 1


586.
placenta-specific 2
PLAC2
NM_153375.1
257000
Hs.515575


587.
plakophilin 1 (ectodermal
PKP1
NM_001005337.1
5317
Hs.497350



dysplasia/skin fragility syndrome)


588.
plakophilin 2
PKP2
NM_001005242.1
5318
Hs.164384


589.
plakophilin 3
PKP3
NM_007183.2
11187
Hs.534395


590.
plasma membrane proteolipid
PLLP
NM_015993.1
51090
Hs.200821



(plasmolipin)


591.
pleckstrin homology domain
PLEKHA1
NM_001001974.1
59338
Hs.287830



containing, family A (phosphoinositide



binding specific) member 1


592.
pleiomorphic adenoma gene-like 1
PLAGL1
NM_002656.2
5325
Hs.444975


593.
poliovirus receptor-related 4
PVRL4
NM_030916.1
81607
Hs.492490


594.
potassium channel, subfamily K,
KCNK1
NM_002245
3775
Hs.376874



member 1


595.
potassium channel, subfamily K,
KCNK6
NM_004823.1
9424
Hs.240395



member 6


596.
potassium channel, subfamily K,
KCNK7
NM_033455.1
10089
Hs.175218



member 7


597.
potassium inwardly-rectifying channel,
KCNJ12
NM_021012.3
3768
Hs.2363



subfamily J, member 12


598.
potassium voltage-gated channel, Shal-
KCND3
NM_004980.3
3752
Hs.535274



related subfamily, member 3


599.
POU domain, class 2, transcription
POU2F3
NM_014352.1
25833
Hs.227115



factor 3


600.
POU domain, class 3, transcription
POU3F3
NM_006236.1
5455
Hs.248158



factor 3


601.
PP12104 mRNA
PP12104
XM_928053.1
643008


602.
pre-B-cell leukemia transcription factor 1
PBX1
NM_002585.1
5087
Hs.493096


603.
premature ovarian failure, 1B
POF1B
NM_024921
79983
Hs.267038


604.
PRKC, apoptosis, WT1, regulator
PAWR
NM_002583
5074
Hs.406074


605.
progastricsin (pepsinogen C)
PGC
NM_002630.1
5225
Hs.1867


606.
progesterone receptor membrane
PGRMC2
NM_006320.1
10424
Hs.507910



component 2


607.
programmed cell death 4 (neoplastic
PDCD4
NM_014456
27250
Hs.232543



transformation inhibitor)


608.
prolactin-induced protein
PIP
NM_002652.2
5304
Hs.99949


609.
proline rich Gla (G-carboxyglutamic
PRRG4
NM_024081.4
79056
Hs.471695



acid) 4 (transmembrane)


610.
prominin 2
PROM2
NM_144707.1
150696
Hs.469313


611.
proprotein convertase subtilisin/kexin
PCSK5
NM_006200.2
5125
Hs.368542



type 5


612.
prostaglandin E receptor 3 (subtype
PTGER3
NM_198712.2
5733
Hs.445000



EP3)


613.
prostaglandin-endoperoxide synthase 1
PTGS1
NM_080591.1
5742
Hs.201978



(prostaglandin G/H synthase and



cyclooxygenase)


614.
protease, serine 27
PRSS27
NM_031948.3
83886
Hs.332878


615.
protease, serine, 12 (neurotrypsin,
PRSS12
NM_003619.2
8492
Hs.445857



motopsin)


616.
protease, serine, 2 (trypsin 2)
PRSS2
NM_002770.2
5645
Hs.367767


617.
protease, serine, 3 (mesotrypsin)
PRSS3
NM_002771.2
5646
Hs.435699


618.
protease, serine, 8 (prostasin)
PRSS8
NM_002773.2
5652
Hs.75799


619.
protein kinase (cAMP-dependent,
PKIA
NM_181839.1
5569
Hs.433700



catalytic) inhibitor alpha


620.
protein phosphatase 1, regulatory
PPP1R13L
NM_006663.2
10848
Hs.560721



(inhibitor) subunit 13 like


621.
protein phosphatase 1, regulatory
PPP1R14C
NM_030949.1
81706
Hs.486798



(inhibitor) subunit 14C
(1R14C)


622.
protein phosphatase 2 (formerly 2A),
PPP2R2C
NM_020416
5522
Hs.479069



regulatory subunit B (PR 52), gamma



isoform


623.
protein phosphatase 2 (formerly 2A),
PPP2R3A
NM_002718.3
5523
Hs.518155



regulatory subunit B′′, alpha


624.
protein tyrosine phosphatase, non-
PTPN21
NM_007039.2
11099
Hs.437040



receptor type 21


625.
protein tyrosine phosphatase, non-
PTPN3
NM_002829.2
5774
Hs.436429



receptor type 3


626.
protein tyrosine phosphatase, receptor
PTPRF
NM_002840
5792
Hs.272062



type, F


627.
protein tyrosine phosphatase, receptor
PTPRK
NM_002844.2
5796
Hs.155919



type, K


628.
protocadherin 21
PCDH21
BC038799.1
92211
Hs.137556




(KIAA1775)


629.
protocadherin gamma subfamily B, 7
PCDHGB7
NM_032101.1
56099
Hs.368160


630.
psoriasis susceptibility 1 candidate 2
PSORS1C2
NM_014069.1
170680
Hs.146824


631.
PTK6 protein tyrosine kinase 6
PTK6
NM_005975.2
5753
Hs.51133


632.
Purkinje cell protein 4 like 1
PCP4L1
XM_938798.1
654790
Hs.433150


633.
pyrin-domain containing protein 1
PYC1
NM_152901
260434
Hs.58314


634.
RAB11 family interacting protein 1
RAB11FIP1
NM_001002233.1
80223
Hs.191179



(class I)


635.
RAB25, member RAS oncogene
RAB25
NM_020387.1
57111
Hs.491308



family


636.
RAB27B, member RAS oncogene
RAB27B
NM_004163.3
5874
Hs.514875



family


637.
RAB3D, member RAS oncogene
RAB3D
NM_004283.2
9545
Hs.567257



family


638.
RAB7B, member RAS oncogene
RAB7B
NM_177403.3
338382
Hs.534612



family


639.
Rap guanine nucleotide exchange
RAPGEFL1
NM_016339.1
51195
Hs.158530



factor (GEF)-like 1


640.
Rap2 binding protein 9
RPIB9
NM_138290
154661
Hs.411488


641.
RAR-related orphan receptor A
RORA
NM_002943.2
6095
Hs.511626


642.
ras homolog gene family, member D
RHOD
NM_014578.2
29984
Hs.15114


643.
ras homolog gene family, member V
RHOV
NM_133639
171177
Hs.447901


644.
RAS p21 protein activator 4
RASA4
NM_006989.3
10156
Hs.558443


645.
RAS-like, estrogen-regulated, growth
RERG
NM_032918.1
85004
Hs.199487



inhibitor


646.
regulating synaptic membrane
RIMS3
NM_014747.2
9783
Hs.434924



exocytosis 3


647.
repetin
RPTN
XM_937200.1
126638
Hs.376144


648.
restin (Reed-Steinberg cell-expressed
RSN
NM_002956.2
6249
Hs.524809



intermediate filament-associated



protein)


649.
retinoic acid early transcript 1E
RAET1E
NM_139165.1
135250
Hs.511818


650.
retinol dehydrogenase 12 (all-trans and
RDH12
NM_152443.1
145226
Hs.415322



9-cis)


651.
retinol dehydrogenase 16 (all-trans and
RDH16
NM_003708.2
8608
Hs.134958



13-cis)


652.
Rhesus blood group, B glycoprotein
RHBG
NM_020407.1
57127
Hs.131835


653.
Rho guanine nucleotide exchange
ARHGEF4
NM_015320.2
50649
Hs.469935



factor (GEF) 4


654.
Rho-guanine nucleotide exchange
RGNEF
XM_932952.1
643607
Hs.33254



factor


655.
rhomboid, veinlet-like 2 (Drosophila)
RHBDL2
NM_017821.3
54933
Hs.524626


656.
ribonuclease, RNase A family, 7
RNASE7
NM_032572.2
84659
Hs.525206


657.
ring finger protein 180
RNF180
NM_178532
285671
Hs.98890


658.
ring finger protein 39
RNF39
NM_170769.1
80352
Hs.121178


659.
RNA binding motif protein 35A
RBM35A
NM_001034915.1
54845
Hs.487471


660.
RNA binding motif protein 35B
RBM35B
NM_024939.2
80004
Hs.436585


661.
S100 calcium binding protein A12
S100A12
NM_005621.1
6283
Hs.19413



(calgranulin C)


662.
S100 calcium binding protein A14
S100A14
NM_020672.1
57402
Hs.288998


663.
S100 calcium binding protein A2
S100A2
NM_005978.3
6273
Hs.516484


664.
S100 calcium binding protein A7
S100A7
NM_002963.2
6278
Hs.112408



(psoriasin 1)


665.
S100 calcium binding protein A7-like 1
S100A7L1
NM_176823.2
338324
Hs.442337


666.
S100 calcium binding protein A8
S100A8
NM_002964.3
6279
Hs.416073



(calgranulin A)


667.
S100 calcium binding protein A9
S100A9
NM_002965.2
6280
Hs.112405



(calgranulin B)


668.
S100 calcium binding protein P
S100P
NM_005980.2
6286
Hs.2962


669.
sciellin
SCEL
NM_003843
8796
Hs.492938


670.
sclerostin domain containing 1
SOSTDC1
NM_015464
25928
Hs.25956


671.
secreted LY6/PLAUR domain
SLURP1
NM_020427.2
57152
Hs.103505



containing 1


672.
secretoglobin, family 2A, member 2
SCGB2A2
NM_002411.1
4250
Hs.46452


673.
secretory leukocyte peptidase inhibitor
SLPI
NM_003064.2
6590
Hs.517070


674.
selenoprotein P, plasma, 1
SEPP1
NM_005410.2
6414
Hs.275775


675.
sema domain, immunoglobulin domain
SEMA3F
NM_004186.2
6405
Hs.32981



(Ig), short basic domain, secreted,



(semaphorin) 3F


676.
serine (or cysteine) proteinase
SERPINB13
NM_012397
5275
Hs.241407



inhibitor, clade B (ovalbumin), member



13


677.
serine palmitoyltransferase, long chain
SPTLC2L
AK075271.1
140911
Hs.425023



base subunit 2-like (aminotransferase



2)


678.
serine peptidase inhibitor, Kazal type 5
SPINK5
NM_006846.2
11005
Hs.331555


679.
serine peptidase inhibitor, Kunitz type 1
SPINT1
NM_003710.3
6692
Hs.233950


680.
serine peptidase inhibitor, Kunitz type, 2
SPINT2
NM_021102.2
10653
Hs.31439


681.
serine/threonine/tyrosine kinase 1
STYK1
NM_018423.1
55359
Hs.24979


682.
serpin peptidase inhibitor, clade A
SERPINA12
NM_173850.2
145264
Hs.99476



(alpha-1 antiproteinase, antitrypsin),



member 12


683.
serpin peptidase inhibitor, clade B
SERPINB12
NM_080474.1
89777
Hs.348541



(ovalbumin), member 12


684.
serpin peptidase inhibitor, clade B
SERPINB2
NM_002575.1
5055
Hs.514913



(ovalbumin), member 2


685.
serpin peptidase inhibitor, clade B
SERPINB3
NM_006919.1
6317
Hs.227948



(ovalbumin), member 3


686.
serpin peptidase inhibitor, clade B
SERPINB4
NM_002974.1
6318
Hs.123035



(ovalbumin), member 4


687.
serpin peptidase inhibitor, clade B
SERPINB5
NM_002639
5268
Hs.55279



(ovalbumin), member 5


688.
serpin peptidase inhibitor, clade B
SERPINB7
NM_001040147.1
8710
Hs.138202



(ovalbumin), member 7


689.
serpin peptidase inhibitor, clade B
SERPINB8
NM_001031848.1
5271
Hs.368077



(ovalbumin), member 8


690.
SH2 domain containing 3A
SH2D3A
NM_005490.1
10045
Hs.439645


691.
SH3 domain containing ring finger 2
SH3RF2
NM_152550.2
153769
Hs.443728


692.
SH3 domain protein D19
SH3D19
NM_001009555.2
152503
Hs.519018


693.
SH3-domain binding protein 2
SH3BP2
NM_003023.2
6452
Hs.167679


694.
SH3-domain GRB2-like endophilin B2
SH3GLB2
NM_020145.2
56904
Hs.460238


695.
sidekick homolog 1 (chicken)
SDK1
NM_152744
221935
Hs.155959


696.
signal transducing adaptor family
STAP2
NM_001013841.1
55620
Hs.194385



member 2


697.
similar to alpha-2-glycoprotein 1, zinc
LOC646282
AC004522
646282
Hs.568109


698.
similar to common salivary protein 1
LOC124220
NM_145252.2
124220
Hs.105887


699.
similar to RIKEN cDNA 1810006A16
LOC91862
NM_052858
91862
Hs.435764



gene


700.
Similar to RIKEN cDNA 2310002J15
MGC59937
NM_199001.1
375791
Hs.512469



gene


701.
similar to WDNM1-like protein
LOC645638
AA149250
645638
Hs.56105


702.
skin aspartic protease
SASP
NM_152792.1
151516
Hs.556025


703.
slit homolog 3 (Drosophila)
SLIT3
NM_003062
6586
Hs.129229


704.
SMAD in the antisense orientation
DAMS
NM_022001
9597
Hs.167700


705.
SMAD, mothers against DPP homolog
SMAD1
NM_005900
4086
Hs.388294



1 (Drosophila)


706.
small breast epithelial mucin
LOC118430
NM_058173
118430
Hs.348419


707.
small proline-rich protein 1A
SPRR1A
NM_005987.2
6698
Hs.46320


708.
small proline-rich protein 1B (cornifin)
SPRR1B
NM_003125.2
6699
Hs.1076


709.
small proline-rich protein 2A
SPRR2A
NM_005988.2
6700
Hs.355542


710.
small proline-rich protein 2G
SPRR2G
NM_001014291.2
6706
Hs.490253


711.
sodium channel, nonvoltage-gated 1
SCNN1A
NM_001038.4
6337
Hs.130989



alpha


712.
sodium channel, nonvoltage-gated 1,
SCNN1B
NM_000336.1
6338
Hs.414614



beta (Liddle syndrome)


713.
sodium channel, nonvoltage-gated 1,
SCNN1G
NM_001039
6340
Hs.371727



gamma


714.
sodium channel, voltage-gated, type
SCN4B
NM_174934.1
6330
Hs.65239



IV, beta


715.
solute carrier family 1 (high affinity
SLC1A6
NM_005071
6511
Hs.515217



aspartate/glutamate transporter),



member 6


716.
solute carrier family 15 (oligopeptide
SLC15A1
NM_005073.1
6564
Hs.436893



transporter), member 1


717.
solute carrier family 16
SLC16A10
NM_018593.3
117247
Hs.520321



(monocarboxylic acid transporters),



member 10


718.
solute carrier family 16
SLC16A14
NM_152527.3
151473
Hs.504317



(monocarboxylic acid transporters),



member 14


719.
solute carrier family 18 (vesicular
SLC18A2
NM_003054.2
6571
Hs.369009



monoamine), member 2


720.
solute carrier family 2 (facilitated
SLC2A12
NM_145176.2
154091
Hs.486508



glucose transporter), member 12


721.
Solute carrier family 22 (extrancuronal
SLC22A3
NM_021977
6581
Hs.242721



monoamine transporter), member 3


722.
Solute carrier family 24
SLC24A3
NM_020689.3
57419
Hs.211252



(sodium/potassium/calcium



exchanger), member 3


723.
solute carrier family 26, member 9
SLC26A9
NM_134325.1
115019
Hs.164073


724.
solute carrier family 28 (sodium-
SLC28A3
NM_022127.1
64078
Hs.535966



coupled nucleoside transporter),



member 3


725.
solute carrier family 39 (zinc
SLC39A2
NM_014579.1
29986
Hs.175783



transporter), member 2


726.
solute carrier family 4, sodium
SLC4A11
NM_032034.1
83959
Hs.105607



bicarbonate transporter-like, member



11


727.
solute carrier family 47, member 2
SLC47A2
NM_152908.2
146802
Hs.126830


728.
solute carrier family 5 (sodium/glucose
SLC5A1
NM_000343.1
6523
Hs.1964



cotransporter), member 1


729.
solute carrier family 6 (amino acid
SLC6A14
NM_007231.1
11254
Hs.522109



transporter), member 14


730.
solute carrier family 6
SLC6A2
NM_001043.2
6530
Hs.78036



(neurotransmitter transporter,



noradrenalin), member 2


731.
spectrin SH3 domain binding protein 1
SSH3BP1
NM_005470
10006
Hs.42710


732.
spectrin, beta, non-erythrocytic 2
SPTBN2
NM_006946.1
6712
Hs.26915


733.
spermatogenesis associated 18
SPATA18
NM_145263.1
132671
Hs.527090



homolog (rat)


734.
sphingomyelin phosphodiesterase 3,
SMPD3
NM_018667.2
55512
Hs.368421



neutral membrane (neutral



sphingomyelinase II)


735.
sphingosine-1-phosphate phosphotase 2
SGPP2
NM_152386.2
130367
Hs.210043


736.
SRY (sex determining region Y)-box
SOX15
NM_006942.1
6665
Hs.95582



15


737.
SRY (sex determining region Y)-box 7
SOX7
NM_031439.2
83595
Hs.213194


738.
START domain containing 5
STARD5
NM_030574.2
80765
Hs.513075


739.
STEAP family member 4
STEAP4
AK026806.1
79689
Hs.521008


740.
steroid-5-alpha-reductase, alpha
SRD5A1
NM_001047.2
6715
Hs.552



polypeptide 1 (3-oxo-5 alpha-steroid



delta 4-dehydrogenase alpha 1)


741.
steroidogenic acute regulator
STAR
NM_000349.2
6770
Hs.521535


742.
stonin 2
STN2
NM_033104
85439
Hs.14248


743.
stratifin
SFN
NM_006142.3
2810
Hs.523718


744.
sulfotransferase family 1E, estrogen-
SULT1E1
NM_005420.2
6783
Hs.479898



preferring, member 1


745.
sulfotransferase family, cytosolic, 2B,
SULT2B1
NM_004605.2
6820
Hs.369331



member 1


746.
suppression of tumorigenicity 14
ST14
NM_021978.3
6768
Hs.504315



(colon carcinoma)


747.
suprabasin
SBSN
NM_198538.1
374897
Hs.433484


748.
surfactant, pulmonary-associated
SFTPD
NM_003019.4
6441
Hs.253495



protein D


749.
sushi domain containing 4
SUSD4
NM_017982.2
55061
Hs.558826


750.
synaptotagmin-like 1
SYTL1
NM_032872.1
84958
Hs.469175


751.
syndecan 1
SDC1
NM_001006946.1
6382
Hs.224607


752.
syndecan binding protein (syntenin) 2
SDCBP2
NM_015685.3
27111
Hs.516836


753.
syntaxin 19
STX19
NM_001001850.1
415117
Hs.533086


754.
synuclein, alpha interacting protein
SNCAIP
NM_005460.2
9627
Hs.426463



(synphilin)


755.
T-box 1
TBX1
NM_005992.1
6899
Hs.173984


756.
T-cell lymphoma invasion and
TIAM1
NM_003253.1
7074
Hs.517228



metastasis 1


757.
t-complex 11 (mouse) like 2
TCP11L2
NM_152772.1
255394
Hs.132050


758.
tensin 4
TNS4
NM_032865.3
84951
Hs.438292


759.
tetra-peptide repeat homeobox-like
TPRXL
NM_182629
348825
Hs.529180


760.
tetraspanin similiar to uroplakin 1
LOC90139
NM_130783
90139
Hs.385634


761.
tetratricopeptide repeat domain 12
TTC12
BC032355.1
54970
Hs.288772


762.
tetratricopeptide repeat domain 18
TTC18
NM_145170.2
118491
Hs.549236


763.
tetratricopeptide repeat domain 22
TTC22
NM_017904.1
55001
Hs.16230


764.
tetratricopeptide repeat domain 9
TTC9
XM_938197.1
23508
Hs.79170


765.
three prime repair exonuclease 2
TREX2
NM_080701.3
11219
Hs.170835


766.
thymic stromal co-transporter
TSCOT
NM_033051.2
57864
Hs.512668


767.
thyroid hormone receptor, beta
THRB
NM_000461.3
7068
Hs.187861



(erythroblastic leukemia viral (v-erb-a)



oncogene homolog 2, avian)


768.
TIGA1
TIGA1
NM_053000
114915
Hs.12082


769.
Tight junction protein 2 (zona
TJP2
NM_201629.1
9414
Hs.50382



occludens 2)


770.
transcription elongation factor A (SII), 3
TCEA3
NM_003196.1
6920
Hs.148105


771.
transcription factor 4
TCF4
NM_003199.1
6925
Hs.200285


772.
transcription factor AP-2 beta
TFAP2B
NM_003221.2
7021
Hs.33102



(activating enhancer binding protein 2



beta)


773.
transforming growth factor, alpha
TGFA
NM_003236.1
7039
Hs.170009


774.
transforming, acidic coiled-coil
TACC2
NM_006997
10579
Hs.501252



containing protein 2


775.
transglutaminase 1 (K polypeptide
TGM1
NM_000359.1
7051
Hs.508950



epidermal type I, protein-glutamine-



gamma-glutamyltransferase)


776.
transglutaminase 3 (E polypeptide,
TGM3
NM_003245.2
7053
Hs.2022



protein-glutamine-gamma-



glutamyltransferase)


777.
transglutaminase 5
TGM5
NM_004245.2
9333
Hs.129719


778.
transient receptor potential cation
TRPV1
NM_018727.4
7442
Hs.558415



channel, subfamily V, member 1


779.
transmembrane protease, serine 11D
TMPRSS11D
NM_004262.2
9407
Hs.132195


780.
transmembrane protease, serine 13
TMPRSS13
NM_032046.1
84000
Hs.266308


781.
transmembrane protease, serine 4
TMPRSS4
NM_019894.2
56649
Hs.161985


782.
transmembrane protein 125
TMEM125
NM_144626.1
128218
Hs.104476


783.
transmembrane protein 154
TMEM154
NM_152680.1
201799
Hs.518900


784.
transmembrane protein 16A
TMEM16A
NM_018043.4
55107
Hs.503074


785.
transmembrane protein 16J
TMEM16J
NM_001012302.1
338440
Hs.501622


786.
transmembrane protein 184A
TMEM184A
NM_152689.2
202915
Hs.556755


787.
transmembrane protein 23
TMEM23
NM_147156.3
259230
Hs.386215


788.
transmembrane protein 30B
TMEM30B
NM_001017970.1
161291
Hs.146180


789.
transmembrane protein 40
TMEM40
NM_018306.2
55287
Hs.475502


790.
transmembrane protein 45A
TMEM45A
NM_018004.1
55076
Hs.126598


791.
transmembrane protein 45B
TMEM45B
NM_138788.2
120224
Hs.504301


792.
transmembrane protein 79
TMEM79
NM_032323.1
84283
Hs.347408


793.
tripartite motif-containing 29
TRIM29
NM_012101
23650
Hs.504115


794.
tripartite motif-containing 31
TRIM31
NM_007028
11074
Hs.91096


795.
tripartite motif-containing 7
TRIM7
NM_203294.1
81786
Hs.487412


796.
trypsinogen C
TRY6
NR_001296.2
154754
Hs.697092


797.
tryptase alpha/beta 1
TPSAB1
NM_003294.3
7177
Hs.405479


798.
tryptase beta 2
TPSB2
NM_024164.5
64499
Hs.592982


799.
tubulin, alpha 1 (testis specific)
TUBA1
NM_006000.1
7277
Hs.75318


800.
tuftelin 1
TUFT1
NM_020127.1
7286
Hs.489922


801.
tumor necrosis factor (ligand)
TNFSF10
NM_003810.2
8743
Hs.478275



superfamily, member 10


802.
tumor necrosis factor receptor
TNFRSF25
NM_003790.2
8718
Hs.462529



superfamily, member 25


803.
tumor protein D52-like 1
TPD52L1
NM_001003395.1
7164
Hs.201482


804.
tumor protein p73-like
TP73L
NM_003722
8626
Hs.137569


805.
tumor-associated calcium signal
TACSTD1
NM_002354.1
4072
Hs.692



transducer 1


806.
tumor-associated calcium signal
TACSTD2
NM_002353.1
4070
Hs.23582



transducer 2


807.
twist homolog 2 (Drosophila)
TWIST2
NM_057179
117581
Hs.422585


808.
ubiquitin protein ligase E3A (human
UBE3A
NM_000462.2
7337
Hs.22543



papilloma virus E6-associated protein,



Angelman syndrome)


809.
Ubiquitin specific peptidase 2
USP2
NM_004205.3
9099
Hs.524085


810.
UDP glucuronosyltransferase 1 familly,
UGT1A1
NM_000463.2
54658
Hs.554822



polypeptide A1


811.
UDP-N-acetyl-alpha-D-
GALNT6
NM_007210.2
11226
Hs.505575



galactosamine:polypeptide N-



acetylgalactosaminyltransferase 6



(GalNAc-T6)


812.
unc-93 homolog A (C. elegans)
UNC93A
NM_018974.2
54346
Hs.145911


813.
vasoactive intestinal peptide receptor 1
VIPR1
NM_004624.2
7433
Hs.348500


814.
vav 3 oncogene
VAV3
NM_006113.3
10451
Hs.267659


815.
vestigial like 3 (Drosophila)
VGLL3
NM_016206.2
389136
Hs.435013


816.
v-ets erythroblastosis virus E26
ETS2
NM_005239.4
2114
Hs.517296



oncogene homolog 2 (avian)


817.
visinin-like 1
VSNL1
NM_003385.4
7447
Hs.444212


818.
v-maf musculoaponeurotic
MAF
NM_005360
4094
Hs.134859



fibrosarcoma oncogene homolog



(avian)


819.
WAP four-disulfide core domain 12
WFDC12
NM_080869.1
128488
Hs.352180


820.
WAP four-disulfide core domain 5
WFDC5
NM_145652.2
149708
Hs.375031


821.
WD repeat domain 66
WDR66
BC036233.1
144406
Hs.507125


822.
wingless-type MMTV integration site
WNT11
NM_004626.2
7481
Hs.108219



family, member 11


823.
wingless-type MMTV integration site
WNT3
NM_030753.3
7473
Hs.445884



family, member 3


824.
wingless-type MMTV integration site
WNT4
NM_030761.3
54361
Hs.25766



family, member 4


825.
wingless-type MMTV integration site
WNT5B
NM_030775.2
81029
Hs.306051



family, member 5B


826.
X Kell blood group precursor-related,
XKRX
NM_212559.1
402415
Hs.364911



X-linked


827.
X102 protein
X102
NM_030879
63969
Hs.248065


828.
Xg blood group (pseudoautosomal
XG
NM_175569.1
7499
Hs.179675



boundary-divided on the X



chromosome)


829.
YOD1 OTU deubiquinating enzyme 1
YOD1
NM_018566.3
55432
Hs.391944



homolog (yeast)


830.
zinc and ring finger 1
ZNRF1
NM_032268.3
84937
Hs.427284


831.
zinc finger and BTB domain containing 3
ZBTB3
NM_024784.2
79842
Hs.558545


832.
zinc finger and BTB domain containing
ZBTB7C
NM_001039360.1
201501
Hs.515388



7C


833.
zinc finger protein 165
ZNF165
NM_003447.2
7718
Hs.55481


834.
zinc finger protein 185 (LIM domain)
ZNF185
NM_007150.1
7739
Hs.16622


835.
zinc finger protein 273
ZNF273
AU132789
10793
Hs.386264


836.
zinc finger protein 42
ZFP42
NM_174900.3
132625
Hs.335787


837.
zinc finger protein 662
ZNF662
NM_207404.2
389114
Hs.293388


838.
zinc finger protein 67 homolog
ZFP67
NM_015872
51043
Hs.159265



(mouse)


839.
zinc finger protein 682
ZNF682
NM_033196.1
91120
Hs.306298


840.
zinc finger protein 750
ZNF750
NM_024702.1
79755
Hs.558544


841.
zinc finger, DHHC-type containing 21
ZDHHC21
NM_178566.2
340481
Hs.561951


842.
similar to cystin 1
LOC649824
XM_938892
649824
Hs.27092


843.
NPC-A-5
LOC642587
AK091113
91170
Hs.301885


844.
hypothetical gene supported by
LOC285259
AI703273
285259
Hs.146159



BC035064


845.
hypothetical gene supported by
LOC284974
AI928242
284974
Hs.119903



BC020554


846.
hypothetical gene supported by
LOC284668
BE672487
284668
Hs.25766



BC007386


847.
hypothetical gene supported by
LOC284456
AL137325
284456
Hs.406781



AL137325


848.
hypothetical gene supported by
LOC284224
BC034640
284224
Hs.382000



BC034640


849.
similar to seven transmembrane helix
LOC283929
BG109230
283929
Hs.374278



receptor


850.
similar to zinc finger protein 366
LOC254647
BE858194
254647
Hs.323053


851.
hypothetical gene supported by
LOC221495
AL117529
221495
Hs.406762



AL117529


852.
hypothetical gene supported by
LOC221042
AL137430
221042
Hs.380965



AL137430


853.
similar to p53-induced protein PIGPC1
LOC204288
AI049608
204288
Hs.355517


854.
hypothetical gene supported by
LOC145739
AL117570
145739
Hs.375657



AL117570


855.
Uncharacterized transcript supported
—
AW195351
—
Hs.250520



by AW195351 found within the



Catenin delta 1 locus


856.
Uncharacterized transcript supported
—
AA418074
—
Hs.110286



by AA418074


857.
Gene supported by sequence info.
—
AI888057
—
—


858.
Gene supported by sequence info.
—
BG484769
342289
Hs.115838


859.
Gene supported by sequence info.
—
XM_933918
646769
Hs.115838


860.
Gene supported by sequence info.
—
AK000090
—
—


861.
Gene supported by sequence info.
—
AA863389
—
—


862.
Gene supported by sequence info.
—
AW135306
—
Hs.444277


863.
Gene supported by sequence info.
—
AF005082
—
Hs.516420


864.
Gene supported by sequence info.
—
R81445
—
—


865.
Gene supported by sequence info.
—
AL050153
—
—


866.
Gene supported by sequence info.
—
AI934364
—
Hs.145761


867.
Gene supported by sequence info.
—
AW131450
—
Hs.121070


868.
Gene supported by sequence info.
—
AI832594
—
Hs.471433


869.
Gene supported by sequence info.
—
N73742
—
Hs.36288


870.
Gene supported by sequence info.
—
BE674309
—
Hs.418279


871.
Gene supported by sequence info.
—
AU158573
—
Hs.288926


872.
Gene supported by sequence info.
—
AW022607
—
Hs.379253


873.
Gene supported by sequence info.
—
R77414
—
Hs.33355


874.
Gene supported by sequence info.
—
AU155612
—
Hs.269545


875.
Gene supported by sequence info.
—
AI089783
—
Hs.123307


876.
Gene supported by sequence info.
—
AL359055
—
Hs.390270


877.
Gene supported by sequence info.
—
BE645279
—
Hs.29792


878.
Gene supported by sequence info.
—
AI939452
—
Hs.445064


879.
Gene supported by sequence info.
—
AW974998
—
Hs.222430


880.
Gene supported by sequence info.
—
AK096998
—
Hs.29952


881.
Gene supported by sequence info.
—
AW025141
—
Hs.432504


882.
Gene supported by sequence info.
—
AW452355
—
Hs.445872


883.
Gene supported by sequence info.
—
AL137535
—
Hs.15806


884.
Gene supported by sequence info.
—
AA516469
—
Hs.433643


885.
Gene supported by sequence info.
—
AU147515
—
Hs.406812


886.
Gene supported by sequence info.
—
AW974077
—
Hs.283349


887.
Gene supported by sequence info.
—
AA890487
—
Hs.24598


888.
Gene supported by sequence info.
—
N66591
—
Hs.440646


889.
Gene supported by sequence info.
—
AU151465
—
Hs.224012


890.
Gene supported by sequence info.
—
AW517412
—
Hs.150757


891.
Gene supported by sequence info.
—
AU147518
—
Hs.499320


892.
Gene supported by sequence info.
—
BF111088
—
Hs.201446


893.
Gene supported by sequence info.
—
AI924046
—
Hs.119567


894.
Gene supported by sequence info.
—
AI971251
—
Hs.443740


895.
Gene supported by sequence info.
—
R48254
—
Hs.344872


896.
Gene supported by sequence info.
—
AI096634
—
Hs.371677


897.
Gene supported by sequence info.
—
BF056273
—
Hs.188920


898.
Gene supported by sequence info.
—
AI457984
—
Hs.165900


899.
Gene supported by sequence info.
—
BG429255
—
Hs.42376


900.
Gene supported by sequence info.
—
AI090487
—
Hs.168325


901.
Gene supported by sequence info.
—
AI659426
—
Hs.443287


902.
Gene supported by sequence info.
—
T51136
—
Hs.421262


903.
Gene supported by sequence info.
—
AW291545
—
Hs.445978


904.
Gene supported by sequence info.
—
AA687916
—
Hs.117295


905.
Gene supported by sequence info.
—
BF114646
—
Hs.19339


906.
Gene supported by sequence info.
—
AW014647
—
Hs.432924


907.
Gene supported by sequence info.
—
W96062
—
Hs.373964


908.
Gene supported by sequence info.
—
AI373107
—
Hs.110334


909.
Gene supported by sequence info.
—
AA758732
—
Hs.473374


910.
Gene supported by sequence info.
—
H15900
—
Hs.31395


911.
Gene supported by sequence info.
—
AL515437
—
Hs.143718


912.
Gene supported by sequence info.
—
AI334358
—
Hs.124597


913.
Gene supported by sequence info.
—
AI458439
—
Hs.159115


914.
Gene supported by sequence info.
—
AL157448
—
Hs.375671


915.
Gene supported by sequence info.
—
AK022350
—
Hs.511707


916.
Gene supported by sequence info.
—
AI972146
—
Hs.192756


917.
Gene supported by sequence info.
—
H22005
—
Hs.120725


918.
Gene supported by sequence info.
—
BF245284
—
Hs.354427


919.
Gene supported by sequence info.
—
AI093221
—
Hs.155965


920.
Gene supported by sequence info.
—
BC019703
—
Hs.145626


921.
Gene supported by sequence info.
—
AU146924
—
Hs.188691


922.
Gene supported by sequence info.
—
AI829605
—
Hs.436077


923.
Gene supported by sequence info.
—
AW301393
—
Hs.493477


924.
Gene supported by sequence info.
—
H88112
—
Hs.234478


925.
Gene supported by sequence info.
—
AW173504
—
Hs.76704


926.
Gene supported by sequence info.
—
AA565852
—
Hs.71947


927.
Gene supported by sequence info.
—
AI022066
—
Hs.372209


928.
Gene supported by sequence info.
—
W68845
—
Hs.324323


929.
Gene supported by sequence info.
—
BI598831
—
Hs.434643


930.
Gene supported by sequence info.
—
AU159446
—
Hs.498954


931.
Gene supported by sequence info.
—
BC040322
—
Hs.44330


932.
Gene supported by sequence info.
—
AA826931
—
Hs.491024


933.
Gene supported by sequence info.
—
BC029440
—
Hs.374843


934.
Gene supported by sequence info.
—
AI950023
—
Hs.270751


935.
Gene supported by sequence info.
—
AV739182
—
Hs.113150


936.
Gene supported by sequence info.
—
AI829721
—
Hs.482381


937.
Gene supported by sequence info.
—
AA876179
—
Hs.134650


938.
Gene supported by sequence info.
—
AK024907
—
Hs.306723


939.
Gene supported by sequence info.
—
AW451197
—
Hs.113418


940.
Gene supported by sequence info.
—
BF224444
—
Hs.127274


941.
Gene supported by sequence info.
—
AW130600
—
Hs.99472


942.
Gene supported by sequence info.
—
AI042373
—
Hs.132917


943.
Gene supported by sequence info.
—
AL038973
—
Hs.144873


944.
Gene supported by sequence info.
—
BE672408
—
Hs.107708


945.
Gene supported by sequence info.
—
AW139091
—
Hs.161158


946.
Gene supported by sequence info.
—
AW025023
—
Hs.234478


947.
Gene supported by sequence info.
—
BE500942
—
Hs.170540


948.
Gene supported by sequence info.
—
AW242920
—
Hs.129368


949.
Gene supported by sequence info.
—
AA603472
—
Hs.28456


950.
Gene supported by sequence info.
—
AU144382
—
Hs.501925


951.
Gene supported by sequence info.
—
AL833150
—
Hs.327631


952.
Gene supported by sequence info.
—
BM992214
—
Hs.314518


953.
Gene supported by sequence info.
—
AL359055
—
Hs.390270


954.
Gene supported by sequence info.
—
AA167323
—
Hs.188682


955.
Gene supported by sequence info.
—
AI970797
—
Hs.133152


956.
Gene supported by sequence info.
—
AI733037
—
Hs.129990


957.
Gene supported by sequence info.
—
H15396
—
Hs.107510


958.
Gene supported by sequence info.
—
BF055060
—
Hs.387100


959.
Gene supported by sequence info.
—
N30188
—
Hs.93739


960.
Gene supported by sequence info.
—
AK056784
—
Hs.224056


961.
Gene supported by sequence info.
—
AU147152
—
Hs.118317


962.
Gene supported by sequence info.
—
AI341837
—
Hs.436105


963.
Gene supported by sequence info.
—
AI051950
—
Hs.99472


964.
Gene supported by sequence info.
—
N91149
—
Hs.279639


965.
Gene supported by sequence info.
—
AI191905
—
Hs.228982


966.
Gene supported by sequence info.
—
BF508208
—
Hs.240074


967.
Gene supported by sequence info.
—
AU147861
—
Hs.188082


968.
Gene supported by sequence info.
—
AA779333
—
Hs.20158


969.
Gene supported by sequence info.
—
AW274846
—
Hs.19339


970.
Gene supported by sequence info.
—
AL137616
—
Hs.30483


971.
Gene supported by sequence info.
—
AK025151
—
Hs.268597


972.
Gene supported by sequence info.
—
BF961733
—
Hs.445604


973.
Gene supported by sequence info.
—
AI079329
—
Hs.271876


974.
Gene supported by sequence info.
—
AW292830
—
Hs.435001


975.
Gene supported by sequence info.
—
BC040965
—
Hs.270114


976.
Gene supported by sequence info.
—
AA933082
—
Hs.126883


977.
Gene supported by sequence info.
—
BC038784
—
Hs.385767


978.
Gene supported by sequence info.
—
AW302207
—
Hs.228982


979.
Gene supported by sequence info.
—
AK025378
—
Hs.466700


980.
Gene supported by sequence info.
—
R97781
—
Hs.247150


981.
Gene supported by sequence info.
—
AI655611
—
Hs.124863


982.
Gene supported by sequence info.
—
BF847120
—
Hs.318887


983.
Gene supported by sequence info.
—
AA461490
—
Hs.66072


984.
Gene supported by sequence info.
—
BC034636
—
Hs.385523


985.
Gene supported by sequence info.
—
N66393
—
Hs.102754


986.
Gene supported by sequence info.
—
AI637733
—
Hs.220624


987.
Gene supported by sequence info.
—
AA583038
—
Hs.349207


988.
Gene supported by sequence info.
—
AU156822
—
Hs.287577


989.
Gene supported by sequence info.
—
BE222843
—
Hs.231852


990.
Gene supported by sequence info.
—
BC040965
—
Hs.270114


991.
Gene supported by sequence info.
—
AI147310
—
Hs.146730


992.
Gene supported by sequence info.
—
AI417988
—
Hs.37648


993.
Gene supported by sequence info.
—
AA825510
—
Hs.124304


994.
Gene supported by sequence info.
—
BG260087
—
Hs.7956


995.
Gene supported by sequence info.
—
AI627679
—
Hs.374420


996.
Gene supported by sequence info.
—
AW070877
—
Hs.432615


997.
Gene supported by sequence info.
—
AA922936
—
Hs.110039


998.
Gene supported by sequence info.
—
AI935541
—
Hs.127009


999.
Gene supported by sequence info.
—
T68445
—
Hs.76704


1000.
Gene supported by sequence info.
—
AK097810
—
Hs.146493


1001.
Gene supported by sequence info.
—
AW081982
—
Hs.59507


1002.
Gene supported by sequence info.
—
AI399889
—
Hs.381411


1003.
Gene supported by sequence info.
—
BC039513
—
Hs.407575


1004.
Gene supported by sequence info.
—
AL512727
—
Hs.232127


1005.
Gene supported by sequence info.
—
AK021990
—
Hs.287466


1006.
Gene supported by sequence info.
—
AK000106
—
Hs.272227


1007.
Gene supported by sequence info.
—
AI819863
—
Hs.106243


1008.
Gene supported by sequence info.
—
AI743489
—
Hs.322679


1009.
Gene supported by sequence info.
—
AL050204
—
Hs.28540


1010.
Gene supported by sequence info.
—
AW006352
—
Hs.159643


1011.
Gene supported by sequence info.
—
BE843544
—
Hs.444613


1012.
Gene supported by sequence info.
—
AI796535
—
Hs.504568


1013.
Gene supported by sequence info.
—
AF086294
—
Hs.125844


1014.
Gene supported by sequence info.
—
BG290650
—
Hs.134876


1015.
Gene supported by sequence info.
—
AV741130
—
Hs.173704


1016.
Gene supported by sequence info.
—
AI928035
—
Hs.282089


1017.
Gene supported by sequence info.
—
AI674565
—
Hs.8379


1018.
Gene supported by sequence info.
—
AI085338
—
Hs.375591


1019.
Gene supported by sequence info.
—
AA034012
—
Hs.37648


1020.
Gene supported by sequence info.
—
AI288186
—
Hs.58611


1021.
Gene supported by sequence info.
—
AK024927
—
Hs.152423


1022.
Gene supported by sequence info.
—
BG149557
—
Hs.37648
















TABLE B







Genes differentially expressed in metastatic melanoma. Expression


of the genes listed in this table is increased relative to non-metastatic samples.














Gene

Entrez




Gene description
Symbol
GenBank ID
Gene ID
UniGene ID
















1023.
ATP-binding cassette, sub-family B
ABCB5
NM_178559.3
340273
Hs.404102



(MDR/TAP), member 5


1024.
abhydrolase domain containing 10
ABHD10
NM_018394.1
55347
Hs.477115


1025.
acyl-CoA synthetase long-chain family
ACSL3
NM_004457
2181
Hs.268012



member 3


1026.
alkylglycerone phosphate synthase
AGPS
NM_003659.2
8540
Hs.516543


1027.
v-akt murine thymoma viral oncogene
AKT3
NM_005465.3
10000
Hs.498292



homolog 3 (protein kinase B, gamma)


1028.
anillin, actin binding protein (scraps
ANLN
NM_018685.2
54443
Hs.62180



homolog, Drosophila)


1029.
adaptor-related protein complex 1,
AP1S2
NM_003916
8905
Hs.121592



sigma 2 subunit


1030.
apolipoprotein C-II
APOC2
NM_000483.3
344
Hs.75615


1031.
ATPase family, AAA domain
ATAD2
NM_014109.2
29028
Hs.370834



containing 2


1032.
activating transcription factor 6
ATF6
NM_007348
22926
Hs.492740


1033.
ataxia telangiectasia mutated (includes
ATM
NM_000051
472
Hs.435561



complementation groups A, C and D)


1034.
ATPase, H+ transporting, lysosomal
ATP6V1C1
NM_001007254.1
528
Hs.86905



42 kDa, V1 subunit C, isoform 1


1035.
ATPase, Class 1, type 8B, member 2
ATP8B2
NM_020452.2
57198
Hs.435700


1036.
antizyme inhibitor 1
AZIN1
NM_148174.2
51582
Hs.459106


1037.
UDP-GlcNAc:betaGal beta-1,3-N-
B3GNT1
NM_006577.5
10678
Hs.173203



acetylglucosaminyltransferase 1


1038.
UDP-Gal:betaGlcNAc beta 1,4-
B4GALT6
NM_004775.2
9331
Hs.464848



galactosyltransferase, polypeptide 6


1039.
bromodomain adjacent to zinc finger
BAZ1B
NM_023005.2
9031
Hs.488671



domain, 1B


1040.
BRCA2 and CDKN1A interacting
BCCIP
NM_016567.2
56647
Hs.370292



protein


1041.
BCL2-related protein A1
BCL2A1
NM_004049.2
597
Hs.227817


1042.
bifunctional apoptosis regulator
BFAR
NM_016561.1
51283
Hs.435556


1043.
bicaudal D homolog 1 (Drosophila)
BICD1
NM_001714
636
Hs.505202


1044.
baculoviral IAP repeat-containing 5
BIRC5
NM_001012270.1
332
Hs.514527



(survivin)


1045.
barren homolog 1 (Drosophila)
BRRN1
NM_015341.3
23397
Hs.308045


1046.
butyrophilin, subfamily 2, member A1
BTN2A1
NM_007049.2
11120
Hs.159028


1047.
BUB1 budding uninhibited by
BUB1
NM_004336.2
699
Hs.469649



benzimidazoles 1 homolog (yeast)


1048.
chromosome 12 open reading frame 11
C12orf11
NM_018164.1
55726
Hs.505077


1049.
chromosome 12 open reading frame 24
C12orf24
NM_013300.1
29902
Hs.436618


1050.
core 1 synthase, glycoprotein-N-
C1GALT1
NM_020156.1
56913
Hs.239666



acetylgalactosamine 3-beta-



galactosyltransferase, 1


1051.
chromosome 1 open reading frame 103
C1orf103
NM_018372.3
55791
Hs.25245


1052.
chromosome 1 open reading frame 67
C1orf67
XM_290922.4
200095
Hs.133977


1053.
chromosome 1 open reading frame 90
C1orf90
BC004269.1
84734
Hs.18449


1054.
chromosome 20 open reading frame
C20orf104
NM_016436
51230
Hs.301055



104


1055.
chromosome 20 open reading frame 30
C20orf30
NM_001009924.1
29058
Hs.472024


1056.
chromosome 7 open reading frame 11
C7orf11
NM_138701.1
136647
Hs.129159


1057.
chromosome 9 open reading frame 100
C9orf100
NM_032818.2
84904
Hs.277026


1058.
calumenin
CALU
NM_001219.2
813
Hs.7753


1059.
cell cycle associated protein 1
CAPRIN1
NM_005898.4
4076
Hs.471818


1060.
cell division cycle 2, G1 to S and G2 to M
CDC2
NM_001786
983
Hs.334562


1061.
CDC42 effector protein (Rho GTPase
CDC42EP3
NM_006449.3
10602
Hs.369574



binding) 3


1062.
CDC45 cell division cycle 45-like (S. cerevisiae)
CDC45L
NM_003504.3
8318
Hs.474217


1063.
CDC6 cell division cycle 6 homolog
CDC6
NM_001254.3
990
Hs.405958



(S. cerevisiae)


1064.
cell division cycle associated 1
CDCA1
NM_031423.2
83540
Hs.234545


1065.
cell division cycle associated 3
CDCA3
NM_031299.3
83461
Hs.524216


1066.
cyclin-dependent kinase 2
CDK2
NM_001798.2
1017
Hs.19192


1067.
centromere protein A, 17 kDa
CENPA
NM_001809
1058
Hs.1594


1068.
centromere protein F, 350/400ka
CENPF
NM_0.16343
1063
Hs.497741



(mitosin)


1069.
centromere protein N
CENPN
NM_018455.3
55839
Hs.283532


1070.
cofilin 2 (muscle)
CFL2
NM_021914.5
1073
Hs.180141


1071.
chromodomain helicase DNA binding
CHD7
NM_017780.2
55636
Hs.20395



protein 7


1072.
carbohydrate (chondroitin 4)
CHST11
NM_018413.2
50515
Hs.17569



sulfotransferase 11


1073.
cytoskeleton associated protein 2-like
CKAP2L
NM_152515.2
150468
Hs.434250


1074.
CDC28 protein kinase regulatory
CKS2
NM_001827.1
1164
Hs.83758



subunit 2


1075.
claspin homolog (Xenopus laevis)
CLSPN
NM_022111.2
63967
Hs.175613


1076.
CSAG family, member 2
CSAG2
NM_004909.1
9598
Hs.522810


1077.
cancer/testis antigen 1A
CTAG1A
NM_139250.1
246100
Hs.559536


1078.
cancer/testis antigen 1B
CTAG1B
NM_001327.1
1485
Hs.534310


1079.
cancer/testis antigen 2
CTAG2
NM_020994.2
30848
Hs.87225


1080.
cystathionase (cystathionine gamma-
CTH
NM_001902.4
1491
Hs.19904



lyase)


1081.
cathepsin L-like 3
CTSLL3
L25629.1
1518
Hs.418123


1082.
cortactin
CTTN
NM_005231
2017
Hs.301348


1083.
DBF4 homolog (S. cerevisiae)
DBF4
NM_006716.3
10926
Hs.208414


1084.
development and differentiation
DDEF1
NM_018482.2
50807
Hs.106015



enhancing factor 1


1085.
DEAD (Asp-Glu-Ala-Asp) box
DDX18
NM_006773.3
8886
Hs.363492



polypeptide 18


1086.
DEP domain containing 1
DEPDC1
NM_017779.3
55635
Hs.445098


1087.
dihydrofolate reductase
DHFR
NM_000791.3
1719
Hs.464813


1088.
hypothetical protein DKFZp762E1312
DKFZp762E1312
NM_018410.3
55355
Hs.532968


1089.
DnaJ (Hsp40) homolog, subfamily C,
DNAJC10
NM_018981.1
54431
Hs.516632



member 10


1090.
dpy-19-like 1 (C. elegans)
DPY19L1
AJ011911.1
23333
Hs.510645


1091.
denticleless homolog (Drosophila)
DTL
NM_016448.1
51514
Hs.126774


1092.
deltex 3 homolog (Drosophila)
DTX3
NM_178502.2
196403
Hs.32374


1093.
dual specificity phosphatase 4
DUSP4
NM_001394.5
1846
Hs.417962


1094.
dual specificity phosphatase 6
DUSP6
NM_001946.2
1848
Hs.298654


1095.
endothelin 3
EDN3
NM_207032.1
1908
Hs.1408


1096.
engrailed homolog 2
EN2
NM_001427.2
2020
Hs.134989


1097.
ets variant gene 1
ETV1
NM_004956.3
2115
Hs.22634


1098.
exonuclease 1
EXO1
NM_130398.2
9156
Hs.498248


1099.
exosome component 3
EXOSC3
NM_016042.2
51010
Hs.493887


1100.
eyes absent homolog 4 (Drosophila)
EYA4
NM_004100
2070
Hs.102408


1101.
family with sequence similarity 126,
FAM126A
NM_032581.2
84668
Hs.85603



member A


1102.
family with sequence similarity 29,
FAM29A
NM_017645.3
54801
Hs.533468



member A


1103.
family with sequence similarity 62 (C2
FAM62B
NM_020728.1
57488
Hs.490795



domain containing) member B


1104.
F-box only protein 32
FBXO32
NM_058229
114907
Hs.403933


1105.
FK506 binding protein 10, 65 kDa
FKBP10
NM_021939.2
60681
Hs.463035


1106.
hypothetical protein FLJ10781
FLJ10781
NM_018215.2
55228
Hs.8395


1107.
hypothetical protein FLJ11029
FLJ11029
NM_018304
55771
Hs.274448


1108.
hypothetical protein FLJ13236
FLJ13236
NM_024902
79962
Hs.170298


1109.
FLJ20105 protein
FLJ20105
NM_001009954.1
54821
Hs.47558


1110.
hypothetical protein FLJ30655
FLJ30655
NM_144643
132320
Hs.404000


1111.
hypothetical protein FLJ30707
FLJ30707
NM_145019
220108
Hs.292590


1112.
FLJ36874 protein
FLJ36874
NM_152716.1
219988
Hs.523698


1113.
fibronectin type III domain containing
FNDC3B
NM_022763.2
64778
Hs.159430



3B


1114.
FERM domain containing 5
FRMD5
NM_032892.3
84978
Hs.368399


1115.
FSH primary response (LRPR1
FSHPRH1
NM_006733
2491
Hs.318398



homolog, rat) 1


1116.
GA binding protein transcription
GABPB2
NM_005254.4
2553
Hs.511316



factor, beta subunit 2


1117.
G antigen 4
GAGE4
NM_001474.1
2576
Hs.460641


1118.
G antigen 8
GAGE8
NM_012196.1
26749
Hs.278606


1119.
UDP-N-acetyl-alpha-D-
GALNT7
NM_017423.1
51809
Hs.127407



galactosamine:polypeptide N-



acetylgalactosaminyltransferase 7



(GalNAc-T7)


1120.
ganglioside-induced differentiation-
GDAP1
NM_018972
54332
Hs.168950



associated protein 1


1121.
growth differentiation factor 15
GDF15
NM_004864.1
9518
Hs.515258


1122.
glutaminase
GLS
NM_014905.2
2744
Hs.116448


1123.
glutamate dehydrogenase 2
GLUD2
BC005111.1
2747
Hs.368538


1124.
golgi transport 1 homolog B (S. cerevisiae)
GOLT1B
NM_016072.2
51026
Hs.62275


1125.
G patch domain containing 2
GPATC2
NM_018040.1
55105
Hs.420757


1126.
glycerol-3-phosphate dehydrogenase 2
GPD2
NM_000408.2
2820
Hs.148266



(mitochondrial)


1127.
G protein-coupled receptor 107
GPR107
NM_020960.3
57720
Hs.512461


1128.
G protein-coupled receptor 19
GPR19
NM_006143.1
2842
Hs.92458


1129.
general transcription factor IIH,
GTF2H2
NM_001515.2
2966
Hs.191356



polypeptide 2, 44 kDa


1130.
general transcription factor IIH,
GTF2H4
NM_001517.4
2968
Hs.485070



polypeptide 4, 52 kDa


1131.
G-2 and S-phase expressed 1
GTSE1
NM_016426.4
51512
Hs.386189


1132.
H2A histone family, member V
H2AFV
NM_201436.1
94239
Hs.157379


1133.
hairy/enhancer-of-split related with
HEY1
NM_012258
23462
Hs.234434



YRPW motif 1


1134.
3-hydroxyisobutyrate dehydrogenase
HIBADH
NM_152740.2
11112
Hs.406758


1135.
histone linker H1 domain, spermatid-
HILS1
NM_194072.1
373861
Hs.25934



specific 1


1136.
histone 1, H2bh
HIST1H2BH
NM_003524.2
8345
Hs.247815


1137.
histone 1, H3d
HIST1H3D
NM_003530
8351
Hs.532144


1138.
hyaluronan-mediated motility receptor
HMMR
NM_012484.1
3161
Hs.72550



(RHAMM)


1139.
HN1 like
HN1L
NM_144570
90861
Hs.437433


1140.
heterogeneous nuclear
HNRPC
NM_004500
3183
Hs.356139



ribonucleoprotein C (C1/C2)


1141.
homeo box A10
HOXA10
NM_018951.3
3206
Hs.110637


1142.
homeo box B6
HOXB6
NM_018952
3216
Hs.98428


1143.
homeo box B7
HOXB7
NM_004502.3
3217
Hs.436181


1144.
homeo box B9
HOXB9
NM_024017
3219
Hs.321142


1145.
homeo box D13
HOXD13
NM_000523.2
3239
Hs.152414


1146.
heat shock 90 kDa protein 1, alpha-like 3
HSPCAL3
NM_001040141.1
3324
Hs.523560


1147.
heat shock 90 kDa protein 1, beta
HSPCB
NM_007355.2
3326
Hs.509736


1148.
heat shock 60 kDa protein 1
HSPD1
NM_002156.4
3329
Hs.113684



(chaperonin)


1149.
heat shock 10 kDa protein 1
HSPE1
NM_002157.1
3336
Hs.558338



(chaperonin 10)


1150.
heat shock 105 kDa/110 kDa protein 1
HSPH1
NM_006644.2
10808
Hs.36927


1151.
insulin-like growth factor 2 mRNA
IGF2BP3
NM_006547
10643
Hs.432616



binding protein 3


1152.
interleukin 1 receptor accessory protein
IL1RAP
NM_002182.2
3556
Hs.478673


1153.
potassium voltage-gated channel,
KCNQ5
NM_019842.2
56479
Hs.98129



KQT-like subfamily, member 5


1154.
KIAA0101
KIAA0101
NM_014736.4
9768
Hs.81892


1155.
KIAA0470
KIAA0470
AK001664.1
9859
Hs.408293


1156.
KIAA1618
KIAA1618
NM_020954.2
57714
Hs.514554


1157.
KIAA1917 protein
KIAA1917
BF056204
114804
Hs.434389


1158.
kinesin family member 18A
KIF18A
NM_031217.2
81930
Hs.301052


1159.
kinesin family member 4A
KIF4A
NM_012310.2
24137
Hs.279766


1160.
kinesin family member C1
KIFC1
NM_002263.2
3833
Hs.436912


1161.
karyopherin alpha 2 (RAG cohort 1,
KPNA2
NM_002266.2
3838
Hs.159557



importin alpha 1)


1162.
lactamase, beta 2
LACTB2
NM_016027.1
51110
Hs.118554


1163.
hypothetical protein LOC144874
LOC144874
AL832853.1
144874
Hs.439363


1164.
hypothetical protein LOC150946
LOC150946
AV751887
150946
Hs.187912


1165.
hypothetical protein LOC152485
LOC152485
NM_178835.2
152485
Hs.133916


1166.
LOC346615
LOC346615
XM_934971.1
645591
Hs.453810


1167.
LOC346616
LOC346616
BC012751.2
645591
Hs.285410


1168.
LOC346658
LOC346658
AI143641
346658
Hs.181400


1169.
LOC346888
LOC346888
XM_294450.5
346887
Hs.127286


1170.
hypothetical gene LOC401431
LOC401431
NM_001008745.1
401431
Hs.556097


1171.
hypothetical gene supported by
LOC440995
BC068085.1
440995
Hs.552645



BC034933; BC068085


1172.
PTD016 protein
LOC51136
NM_016125
51136
Hs.531701


1173.
melanoma antigen
LOC51152
XM_927576.1
644433
Hs.132526


1174.
hypothetical protein DKFZp434D2328
LOC91526
NM_153697
91526
Hs.11571


1175.
hypothetical protein LOC92249
LOC92249
AK001756.1
92249
Hs.31532


1176.
peroxisomal Ion protease 2
LONP2
NM_031490.2
83752
Hs.555994


1177.
leucine zipper protein 5
LUZP5
AK092008.1
54892
Hs.18616


1178.
mannose-6-phosphate receptor (cation
M6PR
NM_002355.2
4074
Hs.134084



dependent)


1179.
MAD2 mitotic arrest deficient-like 1
MAD2L1
NM_002358.2
4085
Hs.28312



(yeast)


1180.
melanoma antigen family A, 1 (directs
MAGEA1
NM_004988.3
4100
Hs.72879



expression of antigen MZ2-E)


1181.
melanoma antigen family A, 12
MAGEA12
NM_005367.4
4111
Hs.169246


1182.
melanoma antigen family A, 2B
MAGEA2B
NM_153488.3
266740
Hs.534597


1183.
melanoma antigen family A, 3
MAGEA3
NM_005362.3
4102
Hs.417816


1184.
melanoma antigen family A, 5
MAGEA5
NM_021049.3
4104
Hs.546265


1185.
melanoma antigen family A, 6
MAGEA6
NM_005363.2
4105
Hs.441113


1186.
mannosidase, endo-alpha-like
MANEAL
NM_152496.1
149175
Hs.534562


1187.
microtubule-associated protein 9
MAP9
NM_001039580.1
79884
Hs.549331


1188.
MARCKS-like 1
MARCKSL1
NM_023009.4
65108
Hs.75061


1189.
MCM10 minichromosome
MCM10
NM_018518.3
55388
Hs.198363



maintenance deficient 10 (S. cerevisiae)


1190.
MCM8 minichromosome maintenance
MCM8
NM_032485.4
84515
Hs.437582



deficient (S. cerevisiae)


1191.
mucolipin 2
MCOLN2
NM_153259.2
255231
Hs.459526


1192.
malic enzyme 2, NAD(+)-dependent,
ME2
NM_002396.3
4200
Hs.233119



mitochondrial


1193.
methyltransferase like 2
METTL2
NM_018396.2
55798
Hs.433213


1194.
milk fat globule-EGF factor 8 protein
MFGE8
NM_005928.1
4240
Hs.3745


1195.
hypothetical protein MGC11082
MGC11082
NM_032691
84777
Hs.326729


1196.
hypothetical protein MGC5509
MGC5509
NM_024093
79074
Hs.409606


1197.
muskelin 1, intracellular mediator
MKLN1
NM_013255
4289
Hs.145599



containing kelch motifs


1198.
matrix metallopeptidase 12
MMP12
NM_002426.2
4321
Hs.1695



(macrophage elastase)


1199.
matrix metallopeptidase 14
MMP14
NM_004995.2
4323
Hs.2399



(membrane-inserted)


1200.
matrix metallopeptidase 8 (neutrophil
MMP8
NM_002424.1
4317
Hs.161839



collagenase)


1201.
meiotic nuclear divisions 1 homolog
MND1
NM_032117.2
84057
Hs.294088



(S. cerevisiae)


1202.
M-phase phosphoprotein 9
MPHOSPH9
NM_022782
10198
Hs.445084


1203.
metallophosphoesterase domain
MPPED2
NM_001584.1
744
Hs.289795



containing 2


1204.
myosin regulatory light chain MRCL3
MRCL3
NM_006471
10627
Hs.233936


1205.
mitochondrial ribosomal protein L44
MRPL44
NM_022915.2
65080
Hs.203559


1206.
musashi homolog 2 (Drosophila)
MSI2
NM_138962.2
124540
Hs.134470


1207.
methylene tetrahydrofolate
MTHFD2
NM_006636
10797
Hs.154672



dehydrogenase (NAD+ dependent),



methenyltetrahydrofolate



cyclohydrolase


1208.
mitochondrial translational release
MTRF1
NM_004294.2
9617
Hs.382176



factor 1


1209.
multiple substrate lipid kinase
MULK
BC009775.1
55750
Hs.521240


1210.
nuclear cap binding protein subunit 1,
NCBP1
NM_002486
4686
Hs.439203



80 kDa


1211.
nuclear cap binding protein subunit 2,
NCBP2
NM_007362
22916
Hs.240770



20 kDa


1212.
neural precursor cell expressed,
NEDD4L
NM_015277.2
23327
Hs.185677



developmentally down-regulated 4-like


1213.
NIMA (never in mitosis gene a)-related
NEK2
NM_002497.2
4751
Hs.153704



kinase 2


1214.
nicotinamide nucleotide
NNT
NM_012343.2
23530
Hs.482043



transhydrogenase


1215.
neuropilin 2
NRP2
NM_003872
8828
Hs.471200


1216.
5′,3′-nucleotidase, cytosolic
NT5C
NM_014595
30833
Hs.67201


1217.
NudC domain containing 1
NUDCD1
NM_032869.2
84955
Hs.558577


1218.
nudix (nucleoside diphosphate linked
NUDT4
NM_019094
11163
Hs.506325



moiety X)-type motif 4


1219.
outer dense fiber of sperm tails 2
ODF2
NM_153437.1
4957
Hs.129055


1220.
procollagen-proline, 2-oxoglutarate 4-
P4HA1
NM_000917.2
5033
Hs.500047



dioxygenase (proline 4-hydroxylase),



alpha polypeptide I


1221.
poly(A) binding protein, cytoplasmic 4
PABPC4
NM_003819.2
8761
Hs.169900



(inducible form)


1222.
P antigen family, member 1 (prostate
PAGE1
NM_003785.3
8712
Hs.128231



associated)


1223.
PDZ binding kinase
PBK
NM_018492.2
55872
Hs.104741


1224.
PDGFA associated protein 1
PDAP1
NM_014891.5
11333
Hs.278426


1225.
phosphodiesterase 4B, cAMP-specific
PDE4B
NM_001037339.1
5142
Hs.198072



(phosphodiesterase E4 dunce homolog,



Drosophila)


1226.
protein disulfide isomerase family A,
PDIA6
NM_005742.2
10130
Hs.212102



member 6


1227.
paternally expressed 10
PEG10
NM_015068.3
23089
Hs.147492


1228.
peroxisome biogenesis factor 13
PEX13
NM_002618.2
5194
Hs.368348


1229.
prefoldin 2
PFDN2
NM_012394.3
5202
Hs.492516


1230.
phosphofructokinase, muscle
PFKM
NM_000289.3
5213
Hs.75160


1231.
profilin 2
PFN2
NM_002628.4
5217
Hs.91747


1232.
prohibitin
PHB
NM_002634.2
5245
Hs.514303


1233.
pleckstrin homology-like domain,
PHLDA1
AK074510.1
652993
Hs.82101



family A, member 1


1234.
proteolipid protein 1 (Pelizaeus-
PLP1
NM_000533.3
5354
Hs.1787



Merzbacher disease, spastic paraplegia



2, uncomplicated)


1235.
phospholipid scramblase 1
PLSCR1
NM_021105.1
5359
Hs.130759


1236.
plexin B3
PLXNB3
NM_005393.1
5365
Hs.380742


1237.
partner of NOB1 homolog (S. cerevisiae)
PNO1
NM_020143.2
56902
Hs.262858


1238.
polymerase (RNA) I polypeptide B,
POLR1B
NM_019014.3
84172
Hs.86337



128 kDa


1239.
polymerase (RNA) III (DNA directed)
POLR3K
NM_016310.2
51728
Hs.437186



polypeptide K, 12.3 kDa


1240.
popeye domain containing 3
POPDC3
NM_022361.3
64208
Hs.458336


1241.
POU domain, class 3, transcription
POU3F2
NM_005604.2
5454
Hs.182505



factor 2


1242.
PTPRF interacting protein, binding
PPFIBP1
NM_003622
8496
Hs.172445



protein 1 (liprin beta 1)


1243.
PR domain containing 13
PRDM13
NM_021620.2
59336
Hs.287386


1244.
prolyl endopeptidase-like
PREPL
AB007896.1
9581
Hs.112916


1245.
protein kinase, cAMP-dependent,
PRKAR1A
NM_002734.3
5573
Hs.280342



regulatory, type I, alpha (tissue specific



extinguisher 1)


1246.
phosphoribosyl pyrophosphate
PRPS1
NM_002764.2
5631
Hs.56



synthetase 1


1247.
proline/serine-rich coiled-coil 1
PSRC1
NM_001005290.2
84722
Hs.405925


1248.
PTK2 protein tyrosine kinase 2
PTK2
NM_005607
5747
Hs.395482


1249.
protein tyrosine phosphatase-like A
PTPLAD1
NM_016395.1
51495
Hs.512973



domain containing 1


1250.
RAD54 homolog B (S. cerevisiae)
RAD54B
NM_012415.2
25788
Hs.30561


1251.
RAD54-like (S. cerevisiae)
RAD54L
NM_003579.2
8438
Hs.523220


1252.
Ras protein-specific guanine
RASGRF1
NM_002891
5923
Hs.459035



nucleotide-releasing factor 1


1253.
regulator of G-protein signalling 1
RGS1
NM_002922.3
5996
Hs.75256


1254.
regulator of G-protein signalling 20
RGS20
NM_003702
8601
Hs.368733


1255.
Ras homolog enriched in brain
RHEB
NM_005614
6009
Hs.283521


1256.
Rho-related BTB domain containing 2
RHOBTB2
NM_015178.1
23221
Hs.372688


1257.
ras homolog gene family, member Q
RHOQ
NM_012249.2
23433
Hs.549125


1258.
ribulose-5-phosphate-3-epimerase
RPE
NM_199229.1
6120
Hs.282260


1259.
Ras-related GTP binding D
RRAGD
NM_021244.2
58528
Hs.485938


1260.
ribonucleotide reductase M2
RRM2
NM_001034
6241
Hs.226390



polypeptide


1261.
RRN3 RNA polymerase I transcription
RRN3
NM_018427.3
54700
Hs.460078



factor homolog (yeast)


1262.
RNA terminal phosphate cyclase
RTCD1
NM_003729.1
8634
Hs.484222



domain 1


1263.
sin3-associated polypeptide, 30 kDa
SAP30
NM_003864
8819
Hs.413835


1264.
src family associated phosphoprotein 2
SCAP2
NM_003930.3
8935
Hs.200770


1265.
SEC22 vesicle trafficking protein-like
SEC22L3
NM_032970.2
9117
Hs.445892



3 (S. cerevisiae)


1266.
SEC24 related gene family, member A
SEC24A
AJ131244
10802
Hs.211612



(S. cerevisiae)


1267.
septin 2
SEPT2
NM_001008491.1
4735
Hs.335057


1268.
septin 9
SEPT9
NM_006640
10801
Hs.288094


1269.
stress-associated endoplasmic
SERP1
NM_014445
27230
Hs.518326



reticulum protein 1


1270.
serine (or cysteine) proteinase
SERPINE2
NM_006216
5270
Hs.21858



inhibitor, clade E (nexin, plasminogen



activator inhibitor type 1), member 2


1271.
seizure related 6 homolog (mouse)-like 2
SEZ6L2
NM_012410.1
26470
Hs.6314


1272.
sarcoglycan, epsilon
SGCE
NM_003919.1
8910
Hs.371199


1273.
solute carrier family 16
SLC16A4
NM_004696.1
9122
Hs.351306



(monocarboxylic acid transporters),
(SL16AJ)



member 4


1274.
solute carrier family 2 (facilitated
SLC2A3
NM_006931.1
6515
Hs.419240



glucose transporter), member 3


1275.
solute carrier family 43, member 3
SLC43A3
NM_014096.2
29015
Hs.99962


1276.
SMC4 structural maintenance of
SMC4L1
NM_001002799.1
10051
Hs.58992



chromosomes 4-like 1 (yeast)


1277.
sorting nexin 25
SNX25
NM_031953.2
83891
Hs.369091


1278.
SRY (sex determining region Y)-box 5
SOX5
NM_006940
6660
Hs.434948


1279.
secreted phosphoprotein 1
SPP1
NM_000582
6696
Hs.313



(osteopontin, bone sialoprotein I, early



T-lymphocyte activation 1)


1280.
sprouty-related, EVH1 domain
SPRED1
NM_152594.1
161742
Hs.525781



containing 1


1281.
sprouty-related, EVH1 domain
SPRED2
NM_181784.1
200734
Hs.59332



containing 2


1282.
sprouty homolog 2 (Drosophila)
SPRY2
NM_005842.2
10253
Hs.18676


1283.
signal sequence receptor, alpha
SSR1
NM_003144.2
6745
Hs.114033



(translocon-associated protein alpha)


1284.
ST6 (alpha-N-acetyl-neuraminyl-2,3-
ST6GALNAC3
NM_152996.1
256435
Hs.337040



beta-galactosyl-1,3)-N-



acetylgalactosaminide alpha-2,6-



sialyltransferase 3


1285.
stress 70 protein chaperone,
STCH
NM_006948.4
6782
Hs.352341



microsome-associated, 60 KDa


1286.
serine/threonine kinase 6
STK6
NM_198433.1
6790
Hs.250822


1287.
TATA box binding protein (TBP)-
TAF1A
NM_005681.2
9015
Hs.153088



associated factor, RNA polymerase I,



A, 48 kDa


1288.
transcription factor 20 (AR1)
TCF20
NM_181492.1
6942
Hs.475018


1289.
transferrin receptor (p90, CD71)
TFRC
NM_003234.1
7037
Hs.529618


1290.
TGFB-induced factor (TALE family
TGIF
NM_170695.2
7050
Hs.373550



homeobox)


1291.
transketolase-like 1
TKTL1
NM_012253.2
8277
Hs.102866


1292.
transmembrane protein 38B
TMEM38B
NM_018112.1
55151
Hs.411925


1293.
transmembrane protein 4
TMEM4
NM_014255
10330
Hs.8752


1294.
transmembrane protein 48
TMEM48
NM_018087.3
55706
Hs.476525


1295.
transmembrane protein 64
TMEM64
NM_001008495.1
169200
Hs.556805


1296.
TRAF2 and NCK interacting kinase
TNIK
NM_015028.1
23043
Hs.34024


1297.
trinucleotide repeat containing 15
TNRC15
NM_015575
26058
Hs.334871


1298.
torsin A interacting protein 1
TOR1AIP1
NM_015602.2
26092
Hs.496459


1299.
TP53TG3 protein
TP53TG3
NM_016212.2
24150
Hs.513537


1300.
TPX2, microtubule-associated,
TPX2
NM_012112.4
22974
Hs.244580



homolog (Xenopus laevis)


1301.
translocation associated membrane
TRAM1
NM_014294.3
23471
Hs.491988



protein 1


1302.
tribbles homolog 2 (Drosophila)
TRIB2
NM_021643.1
28951
Hs.467751


1303.
tripartite motif-containing 51
TRIM51
NM_032681.1
84767
Hs.326734


1304.
trophinin associated protein (tastin)
TROAP
NM_005480.2
10024
Hs.524399


1305.
translin
TSN
NM_004622.2
7247
Hs.75066


1306.
tetratricopeptide repeat domain 26
TTC26
NM_024926.1
79989
Hs.303930


1307.
thymidylate synthetase
TYMS
NM_001071.1
7298
Hs.369762


1308.
ubiquitin-conjugating enzyme E2C
UBE2C
NM_181800.1
11065
Hs.93002


1309.
ubiquitin-conjugating enzyme E2I
UBE2I
NM_003345
7329
Hs.302903



(UBC9 homolog, yeast)


1310.
ubiquitin-conjugating enzyme E2T
UBE2T
NM_014176.1
29089
Hs.5199



(putative)


1311.
ubiquitin family domain containing 1
UBFD1
NM_019116
56061
Hs.3459


1312.
UDP glycosyltransferase 8 (UDP-
UGT8
NM_003360.2
7368
Hs.144197



galactose ceramide



galactosyltransferase)


1313.
X antigen family, member 1
XAGE1
NM_020411.1
9503
Hs.112208


1314.
X antigen family, member 2
XAGE2
NM_130777.1
9502
Hs.522654


1315.
zinc finger protein 697
ZNF697
XM_371286.4
90874
Hs.381105


1316.
hypothetical protein LOC650446
LOC650446
XM_939537
650446
Hs.380331


1317.
musashi homolog 2 (Drosophila)
MSI2
NM_138962
124540
Hs.185084


1318.
neuropilin 2
NRP2
NM_003872
8828
Hs.471200


1319.
hypothetical gene supported by

BF516262
144705
Hs.44817



AF086409


1320.
glutamate dehydrogenase 2
GLUD2
AA909218

Hs.430334


1321.
hypothetical protein LOC647291
LOC647291
NM_001039795.1
647291
—


1322.
hypothetical gene supported by
—
AI631833
347884
Hs.374451



AL832403; BC019824


1323.
Gene supported by sequence info.
—
H38635
—
Hs.391401


1324.
Gene supported by sequence info.
—
BG285837
—
Hs.444096


1325.
Gene supported by sequence info.
—
AW270845
—
—


1326.
Gene supported by sequence info.
—
AI810266
—
Hs.130853


1327.
Gene supported by sequence info.
—
AI911318
—
Hs.224153


1328.
Gene supported by sequence info.
—
AI003508
—
Hs.117689


1329.
Gene supported by sequence info.
—
AI554075
—
Hs.120204


1330.
Gene supported by sequence info.
—
CA424969
—
Hs.146268


1331.
Gene supported by sequence info.
—
AW665538
—
Hs.479714


1332.
Gene supported by sequence info.
—
BF224436
—
Hs.123294


1333.
Gene supported by sequence info.
—
AK024236
—
Hs.476469


1334.
Gene supported by sequence info.
—
BE891646
—
Hs.281434


1335.
Gene supported by sequence info.
—
AI936197
—
Hs.360386


1336.
Gene supported by sequence info.
—
AI374756
—
Hs.116453


1337.
Gene supported by sequence info.
—
AI861893
—
Hs.129967


1338.
Gene supported by sequence info.
—
BC026261
—
Hs.364642
















TABLE C







Genes differentially expressed in metastatic melanoma. Expression


of the genes listed in this table is decreased relative to non-metastatic samples.











Gene




Gene description
Symbol
GenBank ID
Entrez Gene ID













gap junction protein, beta 6 (connexin 30)
GJB6
NM_006783.2
10804


small proline-rich protein 1A
SPRR1A
NM_005987.2
6698


serpin peptidase inhibitor, clade B
SERPINB5
NM_002639.2
5268


(ovalbumin), member 5


calmodulin-like 5
CALML5
NM_017422.3
51806



(CLSP)


desmocollin 1
DSC1
NM_024421.1
1823


plakophilin 1 (ectodermal dysplasia/skin
PKP1
NM_001005337.1
5317


fragility syndrome)


chloride channel, calcium activated, family
CLCA2
NM_006536.4
9635


member 2


desmoglein 1
DSG1
NM_001942.1
1828


corneodesmosin
CDSN
L20815.1
1041


lymphocyte antigen 6 complex, locus D
LY6D
NM_003695.2
8581


late cornified envelope 2B
LCE2B
NM_014357.3
26239


filaggrin
FLG
NM_002016.1
2312


filaggrin 2
RP1-14N1.3
NM_001014342.1
388698


keratin 16 (focal non-epidermolytic
KRT16
NM_005557.2
3868


palmoplantar keratoderma)


suprabasin
SBSN
NM_198538.11
374897


serpin peptidase inhibitor, clade B
SERPINB3
NM_006919.1
6317


(ovalbumin), member 3


serpin peptidase inhibitor, clade B
SERPINB7
NM_001040147.1
8710


(ovalbumin), member 7


keratin 17
KRT17
NM_000422.1
3872


kallikrein 7 (chymotryptic, stratum corneum)
KLK7
NM_005046.2
5650


loricrin
LOR
BC108290.1
4014


secreted LY6/PLAUR domain containing 1
SLURP1
NM_020427.2
57152


hepatocellular carcinoma antigen gene 520
LOC63928
NM_022097.1
63928


keratin 15
KRT15
NM_002275.2
3866


lectin, galactoside-binding, soluble, 7 (galectin
LGALS7
NM_002307.1
3963


7)


cystatin E/M
CST6
NM_001323.2
1474


small proline-rich protein 1B (cornifin)
SPRR1B
NM_003125.2
6699


cornifelin
CNFN
NM_032488.2
84518


triparlite motif-containing 29
TRIM29
NM_058193.1
23650


epiplakin 1
EPPK1
AL137725.1
83481


stratifin
SFN
NM_006142.3
2810


keratin 6B
KRT6B
NM_005555.2
3854


desmoglein 3 (pemphigus vulgaris antigen)
DSG3
BX538327.1
1830


small proline-rich protein 2B
SPRR2B
NM_001017418.1
6701


dermokine
DMKN
NM_033317.2
93099


N-acylsphingosine amidohydrolase (alkaline
ASAH3
NM_133492
125981


ceramidase) 3


serpin peptidase inhibitor, clade B
SERPINB13
NM_012397.2
5275


(ovalbumin), member 13


kallikrein 11
KLK11
NM_006853.2
11012


arylacetamide deacetylase-like 2
AADACL2
NM_207365.1
344752


death associated protein-like 1
DAPL1
NM_001017920.1
92196


ATP-binding cassette, sub-family A (ABC1),
ABCA12
NM_173076.2
26154


member 12


desmocollin 3
DSC3
NM_001941.2
1825


premature ovarian failure, 1B
POF1B
NM_024921.2
79983


GATA binding protein 3
GATA3
NM_001002295.1
2625


LY6/PLAUR domain containing 3
LYPD3
NM_014400.2
27076


keratin 6A
KRT6A
AL569511
140446


Ets homologous factor
EHF
AI763378
26298


protocadherin 21
PCDH21
NM_033100.1
92211


Cas-Br-M (murine) ecotropic retroviral
CBLC
NM_012116.2
23624


transforming sequence c


fibroblast growth factor receptor 2 (bacteria-
FGFR2
NM_022969.1
2263


expressed kinase, keratinocyte growth factor


receptor, craniofacial dysostosis 1, Crouzon


syndrome, Pfeiffer syndrome, Jackson-Weiss


syndrome)


sciellin
SCEL
NM_144777.1
8796


fibroblast growth factor receptor 3
FGFR3
NM_000142.2
2261


(achondroplasia, thanatophoric dwarfism)
















TABLE D







Genes differentially expressed in metastatic melanoma. Expression


of the genes listed in this table is increased relative to non-metastatic samples.











Gene
GenBank reference



Gene description
Symbol
ID
Entrez Gene ID













melanoma antigen family A, 3
MAGEA3
NM_005362.3
4102


melanoma antigen family A, 6
MAGEA6
NM_005363.2
4105


CSAG family, member 2
CSAG2
NM_004909.1
9598



(TRAG3)


melanoma antigen family A, 12
MAGEA12
NM_005367.4
4111


melanoma antigen family A, 2
MAGEA2
NM_005361.2
4101


tripartite motif-containing 51
TRIM51
NM_032681.1
84767


neuropilin 2
NRP2
NM_003872.2
8828


melanoma antigen family A, 1 (directs
MAGEA1
NM_004988.3
4100


expression of antigen MZ2-E)


musashi homolog 2 (Drosophila)
MS12
BF029215
124540


Glycophorin C (Gerbich blood group)
GYPC
H38635
2995


secreted phosphoprotein 1 (osteopontin, bone
SPP1
NM_001040060.1
6696


sialoprotein I, early T-lymphocyte activation


1)


SRY (sex determining region Y)-box 5
SOX5
NM_006940.4
6660


kinesin family member C1
KIFC1
NM_002263.2
3833


histone linker H1 domain, spermatid-specific 1
HILS1
NM_194072.1
373861


regulator of G-protein signalling 20
RGS20
BC018618.1
8601


BUB1 budding uninhibited by benzimidazoles
BUB1
NM_004336.2
699


1 homolog (yeast)


insulin-like growth factor 2 mRNA binding
IGF2BP3
NM_006547.2
10643


protein 3


FERM domain containing 5
FRMD5
NM_032892.3
84978


chromosome 1 open reading frame 90
C1orf90
BC004269.1
84734


eyes absent homolog 4 (Drosophila)
EYA4
BE674583
2070


BCL2-related protein A1
BCL2A1
NM_004049.2
597


solute carrier family 16 (monocarboxylic acid
SLC16A4
NM_004696.1
9122


transporters), member 4


v-akt murine thymoma viral oncogene
AKT3
NM_005465.3
10000


homolog 3 (protein kinase B, gamma)


CDC45 cell division cycle 45-like (S. cerevisiae)
CDC45L
NM_003504.3
8318


SEC22 vesicle trafficking protein-like 3 (S. cerevisiae)
SEC22L3
NM_032970.2
9117


paternally expressed 10
PEG10
NM_015068.3
23089


popeye domain containing 3
POPDC3
NM_022361.3
64208


melanoma antigen family A, 5
MAGEA5
NM_021049.3
4104


glutamate dehydrogenase 2
GLUD2
BC005111.1
2747


ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-
ST6GALNAC3
NM_152996.1
256435


galactosyl-1,3)-N-acetylgalactosaminide


alpha-2,6-sialyltransferase 3


seizure related 6 homolog (mouse)-like 2
SEZ6L2
NM_201575.1
26470


dual specificity phosphatase 4
DUSP4
BE222344
1846


ATP-binding cassette, sub-family B
ABCB5
BC044248.1
340273


(MDR/TAP), member 5


Ras protein-specific guanine nucleotide-
RASGRF1
NM_002891.3
5923


releasing factor 1


dual specificity phosphatase 4
DUSP4
NM_001394.5
1846


FLJ40142 protein
FLJ40142
BF516262
400073


barren homolog 1 (Drosophila)
BRRN1
NM_015341.3
23397


pleckstrin homology-like domain, family A,
PHLDA1
NM_007350.3
22822


member 1


matrix metallopeptidase 14 (membrane-
MMP14
NM_004995.2
4323


inserted)


dual specificity phosphatase 6
DUSP6
NM_001946.2
1848


dpy-19-like 1 (C. elegans)
DPY19L1
XM_371891.2
23333


glutamate dehydrogenase 1
GLUD1
AA909218
2746


LOC346615
LOC346615
XM_934971.1
645591


calumenin
CALU
NM_001219.2
813


ring finger protein 157
RNF157
BF056204
114804


PR domain containing 13
PRDM13
NM_021620.2
59336


PDZ binding kinase
PBK
NM_018492.2
55872


KIAA1618
KIAA1618
NM_020954.2
57714


neural precursor cell expressed,
NEDD4L
NM_015277.2
23327


developmentally down-regulated 4-like


bicaudal D homolog 1 (Drosophila)
BICD1
BC010091.2
636


ribonucleotide reductase M2 polypeptide
RRM2
NM_001034.1
6241









Gene Expression Analysis

As discussed above, combinations of genes are provided herein, for analysis of gene expression in cutaneous tumors (e.g., primary melanoma samples) to determine whether the tumors exhibit a metastatic expression pattern. Methods for analyzing gene expression include methods based on hybridization analysis of polynucleotides, sequencing of polynucleotides, and analysis of protein expression (e.g., proteomics-based methods). Commonly used methods are for the quantification of mRNA expression in a sample include northern blotting and in situ hybridization (Parker & Barnes, Methods in Molecular Biology 106:247-283, 1999); RNAse protection assays (Hod, Biotechniques 13:852 854, 1992); and PCR-based methods, such as reverse transcription polymerase chain reaction (RT-PCR) (Weis et al., Trends in Genetics 8:263 264, 1992). Alternatively, antibodies may be employed that can recognize specific duplexes, including DNA duplexes, RNA duplexes, and DNA-RNA hybrid duplexes or DNA-protein duplexes. Representative methods for sequencing-based gene expression analysis include Serial Analysis of Gene Expression (SAGE), and gene expression analysis by massively parallel signature sequencing (MPSS).
PCR-Based Methods
Combinations of genes indicative of metastatic or non-metastatic melanoma can be analyzed by PCR. PCR is useful to amplify and detect transcripts from a melanoma sample. Various PCR methodologies are useful for gene expression analyses.
Reverse Transcriptase PCR (RT-PCR). RT-PCR is a sensitive quantitative method that can be used to compare mRNA levels in different samples (e.g., non-metastatic and metastatic melanoma samples, or benign cutaneous and melanoma samples) to examine gene expression signatures.
To perform RT-PCR, mRNA is isolated from a sample (e.g., total RNA isolated from a human melanoma sample). mRNA can be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples. Methods for mRNA extraction are known in the art. See, e.g., Ausubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, 1997. Methods for RNA extraction from paraffin embedded tissues are disclosed, for example, in Rupp and Locker, Lab Invest. 56:A67, 1987, and De Andres et al., BioTechniques 18:42044, 1995. Purification kits for RNA isolation from commercial manufacturers, such as Qiagen, can be used. For example, total RNA from a sample can be isolated using Qiagen RNeasy mini-columns. Other commercially available RNA isolation kits include MasterPureTM Complete DNA and RNA Purification Kit (EPICENTRETM, Madison, Wis.), and, Paraffin Block RNA Isolation Kit (Ambion, Inc.). Total RNA from tissue samples can be also isolated using RNA Stat-60 (Tel-Test) or by cesium chloride density gradient centrifugation.
Next, RNA is reverse transcribed into cDNA. The cDNA is amplified in a PCR reaction. Two commonly used reverse transcriptases are avian myeloblastosis virus reverse transcriptase (AMV-RT) and Moloney murine leukemia virus reverse transcriptase (MMLV-RT). The reverse transcription step is typically primed using specific primers, random hexamers, or oligo-dT primers, depending on the conditions and desired readout. For example, extracted RNA can be reverse-transcribed using a GeneAmp RNA PCR kit (Perkin Elmer, Calif., USA), following the manufacturer's instructions. The derived cDNA can then be used as a template in the subsequent PCR reaction. The PCR reaction typically employs the Taq DNA polymerase, which has a 5′-3′ nuclease activity but lacks a 3′-5′ proofreading endonuclease-activity. Two oligonucleotide primers are used to generate an amplicon in the PCR reaction.
Guidelines for PCR primer and probe design are described, e.g., in Dieffenbach et al., “General Concepts for PCR Primer Design” in: PCR Primer, A Laboratory Manual, Cold Spring Harbor Laboratory Press, New York, 133-155, 1995; Innis and Gelfand, “Optimization of PCRs” in: PCR Protocols, A Guide to Methods and Applications, CRC Press, London, 5-11, 1994; and Plasterer, T. N. Primerselect: Primer and probe design. Methods Mol. Biol. 70:520-527, 1997. Factors considered in PCR primer design include primer length, melting temperature (Tm), and G/C content, specificity, complementary primer sequences, and 3′-end sequence. PCR primers are generally 17-30 bases in length, and Tm's between 50-80° C., e.g. about 50 to 7° C. are typically preferred.
For quantitative PCR, a third oligonucleotide, or probe, is used to detect nucleotide sequence located between the two PCR primers. The probe is non-extendible by Taq DNA polymerase enzyme, and typically is labeled with a reporter fluorescent dye and a quencher fluorescent dye. Any laser-induced emission from the reporter dye is quenched by the quenching dye when the two dyes are located close together as they are on the probe. During the amplification reaction, the Taq DNA polymerase enzyme cleaves the probe in a template-dependent manner. The resultant probe fragments disassociate in solution, and signal from the released reporter dye is free from the quenching effect of the second fluorophore. One molecule of reporter dye is liberated for each new molecule synthesized, and detection of the unquenched reporter dye provides the basis for quantitative analysis.
RT-PCR can be performed using commercially available equipment, such as an ABI PRISM 7700TM Sequence Detection System (Perkin-Elmer-Applied Biosystems, Foster City, Calif., USA), or Lightcycler® (Roche Molecular Biochemicals, Mannheim, Germany). Samples can be analyzed using a real-time quantitative PCR device such as the ABI PRISM 7700TM Sequence Detection SystemTM.
To minimize errors and the effect of sample-to-sample variation, RT-PCR is usually performed using an internal standard. A suitable internal standard is expressed at a constant level among different tissues, and is unaffected by the experimental variable. RNAs frequently used to normalize patterns of gene expression are mRNAs for the housekeeping genes glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) and β-actin.
A variation of the RT-PCR technique is real time quantitative PCR, which measures PCR product accumulation through a dual-labeled fluorigenic probe (i.e., TaqManTM probe). Real time PCR is compatible both with quantitative competitive PCR, where internal competitor for each target sequence is used for normalization, and with quantitative comparative PCR using a normalization gene contained within the sample, or a housekeeping gene for RT-PCR. For further details see, e.g. Held et al., Genome Res. 6:986-994, 1996.
Gene expression can be examined using fixed, paraffin-embedded tissues as the RNA source. Briefly, in one exemplary method, sections of paraffin-embedded tumor tissue samples are cut ( ̃10 μm thick). RNA is extracted, and protein and DNA are removed. After analysis of the RNA concentration, RNA repair and/or amplification steps may be performed, if necessary, and RNA is reverse transcribed using gene specific promoters followed by RT-PCR. Methods of examining expression in fixed, paraffin-embedded tissues, are described, for example, in Godfrey et al., J; Molec. Diagn. 2: 84-91, 2000; and Specht et. al., Am. J. Pathol. 158: 419-29, 2001.
Another approach for gene expression analysis employs competitive PCR design and automated, high-throughput matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) MS detection and quantification of oligonucleotides. This method is described by Ding and Cantor, Proc. Natl. Acad. Sci. USA 100:3059-3064, 2003.
See also the MassARRAY-based gene expression profiling method, developed by Sequenom, Inc. (San Diego, Calif.).
Additional PCR-based techniques for gene expression analysis include, e.g., differential display (Liang and Pardee, Science 257:967-971, 1992); amplified fragment length polymorphism (iAFLP) (Kawamoto et al., Genome Res. 12:1305-1312, 1999); BeadArrayTM technology (Illumina, San Diego, Calif.; Oliphant et al., Discovery of Markers for Disease (Supplement to Biotechniques), June 2002; Ferguson et al., Analytical Chemistry 72:5618, 2000); BeadsArray for Detection of Gene Expression (BADGE), using the commercially available Luminex100 LabMAP system and multiple color-coded microspheres (Luminex Corp., Austin, Tex.) in a rapid assay for gene expression (Yang et al., Genome Res. 11:1888-1898, 2001); and high coverage expression profiling (HiCEP) analysis (Fukumura et al., Nucl. Acids. Res. 31(16) e94, 2003).
Microarrays
Evaluating gene expression of a melanoma sample can also be performed with microarrays. Microarrays permit simultaneous analysis of a large number of gene expression products. Typically, polynucleotides of interest are plated, or arrayed, on a microchip substrate. The arrayed sequences are then hybridized with nucleic acids (e.g., DNA or RNA) from cells or tissues of interest (e.g., cutaneous tissue samples). The source of mRNA typically is total RNA (e.g., total RNA isolated from human melanoma samples, and normal skin samples). If the source of mRNA is a primary tumor, mRNA can be extracted, for example, from frozen or archived paraffin-embedded and fixed (e.g. formalin-fixed) tissue samples.
In various embodiments of the microarray technique, probes to at least 10, 25, 50, 100, 200, 500, 1000, 1250, 1500, or 1600 genes (e.g., genes listed in a Table herein, which distinguish metastatic melanoma from other types of cutaneous tissues) are immobilized on an array substrate (e.g., a porous or nonporous solid support, such as a glass, plastic, or gel surface). The probes can include DNA, RNA, copolymer sequences of DNA and RNA, DNA and/or RNA analogues, or combinations thereof.
In some embodiments, a microarray includes a support with an ordered array of binding (e.g., hybridization) sites for each individual gene. The microarrays can be addressable arrays, and more preferably positionally addressable arrays, i.e., each probe of the array is located at a known, predetermined position on the solid support such that the identity (i.e., the sequence) of each probe can be determined from its position in the array.
Each probe on the microarray can be between 10-50,000 nucleotides, e.g., between 300-1,000 nucleotides in length. The probes of the microarray can consist of nucleotide sequences with lengths: less than 1,000 nucleotides, e.g., sequences 10-1,000, or 10-500, or 10-200 nucleotides in length. An array can include positive control probes, e.g., probes known to be complementary and hybridizable to sequences in the test sample, and negative control probes, e.g., probes known to not be complementary and hybridizable to sequences in the test sample.
Methods for attaching nucleic acids to a surface are known. Methods for immobilizing nucleic acids on glass are described, e.g., Schena et al, Science 270:467-470, 1995; DeRisi et al, Nature Genetics 14:457-460, 1996; Shalon et al., Genome Res. 6:639-645, 1996; and Schena et al., Proc. Natl. Acad. Sci. U.S.A. 93:10539-11286, 1995). Techniques are known for producing arrays with thousands of oligonucleotides at defined locations using photolithographic techniques are described by Fodor et al., 1991, Science 251:767-773, 1991; Pease et al., Proc. Natl. Acad. Sci. U.S.A. 91:5022-5026, 1994; Lockhart et al., Nature Biotechnology 14:1675, 1996; U.S. Pat. Nos. 5,578,832; 5,556,752; and 5,510,270). Other methods for making microarrays have been described. See, e.g., Maskos and Southern, Nuc. Acids. Res. 20:1679-1,684, 1992. In principle, and as noted supra, any type of array, for example, dot blots on a nylon hybridization membrane (see Sambrook et al., Molecular Cloning, A Laboratory Manual, 2nd Ed., Vols. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. (1989)) could be used.
The polynucleotide molecules to be analyzed may be from any clinically relevant source, and are expressed RNA or a nucleic acid derived therefrom (e.g., cDNA or amplified RNA derived from cDNA that incorporates an RNA polymerase promoter), including naturally occurring nucleic acid molecules, as well as synthetic nucleic acid molecules. For example, the test polynucleotide molecules include total cellular RNA, poly(A)+ messenger RNA (mRNA), or fraction thereof, cytoplasmic mRNA, or RNA transcribed from cDNA (i.e., cRNA; see, e.g., Linsley & Schelter, U.S. patent application Ser. No. 09/411,074, filed Oct. 4, 1999, or U.S. Pat. No. 5,545,522, 5,891,636, or 5,716,785). Methods for preparing RNA are known and are described, e.g., in Sambrook et al., Molecular Cloning, A Laboratory Manual (2nd Ed.), Vols. 1-3, Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y., 1989. RNA can be fragmented by methods known in the art, e.g., by incubation with ZnCl2, to generate fragments of RNA.
Test polynucleotide molecules that are poorly expressed in particular cells can be enriched using normalization techniques (Bonaldo et al., Genome Res. 6:791-806, 1996).
The test polynucleotides are detectably labeled at one or more nucleotides. Any method known in the art may be used to detectably label the polynucleotides.
Nucleic acid hybridization and wash conditions are chosen so that the test polynucleotide molecules specifically bind or specifically hybridize to the complementary polynucleotide sequences of the array, preferably to a specific array site, wherein its complementary nucleic acid is located. General parameters for specific (i.e., stringent) hybridization conditions for nucleic acids are described in Sambrook et al., supra, and in Ausubel et al., Current Protocols in Molecular Biology, vol. 2, Current Protocols Publishing, New York, 1994. Typically, stringent conditions for short probes (e.g., 10 to 50 nucleotide bases) will be those in which the salt concentration is at least about 0.01 to 1.0 M at pH 7.0 to 8.3 and the temperature is at least about 30° C. Stringent conditions can also be achieved with the addition of destabilizing agents such as formamide. When fluorescently labeled probes are used, the fluorescence emissions at each site of a microarray can be detected by scanning confocal laser microscopy or other methods (see Shalon et al., Genome Research 6:639-645, 1996; Schena et al., Genome Res. 6:639-645, 1996; and Ferguson et al., Nature Biotech. 14:1681-1684, 1996). Signals are recorded and typically analyzed by computer. Methods for evaluating microarray data and classifying samples are described in U.S. Pat. No. 7,171,311.
Serial Analysis of Gene Expression (SAGE)
Gene expression in melanoma samples can also be determined by serial analysis of gene expression (SAGE), which is a method that allows the simultaneous and quantitative analysis of a large number: of gene transcripts, without the need of providing an individual hybridization probe for each transcript (see, e.g. Velculescu et al., Science. 270:484-487, 1995; and Velculescu et al., Cell 88:243-51, 1997). Briefly, a short sequence tag (about 10-14 nucleotides) is generated that contains sufficient information to uniquely identify a transcript, provided that the tag is obtained from a unique position within each transcript. Then, many transcripts are linked together to form long serial molecules, that can be sequenced, revealing the identity of the multiple tags simultaneously. The expression pattern of a population of transcripts can be quantitatively evaluated by determining the abundance of individual tags, and identifying the gene corresponding to each tag.
Protein Detection Methodologies
Immunohistochemical methods are also suitable for detecting the expression of the melanoma signature genes described herein. Antibodies, most preferably monoclonal antibodies, specific for a gene product are used to detect expression. The antibodies can be detected by direct labeling of the antibodies themselves, for example, with radioactive labels, fluorescent labels, hapten labels such as, biotin, or an enzyme such as horse radish peroxidase or alkaline phosphatase. Alternatively, unlabeled primary antibody is used in conjunction with a labeled secondary antibody, comprising antisera, polyclonal antisera or a monoclonal antibody specific for the primary antibody. Immunohistochemistry protocols and kits are well known in the art and are commercially available.
Proteomic methods can allow examination of global changes in protein expression in a sample. Proteomic analysis typically involves separation of individual proteins in a sample by 2-D gel electrophoresis (2-D PAGE), and identification of individual proteins recovered from the gel, e.g. my mass spectrometry or N-terminal sequencing, and analysis of the data using bioinformatics. Proteomics methods can be used alone or in combination with other methods for evaluating gene expression.
In various aspects, the expression of certain genes in a cutaneous sample is detected to provide clinical information (e.g., prognostic information, classification of the tumor from which the sample is derived as a metastatic melanoma or non-metastatic melanoma). Thus, gene expression assays include measures to correct for differences in RNA variability and quality. For example, an assay typically measures and incorporates the expression of certain normalizing genes, such known housekeeping genes, e.g., GAPDH, β-actin, and Cyp1. Alternatively, normalization can be based on the mean or median signal (Ct) of all of the assayed genes or a large subset thereof (global normalization approach). In some embodiments, a normalized test RNA (e.g., from a patient sample) is compared to the amount found in a metastatic melanoma, non-metastatic melanoma, and/or normal skin sample reference set. The level of expression measured in a particular test sample can be determined to fall at some percentile within a range observed in reference sets.
Kits
The technology herein includes kits for evaluating gene expression (e.g., RNA or protein) in melanoma samples. A “kit” refers to a combination of physical elements, e.g., probes, including without limitation specific primers, labeled nucleotic acid probes, antibodies, protein-capture agent(s), reagent(s), instruction sheet(s) and other elements useful to practice the technology described herein. These physical elements can be arranged in any way suitable for carrying out the invention.
A kit for analyzing protein expression can include specific binding agents, such as immunological reagents (e.g., an antibody, e.g., a labeled antibody) for detecting proteins expressed of one or more genes described herein (e.g., one or more genes from Table A, Table B, Table C, or Table D). For example, the kit can include an antibody that detects expression of GJB6, an antibody that detects expression of SPPRR1A, and an antibody that detects expression of SERPINB5, in a tissue section.
Kits for analyzing RNA expression include, for example, a set of oligonucleotide probes for detecting expression of a set of genes described herein (e.g., five or more genes from Table A, Table B, Table C, or Table D). The probes can be provided on a solid support, as in an array (e.g., a microarray), or in separate containers. The kits can include a set of oligonucleotide primers useful for amplifying a set of genes described herein, e.g., to perform PCR analysis. Kits can include further buffers, enzymes, labeling compounds, and the like.
EXAMPLES
To identify the genes involved in the metastatic process of melanoma, various non-metastatic primary skin cancers were compared to metastatic melanoma utilizing a gene microarray approach followed by functional validation of select genes. Distinct gene expression changes occurring along the spectrum of primary melanoma tumor thickness and metastatic melanoma were discovered.
Example 1
Gene Expression Differences Between Primary Cutaneous Cancer and Metastatic Melanoma
Tumor samples were obtained from patients with primary cutaneous melanoma (PCM), squamous cell carcinoma (SCC), basal cell carcinoma (BCC) and metastatic melanoma (MM). Gene expression in the samples was examined by microarray analysis as described in the Materials and Methods, below. An initial training set of 23 tumors revealed 2,014 Affymetrix probe sets with a greater than 2-fold difference in the average gene expression level between the metastatic melanoma (MM) and primary cutaneous cancers. This preliminary list, consisting of 1,141 well characterized and 471 poorly characterized human genes, indicates that a substantial difference exists between the metastatic tumors and the non-metastatic tissue types. The expression differences allow for a relatively robust gene classification of tissue samples into groups of metastatic samples and non-metastatic primary tumors. All tumor samples were clustered utilizing the 2,014 probe sets and individually identified as metastatic or non-metastatic based upon the characteristics of tumor samples in the same cluster. The initial set of samples comprised a training set for which 22 of 23 samples were correctly partitioned into the cluster containing primary melanoma or the cluster containing MM samples. A single primary melanoma with a Breslow's tumor thickness of 90 mm was misclassified as a MM sample. Two independent test sets comprised of primary and MM samples were similarly classified, utilizing the 2,014 probe sets and hierarchical clustering. Co-clustering led to the correct identification of 56 of 60 melanoma samples. In general, the misidentified samples were thick primary melanomas classified as MM. Of note, several normal human skin samples were analyzed and found to classify as non-metastatic by their gene expression profiles.
A subset of melanoma samples were examined in order to generate a more comprehensive list of genes that were differentially expressed between MM and PCM using serial analysis of microarrays (SAM). This analysis identified 1,352 probe sets with higher expression in the metastatic samples and 2,991 probe sets with higher expression in non-metastatic samples. This list was further reduced by removing probe sets that did not appear to have an average difference greater than 2-fold between groups. The resultant complete gene list is shown above in Tables A and B, above. This final list consists of 1,667 Affymetrix probe sets that detect 247 poorly defined transcripts, 84 minimally defined genes, and 1007 well characterized human genes. From this list, 316 genes were highly expressed in MM compared to 1022 genes that were more highly expressed in the non-metastatic: cancers and normal skin.
A subset of the full gene list is shown below in Table 1 below. This table illustrates two main trends. There is a shift in the kind of genes expressed, perhaps related to the fundamental characteristics of the cells comprising the tumors. For example, there is higher expression levels in MM for several melanoma-associated tumor antigens. (MAGE, CSAG2), genes implicated in melanoma progression (GDF15, MMP14, SPP-1), cell cycle progression (CDK2, TYMS, BUB1), and the prevention of apoptosis (BIRC5, BCL2A1). These changes may reflect the higher growth capacity of the metastatic tumors. Conversely, among the 997 genes with reduced expression in MM samples, many are implicated in keratinocyte differentiation and epidermal development, such as loricrin (LOR), involucrin (IVL), and keratin-5 (KRT5), suggesting a loss of epidermal characteristics. These expression changes suggest important comparative differences between non-metastatic and metastatic tumors.
Analysis of the functional classes of genes changed using gene ontology revealed that 15 genes associated with keratinocyte differentiation and 32 genes involved in epidermis development were down-regulated in the metastatic samples (FIG. 1A). These losses were complemented by the increased expression of genes involved in several cellular processes, such as DNA repair, protein transport, melanocyte differentiation, muscle development, nervous: system development and carbohydrate metabolism. Table 1 further illustrates that the magnitude of change in those genes under-expressed was much greater on average than the level of change in over-expressed genes. Overall, the losses in gene expression are both greater in number and magnitude compared to the gains in gene expression in MM samples.
Another observation is that there are a larger number of genes with reduced expression in the metastatic tumors and the degree of decrease is much greater. In other words, the loss of gene expression is greater than the gain of new gene expression. This is consistent with the observation of dedifferentiation which is believed to occur with the development of cancer.
The initial statistical analysis of microarray samples of metastatic melanoma and non-metastatic cutaneous tumors leads to the conclusion that a fundamental difference exists between tumors containing metastatic potential and tumors without demonstrated metastatic potential. In the case of melanoma, it would appear the metastatic potential is associated with a large number of changes in gene expression and fundamental changes in the spectrum of genes expressed. Any measurement of this programmatic shift in gene expression would be useful for the identification of metastatic melanoma cells within a primary melanoma tumor. The data presented in Table 1 addressed the question of whether there were genes differentially expressed (increased or decreased) between primary (BCC/SCC/PCM) and metastatic cancers (metastatic melanoma). The full names of each gene (for named genes), gene symbol, accession number and gene identification for all genes>2-fold up- or down-regulated in metastatic melanoma are provided in Tables A and B above. FIG. 1B is a heatmap depicting the relative gene expression of the full spectrum of genes described herein in the non-metastatic tumors relative to the metastatic tumors. Darker gray shading corresponds to higher than average gene expression, black corresponds to average gene expression, and light gray correspond to lower than average gene expression. FIG. 1B demonstrates that the combination of genes discovered herein dramatically separates metastatic tumors from non-metastatic tumors.







TABLE 1







Differential gene expression between metastatic


melanoma and non-metastatic cutaneous tumors











Increase in

Decrease in



metastatic

metastatic



melanoma

melanoma



relative to

relative to












Gene
MIS/
BCC/SCC/
Gene
MIS/
BCC/SCC/


symbol
Thin
MIS/Thin
symbol
Thin
MIS/Thin















MAGEA3
125
27
CALML5
193
228


MAGEA1
24
13
DSC1
186
198


MAGEA6
119
25
DSC3
64
71


MAGEA2
57
31
PKP1
166
240


MAGEA12
57
29
CLCA2
162
177


MAGEA5
10
6
DSG3
160
119


CSAG2
76
36
DSG1
160
178


TRIM51
51
35
LY6D
143
147


GDF15
30
47
SERPINB3
111
184


GYPC
18
14
SERPINB5
199
227


SPP1
15
7
SERPINB7
10
144


KIFC1
15
3
C19orf33
122
135


RGS20
14
14
FLG
112
112


C1orf90
13
15
KRT5
49
62


BCL2A1
12
12
KRT17
111
196


SOX5
15
8
KRT16
105
274


SLC16A4
12
29
KLK7
99
112


AKT3
11
9
KLK8
23
32


PEG10
11
10
KLK10
27
81


BUB1
14
3
KLK11
6
83


RASGRF1
8
12
LOR
95
98


MMP14
8
6
LGALS7
84
89


SPRED1
6
4
CST6
82
56


GPR19
6
5
TRIM29
79
119


CDK2
6
7
SFN
77
125


HOXA10
3
4
ASAH3
69
56


HOXB6
4
6
GATA3
63
54


HOXB7
5
7
CBLC
60
64


HOXB9
3
3
RAB25
59
78


HEY1
7
16
S100A14
27
44


DUSP4
8
10
S100A7
57
60


DUSP6
8
6
S100A7L1
21
82


CDC45L
7
8
ICEBERG
52
48


CDC6
9
4
IVL
50
76


RRM2
6
4
ELOVL4
38
34


TYMS
4
3
CXCL14
36
37


BIRC5
4
2
FOXN1
33
34





Abbreviations:


PCM, primary cutaneous melanoma,


MIS, melanoma-in-situ,


BCC, basal cell carcinoma,


SCC, squamous cell carcinoma,


Thin, thin melanomas <1.5 mm in Breslow's thickness.






Example 2
Identification of Gene Expression Differences Between Metastatic and Non-Metastatic Tumor Samples
The relative gene expression levels of 177 genes across the spectrum of tissue samples examined is shown graphically in FIG. 1C. This analysis reveals a consistent level of expression through all of the presumed “non-metastatic” samples (normal skin, BCC, SCC, MIS, Thin). A marked change in the gene expression levels is seen, beginning with the I.M. thickness PCM (average Breslow's tumor thickness of 2.1 mm), progressively increasing or decreasing to the expression level representative of MM lesions. All of the thick PCM (average Breslow's thickness 19 mm) exhibited gene expression patterns similar to those of MM samples and daughter MM cell lines. FIG. 1C demonstrates the sharp contrast between metastatic tumors and non-metastatic tumors or normal skin illustrating how gene expression differences could distinguish between these two classes of tissues. The transition zone also illustrates the class of tumors for which a metastatic assessment is particularly useful. A transition appears to occur as primary melanoma tumors thicken. The thicker primary tumors appear to contain gene expression patterns identical to the metastatic melanoma tumors.
The apparent transition zone of gene expression change could represent a critical time period where many tumorigenic events occur or may simply reflect the outgrowth of an aggressive and/or metastatic cell phenotype. To address this issue, a comparative analysis of gene expression patterns in primary melanomas of different Breslow's thickness was performed. PCM and MM samples were compared to elucidate a possible relationship between relative gene expression patterns associated with PCM of increasing Breslow's thickness and that of MM samples. Table 2 (left columns) reveals the relative change in gene expression for a subset of genes throughout the spectrum of primary melanoma tumors to MM samples.
Several genes, such as the MAGE genes, exhibited a steady and consistent increase in gene expression over the entire range of tumor thicknesses. However, a single major shift in expression was observed for most genes when thinner primary tumors were directly compared to thicker ones. This was most apparent when comparing I.M. thickness to thick PCM, with the majority of genes showing the greatest increase in gene expression. Notable exceptions were genes such as SPP1, HOXA10 and MMP14, for which the greatest differential increase in expression was at the comparative interface between thin and I.M. thickness tumor samples. Other genes, such as MMP19, CTH, PDGFRL, C16 orf34 and GPR19, showed the greatest comparative increase in expression when comparing MIS to thin PCM lesions.
A similar phenomenon was observed for genes with decreased expression in primary tumors relative to more advanced lesions (Table 2, right columns). Here, however, the largest proportion of the gene expression change occurred between thick PCM and MM samples. Very little expression of keratins (6B, 16, 17) and SPRR1 (A, B) was observed in MM compared to all primary melanomas, including thick lesions. Several genes, such as TMPRSS4, STAR, ST7L, HAS3, FGFR3, CASZ1 and HR, were found to have gene expression changes at the very earliest stages of tumor thickening. Together, the gene expression patterns do not shift in a coordinated fashion as would be expected as the result of the outgrowth of a clonal aggressive or metastatic cell type. Rather a series of events may occur as PCM tumors thicken that may influence the expression of different groups of genes ultimately leading to the fully metastatic cell type. This data indicates that some gene expression changes may be indicative of earlier events in the progression to full metastasis. The indicated changes in gene expression may signal that cells in primary melanoma tumors are progressing to a fully metastatic-state or that have already acquired the metastatic state. In either case, the genes are useful markers for identifying aggressive tumors which warrant more aggressive treatment.
All annotated genes listed in Table 2 with a “<2” indicates that any difference between tumors for each comparative analysis was less than 2-fold. Underlined numbers indicate the greatest change in gene expression across varying PCM tumor thickness for each gene.







TABLE 2







Comparative analysis of gene expression changes in primary and


metastatic melanoma.











Relative increase in gene expression

Relative decrease in gene expression


















Gene
MIS to
Thin
IM to
Thick
MIS to
Gene
MIS to
Thin
IM to
Thick
MIS to


Symbol
Thin
To IM
Thick
to Met
Met
Symbol
Thin
To IM
Thick
to Met
Met





















MAGEA2
<2
  8.6
9.4
3.1
30.7
SPRR1A
<2
<2
<2  
129.4 
239.3


MAGEA3
<2
  8.1
10.7 
3
83.8
SPRR1B
<2
<2
<2  
52.8 
100.8


MAGE A6
<2
  7.1
9.8
2.7
103
KRT16
<2
<2
<2  
68.3 
195.5


MAGEA1, 2
<2
  2.5
8.9
2.6
81.5
KRT17
<2
  2.6
<2  
27.4 
57.6


MAGE A1
<2
<2
11.1 
<2
25.4
KRT6B
<2
<2
<2  
39.7 
100.9


MAGE A5
<2
  2.2
3.9
<2
11.7
AQP3
<2
<2
3.2
6.1
43.2


MMP19
  5.4
<2
<2  
<2
7.4
CD24
<2
<2
2  
4.4
18.7


PDGFRL
  22.3
  3.6
<2  
<2
6.3
FLG
<2
<2
3  
24.1 
140


C16orf34
  5.4
<2
<2  
<2
18.5
IVL
<2
  2.2
<2  
13.9 
84.1


CTH
  3.9
<2
<2  
<2
8.8
KLK7
<2
<2
6.5
8.9
128


GPR19
  4.2
<2
3  
<2
23.9
LGALS7
<2
<2
3.4
17.3 
109.3


SPPI
<2
  13.1
<2  
<2
44.9
LOR
<2
<2
2.4
22.6 
120.4


HOXA10
<2
  3.3
<2  
<2
3.8
RAB25
<2
<2
3.3
10.3 
88.4


MMP14
<2
  3.6
<2  
2.1
9
SFN
<2
<2
<2  
10.6 
24.2


AKT3
<2
<2
7.5
<2
14.3
C19orf33
  3.1
<2
4.6
13.3 
220.3


BCL2A1
<2
  2.2
4.8
<2
18.7
ASAH3
<2
<2
25.9 
<2  
60


BIRC5
<2
<2
3.7
<2
3.4
KRT15
<2
<2
27.1 
2.2
104.9


BUB1
<2
<2
9.4
<2
10.8
ELOVL4
<2
  2.3
14.7 
<2  
41.9


CDC45L
<2
<2
13  
<2
9.1
GATA3
  2.5
<2
14.3 
<2  
23.5


CDK2
<2
<2
4.8
<2
8.4
MUC15
<2
  2.2
11.9 
<2  
25


CSAG2
<2
<2
19.6 
2.6
54.5
SCEL
<2
<2
28.8 
<2  
71.8


DUSP4
2
<2
5.7
<2
12.5
TP73L
<2
<2
5.5
3.4
41.2


DUSP6
<2
<2
3.7
<2
10.5
RORA
<2
<2
6.2
2.2
26.6


GYPC
<2
<2
12.2 
<2
14.2
POU2F3
<2
<2
13.9 
2.2
73.9


HEY1
<2
<2
5.7
<2
9.3
ICEBERG
<2
  2.7
6.7
4.5
32.3


KIFC1
<2
<2
10.4 
<2
16
CASZ1
<2
  4.8
2.8
<2  
12.3


PEG10
<2
  2.4
4.1
<2
11.3
HR
<2
  3.7
<2  
<2  
7.7


RASGRF1
<2
<2
5.1
<2
9.9
TMPRSS4
  8.7
<2
<2  
3.1
42


RGS20
  3.4
<2
9.2
<2
34.3
STAR
  4.9
<2
<2  
<2  
11.1


SLC16A4
<2
<2
4.4
<2
26.4
ST7L
  4.3
<2
3.6
<2  
8.4


SOX5
<2
<2
12.3 
<2
19.8
LTB4R
 4
<2
2.3
<2  
9.9


TRIM51
<2
  3.1
15.9 
<2
63.6
HAS3
  4.9
<2
<2  
2.5
16.6


TYMS
<2
<2
3.6
<2
4.7
FGFR3
  3.9
<2
3.2
<2  
7.6





Abbreviations:


MIS, melanoma-in-situ,


Thin, thin melanomas <1.0 mm in Breslow's thickness,


I.M., intermediate thickness between 1-4 mm, with thick melanomas >4 mm.






Example 3
Comparative Genomic Analysis of Normal Human Epithelial Melanocytes to Primary and Metastatic Melanoma Samples
Gene expression profiles of cultured NHEM were compared to PCM and MM samples (Table 3), acknowledging the inherent limitations associated with the comparisons of cultured cells and freshly procured tumor samples. Large differences in gene expression were observed between NHEM and early, non-metastatic PCM (MIS/thin lesions only) and MM samples. Concordant over-expression of genes were found for both comparisons, in particular for such genes as KRT14, GJA1, S100A7(A9) and EHF. Other genes, like the melanoma associated antigens, MAGE A2 and TRAG and PRAME were also found to be highly over-expressed in NHEM to early primary or MM samples. Similarly, a marked decrease in gene expression was observed for several genes, although of a lesser magnitude than seen for the over-expressed genes. Several unique genes including PAEP, HES6, ESDN, NR4A3, c6orf168 and BCL2A1, were under-expressed in NHEM compared to thin PCM. Other genes were also identified as under-expressed in both groups, such as CITED-1, GDF15, QPRT, OCA2, c-MET and MME.







TABLE 3







Comparative gene expression levels of normal human epithelial


melanocytes to thin primary cutaneous and metastatic melanoma samples








Comparative Increase
Comparative Decrease


in Gene Expression (Fold Change)
in Gene Expression (Fold Change)

















NHEM c/t



NHEM c/t


Gene
NHEM c/t
Gene
Metastatic
Gene
NHEM c/t

Metastatic


Symbol
MIS/Thin
Symbol
Melanoma
Symbol
MIS/Thin
Gene Symbol
Melanoma

















KRT14
6787
GJA1
759
MME
106
MAP4
20


GJA1
5929
SEPP1
338
CITED1
77
OCA2
10


EHF
5487
KRT14
306
GDF15
64
TRIM7
7


SCEL
3931
MAGEA2
301
PAEP
47
CITED1
6


CLCA2
3689
TRAG3
242
RPEL1
45
TRPM4
6


S100A7
3609
EHF
193
HES6
43
MME
5


KRTDAP
3416
S100A9
160
ESDN
37
TRAP150
5


DSC1
2782
S100A7
129
QPRT
35
FER1L3
4


GJB6
2576
SCEL
126
OCA2
19
QPRT
4


CXCL14
2484
SLC22A3
125
RENBP
17
KLF8
4


LOR
2308
EPHA3
124
NR4A3
16
RPEL1
4


KRT6A
1989
KRTDAP
121
Stat7c
16
PACE4
4


PKP1
1835
S100A8
120
C6orf168
15
HPCAL1
4


SERPINB3
1778
ZIC1
119
BCL2A1
14
ACTR1A
4


S100A9
1768
CXCL14
118
NTT73
14
MET
3


KRT15
1545
IL18
108
PSCD3
14
RAB32
3


GATA3
1347
PRAME
102
HPCAL1
13
TYR
3


PPL
1339
MAGEA6
94.7
MET
12
IRF6
3


IMUP
1250
PLCB4
88
ALS2CR3
12
GDF15
3


ICEBERG
1123
CLCA2
87
PTPLA
12
HINT3
3


KRT6B
1114
GJB6
85
TBC1D7
11
SLC30A1
3


CSTA
693
MAGEA3
84
OA1
11
TRPV2
3


CST6
687
MMP19
59
TYR
11
RSN
3









Example 4
Identification of Putative Oncogenes and Tumor Suppressor Genes in Melanoma
A perusal of the gene expression differences between PCM and MM samples identifies numerous putative oncogenes and tumor suppressor genes (TSG). Table 4 lists several oncogenes and TSG previously implicated in tumor types. The gene with the largest increase in expression (13.2 fold) was SPP-1 or osteopontin. Although not previously identified as an oncogene, osteopontin expression has been shown to correlate with melanoma invasion and tumor progression (Zhou et al., J. Invest. Dermatol. 124:1044-1052, 2005). The lineage-specific oncogene, MITF, previously shown to act as a master regulator of melanocyte development and a critical survival oncogene amplified in melanoma showed a 3.7 fold increase (Garraway et al., Nature. 436:33-35, 2005; Levy et al., Trends Mol. Med. 12:406-14, 2006; McGill et al., J. Biol. Chem. 281:10365-10373, 2006). Of the other genes, GDF15, c-Met and the HOX loci have been shown to act as possible oncogenes in breast cancer, squamous cell lung cancer, prostate and pancreatic cancer. Several of the putative melanoma TSGs have also been previously shown to contribute to the development and progression of cancer in other tumor histologies.
The shifts in gene expression occur at different stages of the thickening process for each of the oncogenes and TSGs listed in Table 4. Some of the genes show a progressive and steady increase or decrease in gene expression as tumors of greater thickness are compared. But for others, such as the oncogenes SPP-1 and GDF15, and the TSGs PITX-1 and CST6, the major shifts in gene expression appear to occur at distinct but different times during the thickening of the primary melanoma tumors. This observation strongly suggests that these changes may occur spontaneously but eventually accumulate to contribute to the final metastatic phenotype.
Table 4 contains a partial list of identified tumor oncogenes and tumor suppressor genes (TSG's) in PCM and MM samples. The fold increase represents the greatest fold change noted throughout all comparisons of each PCM tumor thickness to MM. The activating/suppressive mechanism and affected tumor type are also identified.







TABLE 4





Differential expression of putative tumor oncogenes and suppressor


genes in melanoma







Oncogenes












Fold
Interval of
Activating Mechanisms in other



Gene
Increase
Increase
Tumor Histologies
Affected Tumor Types





SPP-1
13.2
Thin to IM
C-Met activation via αvβ3
Breast, HCC, Prostate,





receptor, Inhibition of apoptosis
CRC, Head & Neck


MITF
3.7
Progressive
Somatic alteration via gene
None, Lineage Specific




increase
amplification (Chr.#3p13-3p14)
for Melanoma


CITED-1
12.4
IM to Thick
Activation of Stat-3, Ras/MAPK
Thyroid


(cbp/p300


kinase signaling via Ets1, Ets2


transactivator)


GDF15
22.7
IM to Thick
Lineage specific activation or
Breast, CRC, Gastric,


(PLAB)


repression of ERK1/2; Integrator of
Prostate, Pancreatic





AKT pathway


c-Met
14.5
Thick to Met
Ras-Associated Protein
CRC, Breast, Ovarian,





(Rap1)/ERK/MAPK, rac1, Grb2,
Pancreatic, Liver





P13K, src activation


HOX Locus
2.1-5.0
Progressive
Downstream activation of WT-1,
AML, Breast, SCLC


(A3, A10, B6,

increase
NFKB, NR4A3, BCI.2, p53


B7, B13)










Tumor Suppressor Genes












Fold
Interval of
Suppressor Mechanisms in other



Gene
Decrease
Decrease
Tumors Histologies
Affected Tumor Types





PITX-1
13.9
Thin to IM
Ras Pathway (RASAL1)
Barrett's [Esophagus]






Prostate, Bladder


CST6 (CST
66.7
IM to Thick
Hypermethylation
Breast, Glioma


E/M)


PDGFRL
7.3
IM to Thick
Gene Deletion from Chr.#
HCC, CRC, NSCLC





8p21.3-p22


DSC3
42.8
Progressive
Hypermethylation
Breast




decrease


POU2F3
49
Thin to IM
Hypermethylation
Cervical


CLCA2
162
MIS/Thin to MM
Hypermethylation
Breast





Abbreviations:


HCC, hepatocellular carcinoma,


CRC, colorectal carcinoma,


NSCLC, non-small cell lung cancer,


SCLC, squamous cell lung cancer,


AML, acute myelogenous leukemia.






Example 5
Validation of Select Candidate Genes by Semi- and Quantitative RT-PCR Analysis
To further validate the expression of putative TSG and oncogenes in our melanoma panel, real-time quantitative polymerase chain reaction (RT-qPCR) assays were performed on 20 previously arrayed samples, comprised of 7 PCM and 13 mM samples. The results are depicted in FIG. 2A, which shows an overall decreased level of mRNA expression of TSG and increased mRNA expression of oncogenes compared to normal skin, which was used to calibrate the expression levels to a value of zero for graphing purposes. FIG. 2A also shows that the MM samples expressed decreased levels of TSGs and increased levels of oncogenes relative to the PCM samples. This was consistent for all PCM samples compared to MM, although not statistically significant for comparisons across different thicknesses of PCM. FIG. 2B shows the original microarray data normalized and graphed in a manner identical to the PCR data. A significant correlation for all TSG and oncogenes examined was found. Utilizing semi-quantitative PCR analysis, several primary and MM: daughter cell lines derived from the freshly procured melanoma samples, normal skin and NHEM, were examined for oncogene and TSG mRNA expression. The results are depicted in FIG. 3A. Several of the cell lines exhibited high levels of expression for several of the reported oncogenes while there was a much higher percentage of loss of TSG expression seen in most cell lines examined. Overall, a favorable correlation was observed between the microarray results and both quantitative and semi-quantitative PCR analysis for daughter and non-daughter primary and MM cell lines. A subset of the genes listed in FIG. 3A are useful for evaluating metastatic and non-metastatic phenotypes. Those genes are included in Tables A and B, above.
FIG. 3B depicts the expression level of several oncogenes an TSGs cell lines derived from normal human melanocytes, normal skin, and cell lines derived from tumor samples. In general, oncogenes are more highly expressed in the cell lines derived from tumors and TSGs are more highly expressed: in the normal skin and normal human melanocytes consistent with their role as possible markers of the metastatic state. These measurements were made with semi-quantitative PCR, demonstrating that alternative measures of gene expression can distinguish the metastatic signature.
Example 6
Functional Analysis of Select Candidate Genes by Western Blot Analysis and Immunohistochemistry
To independently verify and validate the gene expression changes at the protein level, protein expression of several suspected oncogenes and TSG was examined using Western Blot analysis. Osteopontin (SPP-1) protein expression was examined, both from melanoma cell lysates and conditioned cell free media derived from 2 primary and 6 MM daughter cell lines (FIG. 3B, a, b). Interestingly, the protein expression level of 2 subcutaneous melanoma nodules (MCC 12A, 12F) procured from the same patient with MM differed. Similarly, two paired cell lines (MCC80a from a primary melanoma from a synchronous metastatic lymph node, MCC80b), noting a slight increase in SPP-1 protein expression in the latter. Several other melanoma cell lines exhibited minimal SPP-1 protein expression. (MCC12F, 66C, 80a and 89). Similar findings were noted between melanoma cell lysates and conditioned cell media.
Analysis of suspected TSG in 3 primary and 3 metastatic melanoma cell lines revealed a very low level of protein expression of DSC3 in 6/6 cell lines (FIG. 3B, panel c) with 4/6 (2/3 primary and 2/3 MM) cell lines expressing the protein for CLCA2 (FIG. 3B, panel d). Interestingly, PDGFRL protein expression was observed in a single primary cell line, with no evidence of expression in any of the metastatic cell lines (FIG. 3B, panel e). The cellular staining patterns of skin and melanoma samples are available for viewing at the Human Protein Atlas website (world wide web address at proteinatlas.org/). These observations demonstrate that analysis of protein expression (e.g., antibody-based assays) can be used as measures of gene expression for the identification of metastatic melanoma in primary cutaneous tumors.
The molecular analyses described herein clearly identifies distinct molecular profiles associated with MM which are different from PCM, SCC, and BCC as well as normal melanocytes and skin. Using the refined gene list (Tables A and B), the metastatic character of tumors (SCC/BCC/PCM/MM) can be classified correctly greater than 90% of the time. One major difficulty is classification of thick primary melanoma tumors, where occasionally, these tumors appeared to have the gene expression signature of MM. It was discovered that these tumors represent primary tumors which have already acquired the metastatic gene expression pattern. Detection methods that examine expression of the gene combinations described herein allow identification of such tumors and inform subsequent clinical decisions.
In conclusion, a clear pattern of gene expression change was observed in the non-metastatic and metastatic samples examined. There is a clear point of transition in gene expression when comparing I.M. to: thick PCM, revealing specific groupings of genes involved in this process. Several of these genes and combinations thereof have never before revealed as functional or relevant in melanoma. The specific genes involved in this dynamic and fluid change in gene expression provides the basis for the determination of whether a thin, I.M., or thick PCM has the genetic capability to metastasize and facilitate the development of an appropriate treatment strategy.
Example 7
Materials and Methods
Tumor specimens. Tumor samples were surgically procured from patients with primary cutaneous melanoma (PCM), squamous cell carcinoma (SCC), basal cell carcinoma (BCC) and metastatic melanoma (MM) over a 3 year period. All samples were obtained under an Investigational Review Board (IRB) approved tissue procurement protocol (MCC#13448, IRB#101751; PSM#990914-JM, 020318-JM). Upon surgical removal of the primary melanoma, a single surgical oncologist (A.I.R.) utilized a scalpel to macrodissect and procure a portion of the remaining primary tumor, with a similar technique utilized for grossly involved lymph nodes where the melanoma had completely replaced the lymph node. Samples were taken from non-necrotic areas of the tumor. The same process was performed for all distant metastases, with care taken to avoid surrounding tissues and stroma.
All samples were cryopreserved in liquid nitrogen and stored within the Tissue Procurement Laboratory of the Moffitt Cancer Center, securely de-identified through a centralized database. Forty MM samples were analyzed, composed of 22 bulky, macroscopic (replaced) lymph node metastases, 16 subcutaneous and 2 solid organ metastases (adrenal and brain). These MM samples were compared with 42 primary cutaneous cancers (16 PCM, 11 SCC, 15 BCC). PCM consisted of 2 melanoma in situ (MIS), 2 thin melanomas (<1 mm), 3 intermediate-thickness melanomas (1-4 mm), and 9 thick melanomas (>4 mm). Additionally, 4 samples of normal human skin and 1 sample of cultured NHEM were included. All MM samples were procured from patients that had failed multiple previous therapies, ranging from single agent Interferon, single or multi-agent chemotherapy, immunotherapy or other experimental treatment options. All primary cutaneous cancers were procured from previously untreated patients.
RNA isolation, purification and hybridization. A portion of each cryopreserved tissue sample was dissolved in TRIzol® (Invitrogen, Carlsbad, Calif.), purified according to manufacturer's recommendations, and further purified on RNeasy columns (Qiagen Inc., Valencia, Calif.). RNA integrity was verified by both gel electrophoresis and the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, Calif.). A total of 5 μg of RNA was processed using established Affymetrix protocols for the generation of biotin-labeled cRNA and the hybridization, staining, and scanning of arrays as outlined in the Affymetrix technical manuals (Van Gelder et al., Proc. Natl. Acad. Sci. U.S.A. 87:1663-1667, 1990; Warrington et al., Physiol. Genomics. 2:143-147, 2000). The processed RNA was hybridized to Human Genome U133 Plus 2.0 arrays from Affymetrix, Inc. (Santa Clara, Calif.), and scanned on an Affymetrix GeneChip® scanner 3000 at 2.5 μm resolution. A more complete description of this process is available in Dobbin et al., Clin. Can. Res. 11:565-572, 2005. The tissue samples were processed in three independent groups.
Cell lines and tissue culture. Freshly excised melanoma samples were placed into culture media (RPMI 1640+5% FCS) and tissue procurement and expansion of daughter cell lines was established utilizing previously published techniques (Riker et al., Can Detect and Prev, 23(5):387-96, 1999; Riker A I. The isolation and culture of melanoma cell lines. In: Langdon S, editor. Cancer cell culture: Methods and protocols. Totowa: Humana Press; pp. 93-100, 2004). All cell lines were split and passaged<10 times and, characterized by flow cytometry and/or cytospin preparation for cellular confirmation of melanoma cell purity (data not shown). The cell lines, TC077 and TC80a were derived from primary melanoma samples with TC80b derived from a metastatic lymph node (from the same patient). The cell lines, TC12A and TC12F, were derived from 2 different subcutaneous melanoma nodules from: the same patient. There were 3 cell lines examined from metastatic samples, TC66C, TC72 and TC89. The NHEM were cultured according to the manufacturer directions. (Cambrex BioScience, Walkersville, Md.).
Semi and real-time quantitative RT-PCR. First-strand cDNA synthesis was performed using Superscript III RT (Invitrogen). Subsequently, the cDNA was used in semi-quantitative PCR. Each sample was normalized with β-Actin as an internal control, comparing each sample with AlphaEase®FC image analysis software (Alpha Innotech, San Leandro, Calif.), followed by densitometric analysis of the integrated values for each sample. The expression levels of putative oncogenes and tumor suppressor genes were analyzed by real-time quantitative RT-PCR (qPCR) using Assays-on-Demand. Gene Expression Assays (Applied Biosystems, Foster City, Calif.): SPP1 (osteoponin, assay ID Hs00167093_m1), GDF15 (growth differentiation factor 15, assay ID Hs00171132_ml), PITX1 paired-like homeodomain transcription factor1, assay ID Hs00267528 ml), DSC3 (desmocollin 3, assay ID Hs00170032_m1), CST6 (cystatin E/M, assay ID Hs00154599), POU2F3 (POU domain, class 2, transcription factor 3, assay ID Hs00205009) and GAPDH (assay IDHs99999905_m1) as the internal standard. Utilizing normal skin as the calibrator, the relative quantitation values of a target template for each sample were expressed as 2−ΔΔCt. Briefly, qPCR analysis was performed utilizing 40 ng of total cDNA in a 25 μl reaction volume (Applied Biosystems). QPCR was performed utilizing established techniques, with all samples performed in triplicate and run on an ABI/PRISM 7500 Sequence Detector System (Applied Biosystems).
Gene microarray analysis and bioinformatics. Affymetrix MAS 5.0 analysis software was used to generate signal values for all probe sets based upon a mean intensity of 500, subsequently exported and iteratively normalized as a whole group to create the final normalization based upon the most stable gene expression measurements across all samples (Li et al., Proc. Natl. Acad. Sci. U.S.A. 98:31-36, 2001). This process was performed for the initial group of tumor samples to generate the list of normalization probesets that were subsequently used to scale all samples processed for this study to an average intensity of 4000 for the normalization probesets. Following scaling, the calculated signal values were then used to calculate the average expression level for each gene in each tissue type using an initial group of 23 tumor samples. The average expression values derived from this initial set were directly compared to identify genes expressed at high levels in one tumor type but not in the other samples using a t-test and visual inspection to find highly differential expression patterns. Genes highly expressed in metastatic melanomas but not primary melanomas, basal cell carcinomas, or squamous cell carcinomas, were sought. Several genes were initially selected that exhibited the idealized gene expression profiles. Additional candidate genes were then identified by using Pearson's correlation between the idealized gene expression patterns and all other probe sets on the arrays. Positively correlated (r>0.7) and negatively correlated (r<0.7) genes were identified and trimmed to include only those with a 2-fold or greater difference in the average gene expression level between metastatic samples and non-metastatic tumors. This initial gene expression survey identified 2014 Affymetrix probe sets from the U133 Plus 2.0 arrays that showed differential expression between metastatic tumor samples and non-metastatic tumor samples.
The 2014 probe sets identified as correlating with the metastatic phenotype were used to cluster the samples. Following normalization, as described above, the signal values were log 2 transformed. Each probe set was then mean centered across all samples and the resulting values were input into Eisen's cluster. Hierarchical clustering was performed using absolute correlation and a complete linkage. Clustering was performed with various subgroups of the data or with all samples together and resulted in similar sample groupings. Individual samples were classified based on the class of the other samples in the closest cluster. The complete microarray data is available from the Gene Expression Omnibus (world wide web address: ncbi.nlm.nih.gov/geo/) under Accession number GSE7553.
Serial Analysis of Microarrays (SAM) was performed in order to identify a more extensive list of differentially expressed genes expressed between PCM and MM. Two comparisons were made to generate a comprehensive and yet confident list of genes that are differentially expressed between metastatic melanoma and non-metastatic melanomas. In the first comparison, the metastatic melanoma samples were opposed by all the non-metastatic samples including basal and squamous cell carcinoma and normal skin. The false discovery rate threshold used to limit the gene list was 0% for this comparison. Because of the number of samples, this provides good statistical confidence but does not focus on the differences between primary melanoma and metastatic melanoma. A second comparison was performed utilizing 6 thin primary melanoma samples in opposition to 6 randomly selected metastatic melanomas. The only non-random aspects of this sample selection were to avoid selecting samples in which the classifier disagreed with the pathologist's diagnosis and to avoid utilizing more than one sample from the same individual. For this comparison the median false discovery rate threshold was set at 5%. This latter analysis is the preferred grouping of samples, but because of the small sample size it is also more likely to generate false discoveries due to noise and outlier samples. Therefore the more confident gene list generated by combining the two analyses. The intersection of the two approaches yielded 1,352 probe sets with higher expression in the metastatic samples and 2,991 probe sets with higher expression in non-metastatic samples. This list was further reduced by removing probe sets that did not appear to have a difference greater than 2-fold on average between the two groups.
Following all microarray analyses, the identified probe sets were annotated based on the sequence of the probes used on the arrays (Harbig et al., Nucleic Acids Res. 33:e31, 2005).
Western blot analysis. Whole cell extracts from PCM and MM cell lines were prepared by directly lysing cells in SDS sample buffer. Expression of SPP-1 protein was assessed in cell lysate and serum-free conditioned medium. Briefly, 4×106 cells were plated in 5% FBS containing medium; 24 hours later, the growth medium was replaced with serum-free medium. The conditioned media and cell lysates were harvested 24 hours later and resolved using a 12.5% SDS-PAGE. Proteins were transferred to a PVDF membrane and probed with the anti-human SPP-1 mouse monoclonal antibody (Sigma, St. Louis, Mo.) (1:1000) followed by a secondary antibody conjugated to horseradish peroxidase (Amersham Biosciences, Piscataway, N.J.) and detected using chemiluminescence (Santacruz Biotechnology, Santa Cruz, Calif.). The osteopontin band (SPP-1) was visualized at  ̃55-65 kDa. Daughter melanoma cell lines derived from the freshly procured melanoma samples (with the exception of A375) were lysed by M-PERTM Mammalian Protein Extraction Reagent (Pierce, Rockford, Ill.) and processed according to manufacturer instructions. A total of 15 μg of protein from each experimental condition were electrophoresed on 10% SDS-PAGE and transferred to nitrocellulose membranes (Bio-Rad, Hercules, Calif.). Immunostaining was performed with the following primary antibodies: DSC3 (Santa Cruz) 1:200; CLCA2 (Novus Biologicals, Littleton, Colo.) 1:500; PDGFRL (Novus Biologicals) 1:500; α-tubulin (Cell signaling, Danvers, Mass.), 1:1000. Immunocomplexes were visualized using an enhanced chemiluminescence (ECL) Western Blotting Substrate (Pierce). The intensity of the bands were scanned with a Fujifilm intelligent dark box II and analyzed with Fujifilm Las-1000 Lite V1.3 software.
A number of embodiments of the technology have been described. Nevertheless, it will be understood that various modifications may be made without departing from the spirit and scope of the technology. Accordingly, other embodiments are within the scope of the following claims.

## Claims

1. A method of evaluating a melanoma from a patient, the method comprising:
determining mRNA levels of five or more genes selected from the group consisting of: tripartite motif-containing 51 (TRIM51) (SEQ ID NO:1); Glycophorin C (Gerbich blood group) (GYPC) (SEQ ID NO:2); SRY (sex determining region Y)-box 5 (SOX5) (SEQ ID NO:3); kinesin family member C1 (KIFC1) (SEQ ID NO:4); SEC22 vesicle trafficking protein-like 3 (S. cerevisiae) (SEC22L3) (SEQ ID NO:5); and secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1) (SPP1) (SEQ ID NO:6) in a test sample comprising melanoma cells from the patient, and
comparing said mRNA levels to a set of reference levels that represent levels of the mRNAs in a sample comprising cells from a non-metastatic melanoma,
wherein an increase in expression of said five or more genes indicates an increased likelihood that the melanoma is a metastatic melanoma.

2. The method of claim 1, wherein miRNA levels of all six genes are determined.

3. The method of claim 1, wherein mRNA levels of the five or more genes is determined relative to mRNA levels of the five or more genes in a reference set of non-metastatic cutaneous tissue samples, and wherein an increase in expression of said five or more genes, relative to expression of the five or more genes in the reference set, indicates an increased likelihood that the melanoma is a metastatic melanoma.

4. The method of claim 1, wherein mRNA levels of the five or more genes is compared to: (a) mRNA levels in a first reference set of non-metastatic cutaneous tissue samples, and (b) mRNA levels in a second reference set of metastatic melanoma tissue samples; wherein a greater similarity in mRNA levels of the five or more genes in the test sample to the second reference set than to the first reference set indicates an increased likelihood that the melanoma is a metastatic melanoma.

5. The method of claim 1, wherein determining mRNA levels of five or more genes in the test sample comprises isolating RNA from the test sample, and detecting expression of the RNA.

6. The method of claim 5, wherein determining mRNA levels of five or more genes in the test sample comprises performing reverse transcriptase polymerase chain reaction.

7. The method of claim 5, wherein determining mRNA levels of five or more genes in the test sample comprises performing microarray analysis.

8. The method of claim 1, wherein the test sample is a test sample from a primary melanoma.