Supplemental Data Microarray data analysis. In order to identify differentially expressed genes, we compared the melanoma samples to the benign nevi and the normal skin samples separately. The first analysis consisted of the 45 melanoma and 7 normal skin samples; the second analysis consisted of 45 melanoma and 18 nevi samples (Fig. S1). Significance analysis of microarray (SAM) was performed (17). Parameters for SAM were set as ∆=2.5 and fold change = 2.0 with 1,000 permutations. FDR was 1%. There was no missing data and the default random number was used. Next, percentile analysis was conducted. For up-regulated genes, the 30%ile in melanoma samples was compared to the maximum of the normal samples, or that of nevi samples. Student T-test with Bonferroni correction was also performed with cut-off p<0.05 in order to ensure that the selected genes had significant differential expression between the two groups of the samples. As a final step, we identified common genes between the melanoma/benign and melanoma /normal gene lists and reported a single list of genes up-regulated in melanoma (Table S1). 1 Fig. S1. 22,283 genes on Affymetrix U33a chip 15,795 genes with 2 or more “Present” calls Melanoma vs. Skin Melanoma vs. Benign nevi SAM FDR < 1%, fold-change > 2 2,326 up-regulated genes in cancer 828 up-regulated genes in cancer Percentile analysis Up-regulated in > 30% of melanoma 1,941 genes 527 genes T test with Bonferroni correction P < 0.05 592 genes (439 common genes) 492 genes 2 Table S1. Up-regulated genes in melanoma Median Expression Fold Change Fold Change PSID in Melanoma (Can vs Benign) (Can vs skin) 215025_at 2365 149 93 Consensus includes gb:S76476.1 /DEF=trkC {alternatively spliced} human, brain, mRNA, 2225 nt. /FEA=mRNA /GEN= 215311_at 10093 86 30 Consensus includes gb:AL109696.1 /DEF=Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 21920. /F 213960_at 11768 80 29 Consensus includes gb:T87225 /FEA=EST /DB_XREF=gi:715577 /DB_XREF=est:yc81f06.s1 /CLONE=IMAGE:22392 219478_at 5485 80 18 gb:NM_021197.1 /DEF=Homo sapiens WAP four-disulfide core domain 1 (WFDC1), mRNA. /FEA=mRNA /GEN=WFD 206462_s_at 9953 53 24 gb:NM_002530.1 /DEF=Homo sapiens neurotrophic tyrosine kinase, receptor, type 3 (NTRK3), mRNA. /FEA=mRNA / 218839_at 1996 38 7 gb:NM_012258.1 /DEF=Homo sapiens hairyenhancer-of-split related with YRPW motif 1 (HEY1), mRNA. /FEA=mRN 215115_x_at 12421 34 15 Consensus includes gb:AI613045 /FEA=EST /DB_XREF=gi:4622212 /DB_XREF=est:ty68g03.x1 /CLONE=IMAGE:22 221577_x_at 4897 28 38 gb:AF003934.1 /DEF=Homo sapiens prostate differentiation factor mRNA, complete cds. /FEA=mRNA /PROD=prostate 217377_x_at 12402 27 18 Consensus includes gb:AF041811.2 /DEF=Homo sapiens ETS related protein-growth factor receptor tyrosine kinase fusi 213638_at 1827 26 102 Consensus includes gb:AW054711 /FEA=EST /DB_XREF=gi:5920414 /DB_XREF=est:wz96g08.x1 /CLONE=IMAGE 204709_s_at 312 24 16 gb:NM_004856.3 /DEF=Homo sapiens kinesin-like 5 (mitotic kinesin-like protein 1) (KNSL5), mRNA. /FEA=mRNA /G 221909_at 243 22 17 Consensus includes gb:AW299700 /FEA=EST /DB_XREF=gi:6709377 /DB_XREF=est:xs42g04.x1 /CLONE=IMAGE:2 204584_at 9677 21 15 Consensus includes gb:AI653981 /FEA=EST /DB_XREF=gi:4737960 /DB_XREF=est:ty04c03.x1 /CLONE=IMAGE:22 217033_x_at 10961 21 19 Consensus includes gb:S76475.1 /DEF=trkC human, brain, mRNA, 2715 nt. /FEA=mRNA /GEN=trkC /DB_XREF=gi:9 209875_s_at 3038 21 12 gb:M83248.1 /DEF=Human nephropontin mRNA, complete cds. /FEA=mRNA /GEN=nephropontin /PROD=nephropont 217624_at 349 21 20 Consensus includes gb:AA464753 /FEA=EST /DB_XREF=gi:2189637 /DB_XREF=est:zx86c10.s1 /CLONE=IMAGE:8 203071_at 958 19 3 gb:NM_004636.1 /DEF=Homo sapiens sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semap 213587_s_at 10416 18 9 Consensus includes gb:AI884867 /FEA=EST /DB_XREF=gi:5590031 /DB_XREF=est:wl85g03.x1 /CLONE=IMAGE:24 221815_at 3293 17 144 Consensus includes gb:BE671816 /FEA=EST /DB_XREF=gi:10032446 /DB_XREF=est:7a47d01.x1 /CLONE=IMAGE: 219578_s_at 1419 17 26 gb:NM_030594.1 /DEF=Homo sapiens hypothetical protein FLJ13203 similar to cytoplasmic polyadenylation element bi 207144_s_at 593 17 24 gb:NM_004143.1 /DEF=Homo sapiens Cbpp300-interacting transactivator, with GluAsp-rich carboxy-terminal domain, 203069_at 560 15 13 gb:NM_014849.1 /DEF=Homo sapiens KIAA0736 gene product (KIAA0736), mRNA. /FEA=mRNA /GEN=KIAA0736 63825_at 10096 14 74 Cluster Incl. AI557319:PT2.1_16_F08.r Homo sapiens cDNA, 3 end /clone_end=3 /gb=AI557319 /gi=4489682 /ug=Hs 44783_s_at 8503 14 6 Cluster Incl. R61374:yh15e02.s1 Homo sapiens cDNA, 3 end /clone=IMAGE-37665 /clone_end=3 /gb=R61374 /gi=832 218678_at 11356 14 20 gb:NM_024609.1 /DEF=Homo sapiens hypothetical protein FLJ21841 (FLJ21841), mRNA. /FEA=mRNA /GEN=FLJ21 219152_at 365 13 10 gb:NM_015720.1 /DEF=Homo sapiens endoglycan (PODLX2), mRNA. /FEA=mRNA /GEN=PODLX2 /PROD=endogly 205447_s_at 567 13 5 Consensus includes gb:BE222201 /FEA=EST /DB_XREF=gi:8909519 /DB_XREF=est:hu09a10.x1 /CLONE=IMAGE:3 204585_s_at 805 13 17 gb:NM_000425.2 /DEF=Homo sapiens L1 cell adhesion molecule (hydrocephalus, stenosis of aqueduct of Sylvius 1, MA 213274_s_at 18263 12 26 Consensus includes gb:AA020826 /FEA=EST /DB_XREF=gi:1484570 /DB_XREF=est:ze64b04.s1 /CLONE=IMAGE:3 219555_s_at 402 12 21 gb:NM_018455.1 /DEF=Homo sapiens uncharacterized bone marrow protein BM039 (BM039), mRNA. /FEA=mRNA / 203827_at 3380 11 8 gb:NM_017983.1 /DEF=Homo sapiens hypothetical protein FLJ10055 (FLJ10055), mRNA. /FEA=mRNA /GEN=FLJ10 3 205813_s_at 430 11 9 gb:NM_000429.1 /DEF=Homo sapiens methionine adenosyltransferase I, alpha (MAT1A), mRNA. /FEA=mRNA /GEN= 201850_at 11103 10 20 gb:NM_001747.1 DEF=Homo sapiens capping protein (actin filament), gelsolin-like (CAPG), mRNA. FEA=mRNA G 205373_at 579 10 8 gb:NM_004389.1 /DEF=Homo sapiens catenin (cadherin-associated protein), alpha 2 (CTNNA2), mRNA. /FEA=mRNA 214614_at 542 10 9 Consensus includes gb:AI738662 /FEA=EST /DB_XREF=gi:5100643 /DB_XREF=est:wi11f11.x1 /CLONE=IMAGE:23 213217_at 5848 10 6 Consensus includes gb:AU149572 /FEA=EST /DB_XREF=gi:11011093 /DB_XREF=est:AU149572 /CLONE=NT2RM4 204014_at 7184 10 46 gb:NM_001394.2 /DEF=Homo sapiens dual specificity phosphatase 4 (DUSP4), mRNA. /FEA=mRNA /GEN=DUSP4 /P 214893_x_at 214 10 9 Consensus includes gb:AI421964 /FEA=EST /DB_XREF=gi:4267895 /DB_XREF=est:tf40a10.x1 /CLONE=IMAGE:20 220178_at 5915 9 15 gb:NM_021731.1 /DEF=Homo sapiens hypothetical protein PP3501 (PP3501), mRNA. /FEA=mRNA /GEN=PP3501 /PR 202779_s_at 3400 9 55 gb:NM_014501.1 /DEF=Homo sapiens ubiquitin carrier protein (E2-EPF), mRNA. /FEA=mRNA /GEN=E2-EPF /PROD 207038_at 1986 9 47 gb:NM_004694.1 /DEF=Homo sapiens solute carrier family 16 (monocarboxylic acid transporters), member 6 (SLC16A6 219143_s_at 3618 9 13 gb:NM_017793.1 /DEF=Homo sapiens hypothetical protein FLJ20374 (FLJ20374), mRNA. /FEA=mRNA /GEN=FLJ20 214068_at 2148 9 10 Consensus includes gb:AF070610.1 /DEF=Homo sapiens clone 24505 mRNA sequence. /FEA=mRNA /DB_XREF=gi:3 201954_at 25901 9 15 gb:NM_005720.1 /DEF=Homo sapiens actin related protein 23 complex, subunit 1A (41 kD) (ARPC1B), mRNA. /FEA= 214841_at 913 9 11 Consensus includes gb:AF070524.1 /DEF=Homo sapiens clone 24453 mRNA sequence. /FEA=mRNA /DB_XREF=gi:3 206307_s_at 534 8 4 gb:NM_004472.1 /DEF=Homo sapiens forkhead box D1 (FOXD1), mRNA. /FEA=mRNA /GEN=FOXD1 /PROD=forkh 205681_at 1316 8 12 gb:NM_004049.1 /DEF=Homo sapiens BCL2-related protein A1 (BCL2A1), mRNA. /FEA=mRNA /GEN=BCL2A1 /PR 206503_x_at 419 8 9 gb:NM_002675.1 /DEF=Homo sapiens promyelocytic leukemia (PML), mRNA. /FEA=mRNA /GEN=PML /PROD=pro 205690_s_at 9179 8 9 gb:NM_003910.1 /DEF=Homo sapiens maternal G10 transcript (G10), mRNA. /FEA=mRNA /GEN=G10 /PROD=mater 203878_s_at 2036 8 5 gb:NM_005940.2 /DEF=Homo sapiens matrix metalloproteinase 11 (stromelysin 3) (MMP11), mRNA. /FEA=mRNA /G 211013_x_at 498 8 13 gb:AF230411.1 /DEF=Homo sapiens tripartite motif protein TRIM19 lambda mRNA, complete cds. /FEA=mRNA /PRO 209256_s_at 4949 8 6 gb:AF277177.1 /DEF=Homo sapiens PNAS-119 mRNA, complete cds. /FEA=mRNA /PROD=PNAS-119 /DB_XREF=g 215126_at 4940 8 19 Consensus includes gb:AL109716.2 /DEF=Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 208948. / 214896_at 3071 8 11 Consensus includes gb:AL109671.1 /DEF=Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 29222. /F 200838_at 19225 8 17 gb:NM_001908.1 /DEF=Homo sapiens cathepsin B (CTSB), mRNA. /FEA=mRNA /GEN=CTSB /PROD=cathepsin B /D 213836_s_at 2605 8 5 Consensus includes gb:AW052084 /FEA=EST /DB_XREF=gi:5914443 /DB_XREF=est:wy86f07.x1 /CLONE=IMAGE: 209053_s_at 269 7 10 Consensus includes gb:BE793789 /FEA=EST /DB_XREF=gi:10214987 /DB_XREF=est:601589946F1 /CLONE=IMAG 209827_s_at 4884 7 7 Consensus includes gb:NM_004513.1 /DEF=Homo sapiens interleukin 16 (lymphocyte chemoattractant factor) (IL16), m 214023_x_at 1602 7 9 Consensus includes gb:AL533838 /FEA=EST /DB_XREF=gi:12797331 /DB_XREF=est:AL533838 /CLONE=CS0DF00 209848_s_at 32959 7 74 gb:U01874.1 /DEF=Human me20m mRNA, complete cds. /FEA=mRNA /PROD=me20m /DB_XREF=gi:494939 /UG=H 206696_at 6446 7 191 gb:NM_000273.1 /DEF=Homo sapiens ocular albinism 1 (Nettleship-Falls) (OA1), mRNA. /FEA=mRNA /GEN=OA1 /P 218330_s_at 3853 7 4 gb:NM_018162.1 /DEF=Homo sapiens hypothetical protein FLJ10633 (FLJ10633), mRNA. /FEA=mRNA /GEN=FLJ10 213275_x_at 17604 7 3 Consensus includes gb:W47179 /FEA=EST /DB_XREF=gi:1332046 /DB_XREF=est:zc34d07.s1 /CLONE=IMAGE:324 218952_at 2661 7 7 gb:NM_013271.1 /DEF=Homo sapiens granin-like neuroendocrine peptide precursor (SAAS), mRNA. /FEA=mRNA /G 204033_at 2154 7 7 gb:NM_004237.1 /DEF=Homo sapiens thyroid hormone receptor interactor 13 (TRIP13), mRNA.