Keith Hoek - Melanoma Research

105 genes with melanoma metastatic potential-specific expression

The expression of these genes is tied to the proliferative and invasive programs evoked by melanoma cells during disease progression. This gene list was first linked to metastatic potential by us (Hoek et al., 2006).

How to use this information. Below are two tables of probe set lists and their corresponding gene symbol and gene name annotations. If you have properly normalized microarray gene expression data extracted from melanoma lines or cultures, perform sample clustering using the combination of these gene sets. If you have used HG-U133 set chips (Affymetrix) use the probe set information, otherwise use the gene symbols. If you find samples which overexpress motif 1 genes then they are proliferative signature melanoma cells, if samples overexpress motif 2 genes then they are invasive signature melanoma cells.

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motif 1 motif 2 both

Affy IDs Affy IDs Affy IDs

Gene Symbols Gene Symbols Gene Symbols

If you use this information the correct paper to cite for this is (Hoek et al., 2006)

Motif 1

Probe set Gene symbol Gene name

203300_x_at AP1S2 adaptor-related protein complex 1, sigma 2 subunit

204416_x_at APOC1 apolipoprotein C-I

203381_s_at
203382_s_at APOE apolipoprotein E

205681_at BCL2A1 BCL2-related protein A1

211890_x_at
214475_x_at
210944_s_at CAPN3 calpain 3, (p94)

206837_at CART1 cartilage paired-class homeoprotein 1

204995_at CDK5R1 cyclin-dependent kinase 5, regulatory subunit 1 (p35)

207144_s_at CITED1 Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1

209235_at CLCN7 chloride channel 7

209570_s_at D4S234E DNA segment on chromosome 4 (unique) 234 expressed sequence

216513_at
216512_s_at
205337_at
205338_s_at DCT dopachrome tautomerase

221031_s_at APOLD1 Apolipoprotein L domain containing 1

219648_at WDSUB1 WD repeat, sterile alpha motif and U-box domain containing 1

204271_s_at
206701_x_at EDNRB endothelin receptor type B

202454_s_at ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)

203397_s_at GALNT3 polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)

217167_x_at GK glycerol kinase

204187_at GMPR guanosine monophosphate reductase

209169_at
209168_at
209170_s_at
209167_at GPM6B glycoprotein M6B

206696_at GPR143 G protein-coupled receptor 143

206582_s_at
212070_at GPR56 G protein-coupled receptor 56

203632_s_at GPRC5B G protein-coupled receptor, family C, group 5, member B

205862_at GREB1 GREB1 protein

210964_s_at GYG2 glycogenin 2

205376_at INPP4B inositol polyphosphate-4-phosphatase, type II, 105kDa

204562_at IRF4 interferon regulatory factor 4

203723_at ITPKB inositol 1,4,5-trisphosphate 3-kinase B

47550_at
219042_at LZTS1 leucine zipper, putative tumor suppressor 1

221644_s_at
220245_at MATP membrane associated transporter

207323_s_at
209072_at MBP myelin basic protein

207233_s_at MITF microphthalmia-associated transcription factor

206426_at
206427_s_at MLANA melan-A

213638_at PHACTR1 phosphatase and actin regulator 1

207469_s_at PIR pirin (iron-binding nuclear protein)

219584_at PLA1A phospholipase A1 member A

210198_s_at PLP1 proteolipid protein 1

206470_at
213241_at PLXNC1 plexin C1

219412_at RAB38 RAB38, member RAS oncogene family

206617_s_at RENBP renin binding protein

210138_at RGS20 regulator of G-protein signalling 20

221524_s_at RRAGD Ras-related GTP binding D

205334_at S100A1 S100 calcium binding protein A1

209848_s_at SILV silver homolog (mouse)

211546_x_at
207827_x_at
204466_s_at SNCA synuclein, alpha (non A4 component of amyloid precursor)

209843_s_at SOX10 SRY (sex determining region Y)-box 10

213355_at
210942_s_at ST3GAL6 ST3 beta-galactoside alpha-2,3-sialyltransferase 6

204653_at TFAP2A transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)

209354_at TNFRSF14 tumor necrosis factor receptor superfamily, member 14

206479_at TRPM1 transient receptor potential cation channel, subfamily M, member 1

206630_at TYR tyrosinase (oculocutaneous albinism IA)

205694_at TYRP1 tyrosinase-related protein 1

Motif 2

Probe set Gene symbol Gene name

208161_s_at ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member 3

213790_at
202952_s_at ADAM12 a disintegrin and metalloproteinase domain 12 (meltrin alpha)

222108_at AMIGO2 amphoterin induced gene 2

204589_at ARK5 AMP-activated protein kinase family member 5

202686_s_at AXL AXL receptor tyrosine kinase

213905_x_at BGN biglycan

204726_at CDH13 cadherin 13, H-cadherin (heart)

203440_at CDH2 cadherin 2, type 1, N-cadherin (neuronal)

212489_at
203325_s_at
212488_at COL5A1 collagen, type V, alpha 1

209101_at CTGF connective tissue growth factor

209774_x_at CXCL2 chemokine (C-X-C motif) ligand 2

210764_s_at CYR61 cysteine-rich, angiogenic inducer, 61

204602_at DKK1 dickkopf homolog 1 (Xenopus laevis)

214247_s_at DKK3 dickkopf homolog 3 (Xenopus laevis)

201983_s_at EGFR epidermal growth factor receptor

45297_at
221870_at EHD2 EH-domain containing 2

214446_at ELL2 elongation factor, RNA polymerase II, 2

204363_at F3 coagulation factor III (thromboplastin, tissue factor)

202765_s_at
202766_s_at FBN1 fibrillin 1 (Marfan syndrome)

204421_s_at
204422_s_at FGF2 fibroblast growth factor 2 (basic)

206307_s_at FOXD1 forkhead box D1

222020_s_at HNT neurotrimin

219985_at HS3ST3A1 heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1

205207_at IL6 interleukin 6 (interferon, beta 2)

211506_s_at
202859_x_at IL8 interleukin 8

210511_s_at INHBA inhibin, beta A (activin A, activin AB alpha polypeptide)

212942_s_at KIAA1199 KIAA1199

221541_at LCRISP2 LCCL domain containing cysteine-rich secretory protein 2

213640_s_at
215446_s_at
204298_s_at LOX lysyl oxidase

202997_s_at
202998_s_at LOXL2 lysyl oxidase-like 2

212472_at
212473_s_at MICAL2 flavoprotein oxidoreductase MICAL2

204114_at NID2 nidogen 2 (osteonidogen)

202238_s_at NNMT nicotinamide N-methyltransferase

210510_s_at
212298_at NRP1 neuropilin 1

218718_at PDGFC platelet derived growth factor C

202273_at PDGFRB platelet-derived growth factor receptor, beta polypeptide

209318_x_at PLAGL1 pleiomorphic adenoma gene-like 1

201578_at PODXL podocalyxin-like

207177_at PTGFR prostaglandin F receptor (FP)

206157_at PTX3 pentaxin-related gene, rapidly induced by IL-1 beta

218854_at SART2 squamous cell carcinoma antigen recognized by T cells 2

202628_s_at
202627_s_at SERPINE1 serine (or cysteine) proteinase inhibitor, clade E 1

203438_at STC2 stanniocalcin 2

205547_s_at TAGLN transgelin

222146_s_at
212387_at TCF4 transcription factor 4

201506_at TGFBI transforming growth factor, beta-induced, 68kDa

201107_s_at
201110_s_at
201109_s_at
201108_s_at THBS1 thrombospondin 1

213869_x_at
208850_s_at
208851_s_at THY1 Thy-1 cell surface antigen

204932_at
204933_s_at TNFRSF11B tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)

206117_at
206116_s_at
210986_s_at
210987_x_at TPM1 tropomyosin 1 (alpha)

204083_s_at TPM2 tropomyosin 2 (beta)

209946_at VEGFC vascular endothelial growth factor C

205990_s_at WNT5A wingless-type MMTV integration site family, member 5A

221029_s_at WNT5B wingless-type MMTV integration site family, member 5B

motif 1	motif 2	both
Affy IDs	Affy IDs	Affy IDs
Gene Symbols	Gene Symbols	Gene Symbols

Motif 1
Probe set	Gene symbol	Gene name
203300_x_at	AP1S2	adaptor-related protein complex 1, sigma 2 subunit
204416_x_at	APOC1	apolipoprotein C-I
203381_s_at 203382_s_at	APOE	apolipoprotein E
205681_at	BCL2A1	BCL2-related protein A1
211890_x_at 214475_x_at 210944_s_at	CAPN3	calpain 3, (p94)
206837_at	CART1	cartilage paired-class homeoprotein 1
204995_at	CDK5R1	cyclin-dependent kinase 5, regulatory subunit 1 (p35)
207144_s_at	CITED1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1
209235_at	CLCN7	chloride channel 7
209570_s_at	D4S234E	DNA segment on chromosome 4 (unique) 234 expressed sequence
216513_at 216512_s_at 205337_at 205338_s_at	DCT	dopachrome tautomerase
221031_s_at	APOLD1	Apolipoprotein L domain containing 1
219648_at	WDSUB1	WD repeat, sterile alpha motif and U-box domain containing 1
204271_s_at 206701_x_at	EDNRB	endothelin receptor type B
202454_s_at	ERBB3	v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian)
203397_s_at	GALNT3	polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)
217167_x_at	GK	glycerol kinase
204187_at	GMPR	guanosine monophosphate reductase
209169_at 209168_at 209170_s_at 209167_at	GPM6B	glycoprotein M6B
206696_at	GPR143	G protein-coupled receptor 143
206582_s_at 212070_at	GPR56	G protein-coupled receptor 56
203632_s_at	GPRC5B	G protein-coupled receptor, family C, group 5, member B
205862_at	GREB1	GREB1 protein
210964_s_at	GYG2	glycogenin 2
205376_at	INPP4B	inositol polyphosphate-4-phosphatase, type II, 105kDa
204562_at	IRF4	interferon regulatory factor 4
203723_at	ITPKB	inositol 1,4,5-trisphosphate 3-kinase B
47550_at 219042_at	LZTS1	leucine zipper, putative tumor suppressor 1
221644_s_at 220245_at	MATP	membrane associated transporter
207323_s_at 209072_at	MBP	myelin basic protein
207233_s_at	MITF	microphthalmia-associated transcription factor
206426_at 206427_s_at	MLANA	melan-A
213638_at	PHACTR1	phosphatase and actin regulator 1
207469_s_at	PIR	pirin (iron-binding nuclear protein)
219584_at	PLA1A	phospholipase A1 member A
210198_s_at	PLP1	proteolipid protein 1
206470_at 213241_at	PLXNC1	plexin C1
219412_at	RAB38	RAB38, member RAS oncogene family
206617_s_at	RENBP	renin binding protein
210138_at	RGS20	regulator of G-protein signalling 20
221524_s_at	RRAGD	Ras-related GTP binding D
205334_at	S100A1	S100 calcium binding protein A1
209848_s_at	SILV	silver homolog (mouse)
211546_x_at 207827_x_at 204466_s_at	SNCA	synuclein, alpha (non A4 component of amyloid precursor)
209843_s_at	SOX10	SRY (sex determining region Y)-box 10
213355_at 210942_s_at	ST3GAL6	ST3 beta-galactoside alpha-2,3-sialyltransferase 6
204653_at	TFAP2A	transcription factor AP-2 alpha (activating enhancer binding protein 2 alpha)
209354_at	TNFRSF14	tumor necrosis factor receptor superfamily, member 14
206479_at	TRPM1	transient receptor potential cation channel, subfamily M, member 1
206630_at	TYR	tyrosinase (oculocutaneous albinism IA)
205694_at	TYRP1	tyrosinase-related protein 1

Motif 2
Probe set	Gene symbol	Gene name
208161_s_at	ABCC3	ATP-binding cassette, sub-family C (CFTR/MRP), member 3
213790_at 202952_s_at	ADAM12	a disintegrin and metalloproteinase domain 12 (meltrin alpha)
222108_at	AMIGO2	amphoterin induced gene 2
204589_at	ARK5	AMP-activated protein kinase family member 5
202686_s_at	AXL	AXL receptor tyrosine kinase
213905_x_at	BGN	biglycan
204726_at	CDH13	cadherin 13, H-cadherin (heart)
203440_at	CDH2	cadherin 2, type 1, N-cadherin (neuronal)
212489_at 203325_s_at 212488_at	COL5A1	collagen, type V, alpha 1
209101_at	CTGF	connective tissue growth factor
209774_x_at	CXCL2	chemokine (C-X-C motif) ligand 2
210764_s_at	CYR61	cysteine-rich, angiogenic inducer, 61
204602_at	DKK1	dickkopf homolog 1 (Xenopus laevis)
214247_s_at	DKK3	dickkopf homolog 3 (Xenopus laevis)
201983_s_at	EGFR	epidermal growth factor receptor
45297_at 221870_at	EHD2	EH-domain containing 2
214446_at	ELL2	elongation factor, RNA polymerase II, 2
204363_at	F3	coagulation factor III (thromboplastin, tissue factor)
202765_s_at 202766_s_at	FBN1	fibrillin 1 (Marfan syndrome)
204421_s_at 204422_s_at	FGF2	fibroblast growth factor 2 (basic)
206307_s_at	FOXD1	forkhead box D1
222020_s_at	HNT	neurotrimin
219985_at	HS3ST3A1	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1
205207_at	IL6	interleukin 6 (interferon, beta 2)
211506_s_at 202859_x_at	IL8	interleukin 8
210511_s_at	INHBA	inhibin, beta A (activin A, activin AB alpha polypeptide)
212942_s_at	KIAA1199	KIAA1199
221541_at	LCRISP2	LCCL domain containing cysteine-rich secretory protein 2
213640_s_at 215446_s_at 204298_s_at	LOX	lysyl oxidase
202997_s_at 202998_s_at	LOXL2	lysyl oxidase-like 2
212472_at 212473_s_at	MICAL2	flavoprotein oxidoreductase MICAL2
204114_at	NID2	nidogen 2 (osteonidogen)
202238_s_at	NNMT	nicotinamide N-methyltransferase
210510_s_at 212298_at	NRP1	neuropilin 1
218718_at	PDGFC	platelet derived growth factor C
202273_at	PDGFRB	platelet-derived growth factor receptor, beta polypeptide
209318_x_at	PLAGL1	pleiomorphic adenoma gene-like 1
201578_at	PODXL	podocalyxin-like
207177_at	PTGFR	prostaglandin F receptor (FP)
206157_at	PTX3	pentaxin-related gene, rapidly induced by IL-1 beta
218854_at	SART2	squamous cell carcinoma antigen recognized by T cells 2
202628_s_at 202627_s_at	SERPINE1	serine (or cysteine) proteinase inhibitor, clade E 1
203438_at	STC2	stanniocalcin 2
205547_s_at	TAGLN	transgelin
222146_s_at 212387_at	TCF4	transcription factor 4
201506_at	TGFBI	transforming growth factor, beta-induced, 68kDa
201107_s_at 201110_s_at 201109_s_at 201108_s_at	THBS1	thrombospondin 1
213869_x_at 208850_s_at 208851_s_at	THY1	Thy-1 cell surface antigen
204932_at 204933_s_at	TNFRSF11B	tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin)
206117_at 206116_s_at 210986_s_at 210987_x_at	TPM1	tropomyosin 1 (alpha)
204083_s_at	TPM2	tropomyosin 2 (beta)
209946_at	VEGFC	vascular endothelial growth factor C
205990_s_at	WNT5A	wingless-type MMTV integration site family, member 5A
221029_s_at	WNT5B	wingless-type MMTV integration site family, member 5B