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	Supplemental Table 1
	Supplemental Table 2
	Supplemental Table 3
	Supplemental Table 4
	Supplemental Information ISIS splits

	Max Planck Institute for Molecular Genetics
	Deutsche Krebshilfe

Jaeger et al.
Gene expression signatures in melanoma tissues

No.	Affymetrix ID	Gene symbol	Gene description	GOTermsBP	Q value
1.	209875_s_at	SPP1	secreted phosphoprotein 1, (osteopontin)	cell adhesion; cell-cell signaling; cell-matrix adhesion; chemotaxis	<0.01
2.	212353_at	SULF1	sulfatase 1	apoptosis; heparan sulfate proteoglycan metabolism	<0.01
3.	202856_s_at	SLC16A3	solute carrier family 16 (monocarboxylic acid transporters), member 3	monocarboxylic acid transport; organic anion transport; transport	<0.01
4.	213790_at	ADAM12	a disintegrin and metalloproteinase domain 12 (meltrin alpha)	cell adhesion; myoblast fusion; proteolysis and peptidolysis	<0.01
5.	209942_x_at	MAGEA3	melanoma antigen, family A, 3	unknown	<0.01
6.	214612_x_at	MAGEA6	melanoma antigen, family A, 6	unknown	<0.01
7.	203434_s_at	MME	membrane metallo-endopeptidase (CALLA, CD10)	cell-cell signaling; proteolysis and peptidolysis	<0.01
8.	214603_at	psMAGEA	melanoma antigen pseudogene, family A	unknown	<0.01
9.	202952_s_at	ADAM12	a disintegrin and metalloproteinase domain 12 (meltrin alpha)	cell adhesion; myoblast fusion; proteolysis and peptidolysis	0.01
10.	212354_at	SULF1	sulfatase 1	apoptosis; heparan sulfate proteoglycan metabolism; metabolism	0.01
11.	202783_at	NNT	nicotinamide nucleotide transhydrogenase	electron transport; proton transport	0.01
12.	207828_s_at	CENPF	centromere protein F, 350/400ka (mitosin)	DNA replication and chromosome cycle; regulation of mitosis	0.01
13.	202784_s_at	NNT	nicotinamide nucleotide transhydrogenase	electron transport; proton transport	0.01
14.	203435_s_at	MME	membrane metallo-endopeptidase (CALLA, CD10)	cell-cell signaling; proteolysis and peptidolysis	0.01
15.	205066_s_at	ENPP1	ectonucleotide pyrophosphatase/ phosphodiesterase 1	generation of precursor metabolites and energy; nucleotide metabolism; phosphate metabolism; response to nutrients	0.02
16.	201261_x_at	BGN	biglycan	unknown	0.02
17.	210495_x_at	FN1	fibronectin 1	acute-phase response; cell adhesion; cell migration; metabolism; response to wounding	0.02
18.	211719_x_a	FN1	fibronectin 1	acute-phase response; cell adhesion; cell migration; metabolism; response to wounding	0.02
19.	204776_at	THBS4	thrombospondin 4	cell adhesion; substrate-bound cell migration, cell extension	0.02
20.	204030_s_at	SCHIP1	schwannomin interacting protein 1	unknown	0.02
21.	218585_s_at	RAMP	RA-regulated nuclear matrix-associated protein	unknown	0.02
22.	212464_s_at	FN1	fibronectin 1	acute-phase response; cell adhesion; cell migration; metabolism; response to wounding	0.02
23.	213905_x_at	BGN	biglycan	biological process unknown	0.02
24.	212843_at	NCAM1	neural cell adhesion molecule 1	adhesion; cell adhesion; cell-cell signaling; synaptic transmission	0.03
25.	211767_at	SLD5	SLD5 homolog		0.03
26.	206028_s_at	MERTK	c-mer proto-oncogene tyrosine kinase	cell surface receptor linked signal transduction; cell-cell signaling; protein amino acid phosphorylation; visual perception	0.03
27.	202620_s_at	PLOD2	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	protein metabolism; protein modification	0.03
28.	218375_at	NUDT9	nudix (nucleoside diphosphate linked moiety X)-type motif 9	Purine metabolism cation transport	0.03
29.	203968_s_at	CDC6	CDC6 cell division cycle 6 homolog (S. cerevisiae)	DNA replication; DNA replication checkpoint; cell cycle; cytokinesis; mitosis; negative regulation of DNA replication; negative regulation of cell proliferation;	0.03
30.	214511_x_at	LOC440607	Fc-gamma receptor I B2	immune response	0.03
31.	201521_s_at	NCBP2	nuclear cap binding protein subunit 2, 20kDa	mRNA processing; mRNA-nucleus export; snRNA-nucleus export; transport	0.03
32.	204170_s_at	CKS2	CDC28 protein kinase regulatory subunit 2	cell cycle; cytokinesis; regulation of cyclin dependent protein kinase activity	0.03
33.	216442_x_at	FN1	fibronectin 1	acute-phase response; cell adhesion; cell migration; metabolism; response to wounding	0.03
34.	209408_at	KIF2C	kinesin family member 2C	cell proliferation; mitosis	0.03
35.	209773_s_at	RRM2	ribonucleotide reductase M2 polypeptide	DNA replication; deoxyribonucleoside diphosphate metabolism	0.04
36.	209094_at	DDAH1	dimethylarginine dimethylaminohydrolase 1	arginine catabolism; nitric oxide mediated signal transduction	0.04
37.	212414_s_at	SEPT6	septin 6	cell cycle; cytokinesis	0.04
38.	202508_s_at	SNAP25	synaptosomal-associated protein, 25kDa	neurotransmitter secretion; neurotransmitter uptake; synaptic transmission; synaptic vesicle docking during exocytosis	0.04
39.	208308_s_at	GPI	glucose phosphate isomerase	carbohydrate metabolism; gluconeogenesis; glycolysis; hemostasis; humoral immune response; neurogenesis	0.04
40.	218308_at	TACC3	transforming, acidic coiled-coil containing protein 3	unknown	0.04
41.	210467_x_at	MAGEA12	melanoma antigen, family A, 12	biological process unknown	0.04
42.	202983_at	SMARCA3	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3	DNA repair; protein ubiquitination; regulation of transcription, DNA-dependent	0.04
43.	203510_at	MET	met proto-oncogene (hepatocyte growth factor receptor)	cell proliferation; protein amino acid phosphorylation; signal transduction	0.04
44.	218663_at	HCAP-G	chromosome condensation protein G	cell cycle; mitosis; mitotic chromosome condensation	0.04
45.	202609_at	EPS8	epidermal growth factor receptor pathway substrate 8	cell proliferation; epidermal growth factor receptor signaling pathway; signal transduction	0.04
46.	212350_at	TBC1D1	TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1		0.04
47.	218662_s_at	HCAP-G	chromosome condensation	protein G cell cycle; mitosis; mitotic chromosome condensation	0.04
48.	201664_at	SMC4L1	SMC4 structural maintenance of chromosomes 4-like 1 (yeast)	cell cycle; chromosome organization and biogenesis (sensu Eukaryota); mitosis; mitotic chromosome condensation; mitotic sister chromatid segregation	0.04
49.	209374_s_at	IGHM	immunoglobulin heavy constant mu	immune response	0.04
50.	201663_s_at	SMC4L1	SMC4 structural maintenance of chromosomes 4-like 1 (yeast)	cell cycle; chromosome organization and biogenesis (sensu Eukaryota); mitosis; mitotic chromosome condensation; mitotic sister chromatid segregation	0.04
51.	208079_s_at	STK6	serine/threonine kinase 6	cell cycle; mitosis; protein amino acid phosphorylation	0.05
52.	203060_s_at	PAPSS2	3'-phosphoadenosine 5'-phosphosulfate synthase 2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism; skeletal development; sulfate assimilation	0.05
53.	204597_x_at	STC1	stanniocalcin 1	calcium ion homeostasis; cell surface receptor linked signal transduction; cell-cell signaling; response to nutrients	0.05
54.	214023_x_at	MGC8685	tubulin, beta polypeptide paralog	microtubule polymerization; microtubule-based movement	0.05
55.	220445_s_at	CSAG2	CSAG family, member 2 r	response to drug	0.05
56.	202487_s_at	H2AFV	H2A histone family, member V	chromosome organization and biogenesis (sensu Eukaryota); nucleosome assembly	0.05
57.	201387_s_at	UCHL1	ubiquitin carboxyl-terminal esterase L1 (ubiquitin thiolesterase)	protein deubiquitination; ubiquitin-dependent protein catabolism	0.05

Supplementary Table 2 List of up-regulated genes in melanoma metastases compared with primary melanomas. 389 differentially expressed probe sets (representing 308 genes) between melanoma metastases and primary melanomas were identified with a FDR <0.05. Of these, 57 probe sets showed up-regulation in metastases and are listed in this table together with their main biological functions. Q value indicates FDR after applying 10,000 permutations (see Materials and methods section).