Table 1. The most significantly over-expressed genes^a shared in comparisons of primary melanomas vs benign nevi and metastatic vs non-metastatic primary melanomas by Significance Analysis of Microarrays (SAM) (ordered by SAM score of metastatic vs non-metastatic primary melanomas).

Gene	Gene description	Probe set ID	Mean ± Sthev		Foldb	SAM Scorec	Foldb
			Non-metastatic primary melanomas	Metastatic primary melanomas	Metastatic vs non-metastatic	Metastatic vs non-metastatic	Melanomas vs nevi
TIMP1	TIMP metallopeptidase inhibitor 1	201666_at	1854 ± 833	5666 ± 2639	3.1	3.863	2.3
VCAN	Versican	204620_s_at	1047 ± 434	2466 ± 943	2.4	3.788	2.8
SPP1	Secreted phosphoprotein 1	209875_s_at	323 ± 218	4053 ± 3159	12.6	3.258	50.2
CTHRC1	Collagen triple helix repeat containing 1	225681_at	1307 ± 610	3127 ± 1450	2.4	3.240	4.1
SERPINH1	Serpin peptidase inhibitor, clade H, member 1	207714_s_at	536 ± 147	1114 ± 443	2.1	3.221	1.9
LGALS1	Lectin, galactoside-binding, soluble, 1	201105_at	3938 ± 1119	8473 ± 3897	2.2	3.144	1.6
SULF1	Sulfatase 1	212354_at	173 ± 58	483 ± 231	2.8	3.093	3.1
COL4A1	Collagen, type IV, alpha 1	211981_at	496 ± 222	953 ± 336	1.9	3.011	3.0
THY1	Thy-1 cell surface antigen	213869_x_at	347 ± 116	659 ± 242	1.9	2.869	2.6
MME	Membrane metallo-endopeptidase	203435_s_at	185 ± 50	401 ± 165	2.2	2.825	2.1
LOC541471 / NCRNA00152	Hypothetical LOC541471 / non-protein coding RNA 152	225799_at	448 ± 237	1140 ± 623	2.5	2.786	4.7
C13orf18	Chromosome 13 open reading frame 18	219471_at	184 ± 74	363 ± 124	2.0	2.763	1.7
HEY1	Hairy/enhancer-of-split related with YRPW motif 1	44783_s_at	564 ± 353	1720 ± 1093	3.1	2.762	2.7
LOXL2	Lysyl oxidase-like 2	202998_s_at	211 ± 88	416 ± 147	2.0	2.756	2.0
IGKC	Immunoglobulin kappa constant	221651_x_at	2934 ± 3593	8942 ± 5389	3.0	2.739	8.4
A2M	Alpha-2-macroglobulin	217757_at	2025 ± 800	3437 ± 1277	1.7	2.687	2.8
ADAM12	ADAM metallopeptidase domain 12	226777_at	63 ± 35	283 ± 183	4.5	2.672	6.1
PARVB	Parvin, beta	37966_at	250 ± 78	490 ± 198	2.0	2.660	1.5
OLFML2B	Olfactomedin-like 2B	213125_at	217 ± 124	457 ± 190	2.1	2.600	2.8
SLC2A3	Solute carrier family 2, member 3	202499_s_at	136 ± 69	446 ± 285	3.3	2.594	3.7
IGHG1 / G2 / M / V4-31	Immunoglobulin heavy constant gamma 1 / gamma 2 / mu / variable 4-31	211430_s_at	2376 ± 3258	8114 ± 5601	3.4	2.585	21.7
ARPC1B	Actin related protein 2/3 complex, subunit 1B	201954_at	1341 ± 451	3177 ± 1927	2.4	2.566	2.1
DAB2	Disabled homolog 2, mitogen-responsive phosphoprotein	201279_s_at	730 ± 401	1528 ± 764	2.1	2.559	1.9
NES	Nestin	218678_at	504 ± 251	1201 ± 691	2.4	2.552	1.6
RNASE1	Ribonuclease, RNase A family, 1 (pancreatic)	201785_at	1494 ± 829	3831 ± 2434	2.6	2.551	2.7
C20orf112	Chromosome 20 open reading frame 112	225224_at	213 ± 70	470 ± 233	2.2	2.532	1.7
KDELR3	KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 3	204017_at	372 ± 118	657 ± 256	1.8	2.520	2.0
THBS1	Thrombospondin 1	201108_s_at	154 ± 48	274 ± 81	1.8	2.491	2.1
VSIG4	V-set and immunoglobulin domain containing 4	204787_at	187 ± 97	553 ± 362	3.0	2.470	2.1
SLC20A1	Solute carrier family 20, member 1	201920_at	499 ± 239	1208 ± 739	2.4	2.461	3.8
RRM2	Ribonucleotide reductase M2	209773_s_at	303 ± 140	693 ± 389	2.3	2.434	3.8
EGR1	Early growth response 1	227404_s_at	2576 ± 936	5552 ± 3324	2.2	2.417	1.9
TMEM158	Transmembrane protein 158	213338_at	175 ± 42	630 ± 484	3.6	2.405	2.7
FN1	Fibronectin 1	210495_x_at	3032 ± 1186	6006 ± 3292	2.0	2.402	2.2
CCL4	Chemokine (C-C motif) ligand 4	204103_at	225 ± 111	557 ± 338	2.5	2.360	3.9
IGKC / IGKV1-5	Immunoglobulin kappa constant / variable 1-5	214836_x_at	600 ± 548	1766 ± 1267	2.9	2.360	4.6
PLAUR	Plasminogen activator, urokinase receptor	210845_s_at	192 ± 88	499 ± 315	2.6	2.336	2.4
FCGR2A	Fc fragment of IgG, low affinity IIa, receptor	203561_at	97 ± 54	490 ± 425	5.1	2.333	4.9
CALU	Calumenin	200755_s_at	702 ± 231	1251 ± 591	1.8	2.317	2.0
CDKN3	Cyclin-dependent kinase inhibitor 3	209714_s_at	157 ± 57	291 ± 109	1.9	2.313	3.0
SH2B3	SH2B adaptor protein 3	203320_at	287 ± 145	593 ± 307	2.1	2.306	2.3
RAB20	RAB20, member RAS oncogene family	219622_at	198 ± 64	562 ± 395	2.8	2.297	1.9
ATP6V0E2	ATPase, H+ transporting V0 subunit e2	213587_s_at	340 ± 92	751 ± 457	2.2	2.272	1.8
IGLC7 / IGLV1-44	Immunoglobulin lambda constant 7 / variable 1-44	215379_x_at	655 ± 752	2434 ± 2071	3.7	2.266	11.6
PLA2G16	Phospholipase A2, group XVI	209581_at	219 ± 145	408 ± 152	1.9	2.244	2.9
GRB10	Growth factor receptor-bound protein 10	209409_at	217 ± 76	463 ± 257	2.1	2.234	1.8
IGLV1-44 / LOC100290481	Immunoglobulin lambda variable 1-44 / immunoglobulin lambda light chain-like	214677_x_at	1483 ± 1970	5704 ± 5106	3.8	2.196	19.4
CYR61	Cysteine-rich, angiogenic inducer, 61	201289_at	350 ± 93	740 ± 451	2.1	2.179	3.3
PCOLCE	Procollagen C-endopeptidase enhancer	202465_at	726 ± 289	1332 ± 712	1.8	2.142	2.1
CHN1	Chimerin (chimaerin) 1	212624_s_at	247 ± 101	457 ± 216	1.8	2.130	2.8
PAPSS2	3′-phosphoadenosine 5′-phosphosulfate synthase 2	203058_s_at	159 ± 74	335 ± 180	2.1	2.113	2.6
FCGR2C	Fc fragment of IgG, low affinity IIc, receptor	210992_x_at	225 ± 90	582 ± 427	2.6	2.095	2.0
MCAM	Melanoma cell adhesion molecule	209086_x_at	326 ± 62	649 ± 387	2.0	2.079	1.6
CCL2	Chemokine (C-C motif) ligand 2	216598_s_at	385 ± 206	1346 ± 1242	3.5	2.076	4.6
CCR1	Chemokine (C-C motif) receptor 1	205099_s_at	109 ± 74	391 ± 333	3.6	2.064	4.0
SLC2A14 / SLC2A3	Solute carrier family 2, member 14 / solute carrier family 2, member 3	216236_s_at	272 ± 71	536 ± 311	2.0	2.050	1.8
FKBP11	FK506 binding protein 11	219118_at	269 ± 119	605 ± 404	2.2	2.047	3.0
BCL2A1	BCL2-related protein A1	205681_at	292 ± 306	682 ± 424	2.3	2.047	3.6
IGLL3P	Immunoglobulin lambda-like polypeptide 3, pseudogene	215946_x_at	175 ± 104	446 ± 317	2.5	2.038	2.8
BST2	Bone marrow stromal cell antigen 2	201641_at	297 ± 145	660 ± 440	2.2	2.037	2.2
EMILIN2	Elastin microfibril interfacer 2	224374_s_at	272 ± 136	593 ± 382	2.2	2.034	1.8

^aOnly annotated genes and the first probe set for each gene are shown. Full gene list is available by request.

^bGenes with ≥2-fold change at least in one of the comparisons are shown.

^cThe FDR q-value for each was <0.001.