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 ...
Pigment Cell Res. 19(4):290-302.
Metastatic potential of melanomas defined by specific gene expression profiles with no BRAF signature.
Hoek KS, Schlegel NC, Brafford P, Sucker A, Ugurel S, Kumar R, Weber BL, Nathanson KL, Phillips DJ, Herlyn M, Schadendorf D, Dummer R.
| 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 |