Table 2

Classifiers of immune responsiveness

Clone IDAbbrev.TitleWilcoxont testPutative functionaWilcoxont testRelative expressionb
Genes that discriminate between pretreatment melanoma lesions that regressed completely or did not (13 versus 21)13 cr vs. 11 nr
195458ESTEST0.000040.00003Unknown0.000400.00031Suppressed
768496EBI3EBI30.000040.00051 IL-12 facilitator 0.000050.00138 Enhanced
269815INHBAInhibin, βA0.000080.00013 TGF-β family 0.003120.00344 Enhanced
280752RBL2Retinoblastoma-like 2 (p130)0.000180.00010Putative tumor suppressor0.020350.00500Suppressed
811116ESTEST0.000290.00022Unknown0.004790.00520 Enhanced
504469ODF2Outer dense fibre of sperm tails 20.000400.00019Cell migration0.008850.00606 Enhanced
588637ACTG1Actin-cytoskeleton γ actin0.000400.00022Cell migration0.003890.00184Suppressed
323917EHD1EH domain containing 10.000440.00554 Ligand-induced endocytosis 0.000560.00397 Enhanced
365098BNIP3LBCL2/adenovirus E1B 19kD-interacting protein 3-like0.000470.00027Putative tumor suppressor0.000920.00138Suppressed
814095LTA4HLeukotriene A4 hydrolase0.000470.00146 Immediate hypersensitivity 0.003850.00743Suppressed
321739IRF2IFN-γ regulatory factor 20.000550.00019 IFN expression regulation 0.007270.00289 Enhanced
109316Serpina3α1-antichymotrypsin0.000550.00872Proteinase inhibitor0.01075NSc Enhanced
1457955ESTEST0.000760.00019Unknown0.003850.00175Suppressed
51463BIRC1Neuronal apoptosis inhibitory protein0.000950.00129Apoptosis regulator0.005620.01252Suppressed
323371APPAmyloid β (A4) precursor protein0.001000.00099Intracellular signaling0.005940.00402 Enhanced
142259FIP2Tumor necrosis factor α-inducible cellular protein0.001180.00041 TNF pathway 0.007270.00441Suppressed
854138CSNK1ECasein kinase 1, epsilon0.001180.01792DNA replication repair0.000300.00258 Enhanced
322160PTENMMAC1-PTEN-Tumor suppressor gene0.001180.00067Putative tumor suppressor0.004820.00338Suppressed
796297KIAA1605KIAA16050.001360.00051Unknown0.000920.00055 Enhanced
345935MADHMADH30.001570.00044 TGF-β response regulator 0.000530.00030 Enhanced
588915IFI27IFN, α-inducible protein 270.001760.01109 IFN-induced tumor suppressor 0.00098NSSuppressed
344080SHMT2Serine hydroxymethyltransferase mitochondrial precursor0.002060.00097Cell metabolism0.004740.02665 Enhanced
240109FLJ10632Homo sapiens cDNA FLJ106320.002160.00065Unknown0.015870.01430Suppressed
725284PHKG2Phosphorylase kinase, gamma 20.002380.00301Kinase0.002190.00091 Enhanced
240099ESTEST0.003270.01459Unknown0.000860.00514Suppressed
324210SR-BP1Sigma receptor (SR31747 binding protein 1)0.003540.00271Cell proliferation regulation0.001970.00085 Enhanced
43884PPIFPeptidylprolyl isomerase F (cyclophilin F)0.004020.00099Cell metabolismNS0.04096 Enhanced
563423JAK1JAK10.008300.01792 IL-2 receptor regulation 0.000080.00007Suppressed
136218TIA1TIA1 cytotoxic granule-associated RNA-binding protein0.011110.00642 CTL-mediated cytolysis 0.000560.00168 Enhanced
1103633KIAA0515KIAA05150.021790.03866Unknown0.00053NSSuppressed
322961CAPZBCapping protein (actin filament) muscle Z-line, beta0.037560.02295Cell migration0.000550.00027 Enhanced
221846CHES1Checkpoint suppressor 10.046120.04285DNA-damage checkpoint0.001540.00071Suppressed
148421TXKTXK tyrosine kinaseNSNS T-cell regulation 0.001560.00012Suppressed
Abundance of immune cell marker genes in pretreatment melanoma lesions that regressed completely or did not (13 versus 21)13 cr vs. 11 nr
377560CD3 deltaCD3 δND0.46798T-cell markerND0.50000Equal
306841TCRT cell receptor beta locusND0.68111T-cell markerND0.75879Equal
771258CD8 alphaCD8 α chainND0.85709Cytotoxic T-cell markerND0.39163Equal
86189CD4CD4 (p55)ND0.09511Helper T-cell markerND0.34623Equal
282679CD16CD16-Fcγ receptor IIIaND0.62066NK cell markerND0.95314Equal
154015CD11ACD11A-Integrin, α L-LFA-1 α chainND0.84775Leukocyte-associated markerND0.80301Equal
435434CD14CD14ND0.42577Macrophage markerND0.56275Equal
50214CD86CD86, B72, CD28/CTLA-4 ligandND0.37608Macrophage/B-cell markerND0.97991Equal
564503CD83CD83-B-G antigen IgV domain homolog-HB15ND0.38766Activated B cells and dendritic cellsND0.69852Equal
  • a Boldface entries show genes associated with immune/inflammatory function.

  • b Relative expression of individual genes in responding compared with nonresponding lesions.

  • c NS, not significant; ND, not done.