Method to use gene expression to determine likelihood of clinical outcome of renal cancer

1. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient, comprising:

measuring a level of an RNA transcript, in a renal tumor sample from the patient, of a panel of genes consisting of:

(a) a set of genes consisting of one or more genes selected from: YBX1, XIAP, WWOX, VWF, VEGFA, VCAM1, USP34, UMOD, UGCG, UBB, UBA3, TYMS, TUSC4, TSPAN7, TSC2, TSC1, TP53, TOP2B, TNFSF12, TNFSF10, TNFRSF11B, TNFRSF10D, TNFRSF10B, TNFAIP6, TMEM47, TM2M27, TLR3, TIMP3, TIMP2, THBS1, TGFBR2, IGF1R, IF127, ID3, ID2, ID1, ICAM2, HYAL2, HYAL1, HSPG2, HSD11B2, HPN, HPCAL1, HMGB1, HLA-DPB1, HIF1AN, HDAC1, HAVCR1, HADH, GZMA, GSTP1, GSTM3, GSTM1, GRB7, GPX3, GJA1, GFRA1, GCLC, GBP2, GATM, GATA3, FOS, TGFBR1, TGFB2, TGFA, TEK, TCF4, TAP1, TAGLN, TACSTD2, SUCLG1, STK11, STAT5B, STAT5A, STATS, SPRY1, SPARCL1, SPARC, SOD1, SNRK, SNAI1, SMAD4, SMAD2, SLC34A1, SLC22A6, SKIL, SHANKS, SGK1, SFRP1, SEMA3F, SELENBP1, SDPR, SDHA, SCNN1A, FOLR1, FLT4, FLT3LG, FLT1, FILIP1, FIGF, FHL1, FHIT, FH, FGFR2, FGFR1, FGF2, FGF1, FDPS, FBXW7, FAS, FABP1, ESRRG, ERG, ERCC1, ERBB3, ERBB2, EPHB4, EPHA2, EPAS1, ENPP2, ENPEP, ENG, EMP1, EMCN, ELTD1, EIF2C1, SCN4B, RPTOR, RPS6KB1, RPS6KA1, RPS23, ROCK2, ROCK1, RIPK1, RHOC, RHOB, RHOA, RGS5, RERGL, RELA, RB1, RASSF1, BARB, RALBP1, RAF1, PTPRG, PTPRB, PTN, PTK2, PTH1R, PTEN, PSMB9, PSMB8, PRSS8, PRPS2, PRKCH, PPP2CA, EGR1, EGLN3, EGFR, EFNB2, EFNB1, EEF1A1, EDNRB, EDN2, EDN1, EBAG9, DUSP1, DPYS, DPEP1, DLL4, DLC1, DKFZP564O0823, DICER1, DIAPH1, DIABLO, DHPS, DET1, DEFB1, DDC, DCXR, DAPK1, CYR61, CYP3A4, CXCL9, CXCL12, CX3CR1, CX3CL1, PPARG, PPAP2B, PLG, PLAT, PLA2G4C, PIK3CA, PIK3C2B, PFKP, PECAM1, PDZK3, PDZK1, PDGFRB, PDGFD, PDGFC, PDGFB, PDGFA, PCK1, PCCA, PARD6A, PAK1, PAH, OGG1, NUDT6, NRG1, NPR1, NPM1, NOTCH3, NOTCH2, NOTCH1, NOS3, NOS2, NOL3, NFX1, CUL1, CUBN, CTSS, CTSH, CTNNB1, CTNNA1, CTGF, CSF1R, CSF1, CRADD, COL4A2, COL18A1, CLU, CLDN7, CLDN10, CLCNKB, CFLAR, CEACAM1, CDKN1B, CDKN1A, CDH6, CDH5, CDH16, CDH13, CD4, CD36, CD34, CCR7, CCR4, CCND1, CCL4, CCL2, CAT, NFKB1, NFATC2, NFAT5, MYRIP, MYH11, MYC, MVP, MUC1, MTOR, MSH3, MSH2, MLST8, MIF, MICA, MGMT, MCM3, MCAM, MARCKS, MAPK3, MAPK1, MAP4, MAP2K3, MAP2K1, MAL2, MAL, LYZ, LTF, LRP2, LMO2, LDB2, LDB1, LAMA4, KRT7, CASP6, CASP10, CALD1, CA9, CA2, C7, C2 orf40, C13orf15, BUB3, BTRC, BIRC2, BIN1, BGN, BCL2L12, BCL2L1, BCL2, BBC3, BAG1, BAD, ATP6V1B1, ASS1, ARRB1, ARHGDIB, AQP1, APOLD1, APC, ANXA4, ANXA1, ANTXR1, ANGPTL4, ANGPTL3, ANGPT1, ALDOB, KRAS, KL, KITLG, KIT, KDR, KCNJ15, KAT5, JUP, JUN, JAG1, ITGB1, ITGA7, ITGA6, ITGA4, ITGA3, IQGAP2, INSR, IMPS, IL6ST, IL15, IGFBP6, IGFBP3, IGFBP2, ALDH6A1, ALDH4A1, AKT3, AKT2, AKT1, AIF1, AHR, AGTR1, ADH1B, ADFP, ADD1, ADAMTS5, ADAMTS1, ACE2, ACADSB, ABCG2, ABCC4, ABCC3, ABCC1, ABCB1, ABAT, AAMP, and A2M;

(b) a set of genes consisting of one or more genes selected from: WT1, VTN, VDR, VCAN, UBE2T, TPX2, TOP2A, TK1, TIMP1, TGFBI, SQSTM1, SPP1, SPHK1, SLC7A5, SLC2A1, SLC16A3, SLC13A3, SHC1, SFN, SERPINA5, SEMA3C, SAA2, S100A1, RRM2, RPLP1, PTTG1, PTGS2, PLAUR, PF4, PCSK6, MYBL2, MT1X, MMP9, LGALS1, LAMBS, LAMB1, L1CAM, IL8, IL6, ICAM1, HIST1H1D, FN1, F3, F2, ESPL1, EPHB2, EPHB1, ENO2, EIF4EBP1, CXCR4, CXCL1, CTSB, CRP, CP, COL7A1, COL1A1, CHEK1, CENPF, CD82, CD44_s, CCNE1, CCNB1, CCL20, CA12, C3, BUB1, MMP7, MMP14, MKI67, MGST1, MDK, LOX, LMNB1, LIMK1, BIRC5, BIRC3, BCL2A1, AURKA, ANXA2, ALOX5, ADAM8, and ABCC2;

(c) a set of genes consisting of one or more genes selected from: ACE2, ADD1, ALDOB, ANGPTL3, APOLD1, AQP1, NUDT6, CASP10, CAV2, CCL4, CCL5, CCR2, CCR4, CCR7, CD4, CD8A, CEACAM1, CFLAR, CTSS, CX3CL1, CXCL10, CXCL9, CXCR6, DAPK1, DDC, DLC1, C2 orf40, EDNRB, EMCN, EPAS1, FAS, FH, GATA3, GZMA, HLA-DPB1, HSPG2, ICAM2, ICAM3, ID1, IGF1R, IL15, IQGAP2, KLRK1, LDB2, LRP2, LTF, MAP4, ABCC1, NOS3, PIK3C2B, PLA2G4C, PPAP2B, PRCC, PRKCB, PRKCH, PRSS8, PSMB9, PTPRB, RGS5, SDPR, SELE, SGK1, SHANKS, SNRK, TEK, TGFBR2, TIMP3, TMEM27, TSPAN7, UBB, and WWOX; and

(d) a set of consisting of one or more genes selected from: BIRC2, BUB1, CCNB1, ENO2, ITGB1, ITGB5, LAMB1, MMP14, MMP9, PSMA7, RUNX1, SPHK1, SPP1, SQSTM1, TPX2, TUBBA2, and VCAN;

wherein the gene(s) of the sets do not overlap, and wherein one or more of AAMP, RPS23, SDHA, UBB, and RPLP1 is a member of the panel.

2. The method of claim 1 , wherein the renal cancer is renal cell carcinoma (RCC).

3. The method of claim 2 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).

4. The method of claim 1 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.

5. The method of claim 1 , wherein the renal tumor sample is obtained from a biopsy.

6. The method of claim 1 , wherein the renal tumor sample is paraffin-embedded and fixed.

7. The method of claim 1 , wherein one or more angiogenesis genes selected from: ADD1, ANGPTL3, APOLD1, CEACAM1, EDNRB, EMCN, ENG, EPAS1, FLT1, JAG1, KDR, KT, LDB2, NOS3, NUDT6, PPAP2B, PRKCH, PTPRB, RGS5, SHANK3, SNRK, TEK, ICAM2, and VCAM1;

one or more immune response genes selected from: CCL5, CCR7, CD8A, CX3CL1, CXCL10, CXCL9, HLA-DPB1, IL6, IL8, and SPP1;

a transport gene selected from AQP1, SGK1, and both AQP1 and SGK1;

one or more cell adhesion/extracellular matrix genes selected from: ITGB1, A2M, ITGB5, LAMB1, LOX, MMP14, TGFBR2, TIMP3, and TSPAN7;

one or more cell cycle genes selected from: BUB1, C13 orf15, CCNB1, PTTG1, TPX2, LMNB1, and TUBB2A; and/or

CASP10

is a member of the panel of genes.

8. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient, comprising:

measuring a level of an RNA transcript, in a renal tumor sample from the patient, of a panel of genes consisting of:

(a) a set of genes consisting of one or more genes selected from: YBX1, XIAP, WWOX, VWF, VEGFA, VCAM1, USP34, UMOD, UGCG, UBB, UBA3, TYMS, TUSC4, TSPAN7, TSC2, TSC1, TP53, TOP2B, TNFSF12, TNFSF10, TNFRSF11B, TNFRSF10D, TNFRSF10B, TNFAIP6, TMEM47, TMEM27, TLR3, TIMP3, TIMP2, THBS1, TGFBR2, IGF1R, IFI27, ID3, ID2, ID1, ICAM2, HYAL2, HYAL1, HSPG2, HSD11B2, HPN, HPCAL1, HMGB1, HLA-DPB1, HIF1AN, HDAC1, HAVCR1, HADH, GZMA, GSTP1, GSTM3, GSTM1, GRB7, GPX3, GJA1, GFRA1, GCLC, GBP2, GATM, GATA3, FOS, TGFBR1, TGFB2, TGFA, TEK, TCF4, TAP1, TAGLN, TACSTD2, SUCLG1, STK11, STAT5B, STAT5A, STATS, SPRY1, SPARCL1, SPARC, SOD1, SNRK, SNAI1, SMAD4, SMAD2, SLC34A1, SLC22A6, SKIL, SHANKS, SGK1, SFRP1, SEMA3F, SELENBP1, SDPR, SDHA, SCNN1A, FOLR1, FLT4, FLT3LG, FLT1, FILIP1, FIGF, FHL1, FHIT, FH, FGFR2, FGFR1, FGF2, FGF1, FDPS, FBXW7, FAS, FABP1, ESRRG, ERG, ERCC1, ERBB3, ERBB2, EPHB4, EPHA2, EPAS1, ENPP2, ENPEP, ENG, EMP1, EMCN, ELTD1, EIF2C1, SCN4B, RPTOR, RPS6KB1, RPS6KA1, RPS23, ROCK2, ROCK1, RIPK1, RHOC, RHOB, RHOA, RGS5, RERGL, RELA, RB1, RASSF1, BARB, RALBP1, RAF1, PTPRG, PTPRB, PTN, PTK2, PTH1R, PTEN, PSMB9, PSMB8, PRSS8, PRPS2, PRKCH, PPP2CA, EGR1, EGLN3, EGFR, EFNB2, EFNB1, EEF1A1, EDNRB, EDN2, EDN1, EBAG9, DUSP1, DPYS, DPEP1, DLL4, DLC1, DKFZP56400823, DICER1, DIAPH1, DIABLO, DHPS, DET1, DEFB1, DDC, DCXR, DAPK1, CYR61, CYP3A4, CXCL9, CXCL12, CX3CR1, CX3CL1, PPARG, PPAP2B, PLG, PLAT, PLA2G4C, PIK3CA, PIK3C2B, PFKP, PECAM1, PDZK3, PDZK1, PDGFRB, PDGFD, PDGFC, PDGFB, PDGFA, PCK1, PCCA, PARD6A, PAK1, PAH, OGG1, NUDT6, NRG1, NPR1, NPM1, NOTCH3, NOTCH2, NOTCH1, NOS3, NOS2, NOL3, NFX1, CUL1, CUBN, CTSS, CTSH, CTNNB1, CTNNA1, CTGF, CSF1R, CSF1, CRADD, COL4A2, COL18A1, CLU, CLDN7, CLDN10, CLCNKB, CFLAR, CEACAM1, CDKN1B, CDKN1A, CDH6, CDH5, CDH16, CDH13, CD4, CD36, CD34, CCR7, CCR4, CCND1, CCL4, CCL2, CAT, NFKB1, NFATC2, NFAT5, MYRIP, MYH11, MYC, MVP, MUC1, MTOR, MSH3, MSH2, MLST8, MIF, MICA, MGMT, MCM3, MCAM, MARCKS, MAPK3, MAPK1, MAP4, MAP2K3, MAP2K1, MAL2, MAL, LYZ, LTF, LRP2, LMO2, LDB2, LDB1, LAMA 4, KRT7, CASP6, CASP10, CALD1, CA9, CA2, C7, C2 orf40, C13 orf15, BUB3, BTRC, BIRC2, BIN1, BGN, BCL2L12, BCL2L1, BCL2, BBC3, BAG1, BAD, ATP6V1B1, ASS1, ARRB1, ARHGDIB, AQP1, APOLD1, APC, ANXA4, ANXA1, ANTXR1, ANGPTL4, ANGPTL3, ANGPT1, ALDOB, KRAS, KTKITLG, KIT, KDR, KCNJ15, KAT5, JUP, JUN, JAG1, ITGB1, ITGA7, ITGA6, ITGA4, ITGA3, IQGAP2, INSR, IMPS, IL6ST, IL15, IGFBP6, IGFBP3, IGFBP2, ALDH6A1, ALDH4A1, AKT3, AKT2, AKT1, AIF1, AHR, AGTR1, ADH1B, ADFP, ADD1, ADAMTS5, ADAMTS1, ACE2, ACADSB, ABCG2, ABCC4, ABCC3, ABCC1, ABCB1, ABAT, AAMP, and A2M;

(b) a set of genes consisting of one or more genes selected from: WT1, VTN, VDR, VCAN, UBE2T, TPX2, TOP2A, TK1, TIMP1, TGFBI, SQSTM1, SPP1, SPHK1, SLC7A5, SLC2A1, SLC16A3, SLC13A3, SHC1, SFN, SERPINA5, SEMA3C, SAA2, S100A1, RRM2, RPLP1, PTTG1, PTGS2, PLAUR, PF4, PCSK6, MYBL2, MT1X, MMP9, LGALS1, LAMB3, LAMB1, L1CAM, IL8, IL6, ICAM1, HIST1H1D, FN1, F3, F2, ESPL1, EPHB2, EPHB1, ENO2, EIF4EBP1, CXCR4, CXCL1, CTSB, CRP, CP, COL7A1, COL1A1, CHEK1, CENPF, CD82, CD44_s, CCNE1, CCNB1, CCL20, CA12, C3, BUB1, MMP7, MMP14, MKI67, MGST1, MDK, LOX, LMNB1, LIMK1, BIRC5, BIRC3, BCL2A1, AURKA, ANXA2, ALOX5, ADAM8, and ABCC2;

(c) a set of genes consisting of one or more genes selected from: WT1, VTN, VDR, UBE2T, TSPAN8, TPX2, TOP2A, TK1, TIMP1, TGFBI, SPP1, SLC7A5, SLC16A3, SFN, SEMA3C, SELL, SAA2, RRM2, RPLP1, RAD51, PTTG1, PTGS2, PTGIS, PLAUR, PF4, PDGFRA, PCSK6, NNMT, NME2, MYBL2, MT1X, MMP9, MMP7, MMP14, LAMA 3, L1CAM, ISG20, IL8, IL6, IGF1 ICAM1, HIST1H1D, GPX2, FN1, FAP, F3, F2, ESPL1, EPB41L3, ENO2, EIF4EBP1, E2F1, DCN, CXCR6, CXCR5, CXCR4, CXCL1, CTSB, CRP, CP, COL7A1, COL1A1, CHEK2, CHEK1, CENPF, CD82, CD44_s, CCNE2_2, CCNB1, MKI67, MGST1, MDK, MDH2, LRRC2, LOX, LMNB1, LIMK1, LAPTM5, LAMB3, LAMB1, CCL20, CA12, C3, BUB1, BIRC5, BCL2A1, AURKA, APOL1, ANXA2, ADAM8, and ABCC2;

(d) a set of genes consisting of one or more genes selected from: YBX1, XIAP, WWOX, WISP1, VWF, VEGF, VCAM1, USP34, UMOD, UGCG, UBB, UBA3, TYMS, TUSC4, TUSC2, TSPAN7, TSC2, TSC1, TP53, TOP2B, TNIP2, TNFSF12, TNFSF10, TNFRSF11B, TNFRSF10D, TNFRSF10B, TNFAIP6, TNF, TMEM47, TMEM27, TLR3, TIMP3, TIMP2, THBS1, TGFBR2, IL7, IL6ST, IL15, IGFBP6, IGFBP3, IGF1R, ID3, ID2, ID1, ICAM2, HYAL2, HYAL1, HSPG2, HSD11B2, HPN, HPCAL1, HNRNPAB, HMGB1, HLA-DPB1, HIF1AN, HIF1A, HGF, HDAC1, HAVCR1, HADH, GSTT1, GSTP1, GSTM3, GSTM1, GRB7, GRB14, GPX3, GNAS, GJA1, GFRA1, TGFBR1, TGFB2, TGFB1, TGFA, TEK, TCF4, TAP1, TAGLN, TACSTD2, SUCLG1, STK11, STAT5B, STAT5A, STATS, STAT1, SPRY1, SPAST, SPARCL1, SPARC, SOD1, SNRK, SNAI1, SMAD4, SMAD2, SLC9A1, SLC34A1, SLC22A6, SKIL, SIRPA, SHANKS, SGK1, SFRP1, SEMA3F, SELPLG, SELENBP1, GCLM, GCLC, GBP2, GATM, GATA3, FOS, FOLR1, FLT4, FLT3LG, FLT1, FILIP1, FIGF, FHL1, FHIT, FH, FGFR2, FGFR1, FGF2, FGF1, FDPS, FBXW7, FAS, ESRRG, ERG, ERCC1, ERBB4, ERBB3, ERBB2, EPHB4, EPHA2, ENPP2, ENPEP, ENG, EMP1, SDPR, SDHA, SCNN1A, SCN4B, S100A2, RPTOR, RPS6KB1, RPS6KA1, RPS23, ROCK2, ROCK1, RIPK1, RHOC, RHOB, RHOA, RHEB, RGS5, RERGL, RB1, RASSF1, BARB, RALBP1, RAF1, RAC1, PTPRG, PTPRB, PTN, PTK2, PTH1R, PTEN, PSMB9, PSMB8, PSMA7, PRSS8, EMCN, ELTD1, EIF2C1, EGR1, EGLN3, EGFR, EGF, EFNB2, EFNB1, EEF1A1, EDNRB, EDN2, EDN1, EBAG9, DUSP1, DPYS, DPEP1, DLL4, DLC1, DKFZP56400823, DICER1, DIAPH1, DIABLO, DHPS, DET1, DEFB1, DDC, DAPK1, CYR61, CXCL12, CX3CR1, CX3CL1, CUL1, CUBN, PRPS2, PRKCH, PRKCD, PPP2CA, PPARG, PPAP2B, PLG, PLAT, PLA2G4C, PIK3CA, PIK3C2B, PFKP, PECAM1, PDZK3, PDZK1, PDGFRB, PDGFD PDGFC, PDGFB, PDGFA, PCK1, PCCA, PARD6A, PAK1, PAH, OGG1, NUDT6, NPRP1, NPM1, NOTCH3, NOTCH2, NOTCH1, NOS3, NOS2A, NOL3, CTSS, CTSH, CTNNB1, CTNNA1, CTGF, CSF2RA, CSF1R, CSF1, CRADD, COL4A2, COL4A1, COL18A1, CLU, CLDN10, CLCNKB, CFLAR, CEACAM1, CDKN1A, CDH6, CDH5, CDH2, CDH16, CDH13, CDC25B, CD4, CD36, CD34, CD24, CD14, CCND1, CCL4, CCL2, CAT, CASP10, CALD1, NFX1, NFKB1, NFATC2, NFAT5, MYRIP, MYH11, MYC, MX1, MVP, MUC1, MTOR, MSH3, MSH2, MMP11, MLST8, MIF, MICA, MGMT, MCM3, MCAM, MARCKS, MAPK3, MAPK1, MAP4, MAP2K3, MAP2K1, MAL2, MAL, LYZ, LTF, LRP2, LMO2, LDB2, LDB1, LAMA 4, CACNA2D1, CA9, CA2, C3AR1, C2 orf40, C1QA, C13 orf15, BUB3, BTRC, BIRC2, BIN1, BGN, BCL2L1, BCL2, BAX, BAK1, BAG1, ATP6V1B1, ATP1A1, ASS1, ARRB1, ARHGDIB, AQP1, APOLD1, APC, ANXA4, ANXA1, ANTXR1, ANGPTL4, ANGPTL3, ANGPTL2, ANGPT2, ANGPT1, ALDOB, ALDH6A1, KRT7, KRAS, KIT, KITLG, KIT, KDR, KCNJ15, KAT5, JUP, JUN, JAG1, ITGB5, ITGB1, ITGA7, ITGA6, ITGA5, ITGA4, ITGA3, IQGAP2, INSR, IMP3, ALDH4A1, AKT3, AKT2, AKT1, AIF1, AHR, AGTR1, ADH1B, ADD1, ADAMTS5, ADAM17, ACE2, ACADSB, ABCG2, ABCC4, ABCC3, ABCC2, ABCB1, ABAT, AAMP, and A2M;

(e) a set of genes consisting of one or more genes selected from: WT1, VTN, VDR, UBE2T, TYMP, TPX2, TOP2A, TNFSF13B, TK1, TGFBI, STAT1, SQSTM1, SPP1, SLC7A5, SLC16A3, SLC13A3, SFN, SEMA3C, SAA2, S100A1, RRM2, RPLP1, RAD51, PTTG1, PSMB9, PSMB8, PRKCB, PDCD1, PCSK6, PCNA, NME2, MYBL2, MMP9, MMP14, MKI67, HPD, HIST1H1D, HGD, GZMA, GPX2, GPX1, FCGR3A, FASLG, FABP1, F2, ESPL1, E2F1, CXCR6, CXCR5, CXCL9, CXCL10, CXCL1, CTSD, CTSB, CRP, CP, CHEK2, CHEK1, CENPF, CD8A, CD82, CD70, CCNE1, CCNB1, CCL5, CCL20, CAV2, CA12, C3, C1QB, MGST1, MET, MDK, MDH2, MCM2, LOX, LMNB1, LIMK1, LAPTM5, LAMBS, L1CAM, KLRK1, ITGB2, IL8, IL6, ICAM1, HSPA8, BUB1, BRCA1, BIRC5, BIRC3, AURKA, ATP5E, APOL1, APOE, APOC1, ANXA2, ANGPTL3, AMACR, ALOX5, ALDH4A1, ADAMS, and ABCC2;

(f) a set of genes consisting of one or more genes selected from: ZHX2, YBX1, XPNPEP2, XIAP, WISP1, VWF, VHL, VEGFA, VCAN, VCAM1, USP34, UMOD, UGCG, UBB, UBA3, TUSC4, TUSC2, TSPAN7, TSC2, TSC1, TP53, TOP2B, TNIP2, TNFSF12, TNFRSF11B, TNFRSF10D, TNFR5F10C, TNFRSF10B, TNFAIP6, TNFAIP3, TNF, TMEM47, TMEM27, TIMP3, ITGA4, ITGA3, IQGAP2, INSR, INHBA, IMP3, IL6ST, IL1B, IL15, IL10, IGFBP6, IGFBP5, IGFBP2, IGF2, IGF1R ID3, ID2, ID1, ICAM2, HYAL2, HYAL1, HSPG2, HSPA1A, HSP90AB1, HSD11B2, HPCAL1, HNRNPAB, HMGB1, HIF1AN, HIF1A, HGF, HDAC1, HADH, GSTP1, TIMP2, THBS1, THBD, TGFBR2, TGFBR1, TGFB2, TGFB1, TGFA, TEK TDGF1, TCF4, TAGLN, TACSTD2, SUCLG1, STK11, STC2, STAT5B, STAT5A, STATS, SPRY1, SPAST, SPARCL1, SPARC, SNRK, SNAI1, SMAD4, SMAD2, SLC9A1, SLC34A1, SKIL, SHC1, SHANKS, SGK1, SFRP1, GSTM3, GSTM1, GRB7, GRB14, GPC3, GNAS, GMNN, GJA1, GCLM, GCLC, GATM, GATA3, GAS2, GADD45B, FST, FOS, FOLR1, FLT4, FLT3LG, FLT1, FILIP1, FIGF, FHL1, FHIT, FH, FGFR2, FGFR1, FGF2, FGF1, FDPS, FBXW7, FAP, ESRRG, ERG, SERPINE1, SEMA3F, SELENBP1, SELE, SDPR, SDHA, SCNN1A, SCN4B, S100A2, RUNX1, RRM1, RPTOR, RPS6KB1, RPS23, ROCK2, ROCK1, RIPK1, RHOC, RHOB, RHOA, RHEB, RGS5, RERGL, RELA, RB1, RASSF1, RARB, RALBP1, RAF1, RAC1, PXDN, PTPRG, PTPRB, PTN, ERCC4, ERCC1, ERBB4, ERBB2, EPHB4, EPHA2, EPAS1, ENPP2, ENPEP, ENO2, ENG, EMP1, EMCN, ELTD1, EIF2C1, EGR1, EGLN3, EGF, EFNB2, EFNB1, EEF1A1, EDNRB, EDN2, EDN1, EBAG9, DUSP1, DPEP1, DLL4, DLC1, DKFZP564O0823, DICER1, DIAPH1, DIABLO, DHPS, PTK2, PTH1R, PTEN, PSMA7, PRPS2, PROM2, PRKCH, PRKCD, PPP2CA, PPARG, PPAP2B, PMP22, PLG, PLAT, PLA2G4C, PIK3CA PIK3C2B, PI3K, PGF, PFKP, PECAM1, PDZK3, PDZK1, PDGFRB, PDGFRA, PDGFD, PDGFC, PDGFB, PDGFA, PCK1, PCCA, PARD6A, PAK1, PAH, OGG1, NUDT6, DET1, DEFB1, DAPK1, DAG1, CYR61, CXCL12, CX3CR1, CX3CL1, CUL1, CUBN, CTSL1, CTNNB1, CTNNA1, CTGF, CSF1, CRADD, COL5A2, COL4A2, COL4A1, COL1A2, COL18A1, CLDN10, CLCNKB, CFLAR, CEACAM1, CDKN1B, CDKN1A, CDK4, CDH5, CDH16, CDH13, CD99, CD44_1, CD36, CD34, NPR1, NPM1, NOTCH3, NOTCH2, NOTCH1, NOS3, NOS2, NOL3, NFX1, NFKB1, NFATC2, NFAT5, MYRIP, MYH11, MYC, MX1, MVP, MUC1, MTOR, MT1X, MSH3, MMP2, MMP11, MIF, MICA, MGMT, MCM3, MCAM, MARCKS, MAPK3, MAPK1, MAP4, MAP2K3, MAP2K1, CD14, CCND1, CCL2, CAT, CASP10, CALD1, CACNA2D1, CA9, CA2, C7, C3AR1, C, C2 orf40, C13 orf15, BUB3, BTRC, BNIP3, BIRC2, BGN, BCL2L1, BCL2, BAG1, AXL, ATP6V1B1, ASS1, ARRB1, ARHGDIB, ARF1, AREG, AQP1, APOLD1, APC, APAF1, ANXA1, ANTXR1, ANGPTL4, MAL, LRP2, LMO2, LDB2, LDB1, LAMB1, LAMA 4, KRT7, KRAS, KL, KITLG, KIT, KDR, KCNJ15, KAT5, JUP, JUN, JAG1, ITGB5, ITGB3, ITGB1, ITGA7, ITGA6, ITGA5, ANGPTL2, ANGPT2, ANGPT1, ALDOB, ALDH6A1, AKT3, AKT2, AKT1, AHR, AGTR1, ADH1B, ADD1, ADAMTS9, ADAMTS5, ADAMTS4, ADAMTS2, ADAMTS1, ADAM17, ACADSB, ABCG2, ABCC4, AAMP, and A2M;

(g) a set of genes consisting of one or more genes selected from: WT1, VTN, VDR, UBE2T, TYMP, TSPAN8, TPX2, TOP2A, TNFSF13B, TK1, TIMP1, SPP1, SPHK1, SLC7A5, SLC2A1, SLC13A3, SHC1, SFN, SERPINE1, SERPINA5, SEMA3C, SELL, SAA2, RRM2, RPLP1, RND3, RAD51, PTTG1, PTGS2, PRKCB, PRKCA, PLAUR, KRT19, ITGB4, ISG20, IL8, IL6, ICAM1, HSPA8, HIST1H1D, GPX1, FZD2, FN1, FCGR3A, FCER1G, FAP, F3, F2, ESPL1, EPHB2, EPHB1, EPB41L3, ENO2, EIF4EBP1, E2F1, CXCR6, CXCR4, CXCL1, CTSB, CRP, CP, COL7A1, COL1A1, CHEK2, CHEK1, CENPF, PLAU, PF4, PDCD1, PCSK6, PCNA, NNMT, NME2, MYBL2, MT1X, MMP9, MMP7, MMP14, MKI67, MGST1, MET, MDK, MCM2, LRRC2, LOX, LMNB1, LIMK1, LGALS9, LGALS1, LAPTM5, LAMBS, L1CAM, CD82, CD68, CD44_S, CCNE2_2, CCNE1, CCNB1, CCL5, CCL20, CAV2, CA12, C3, C1QB, BUB1, BRCA1, BIRC5, BIRC3, BCL2A1, AURKA, ATAD2, APOL1, APOC1, ANXA2, ALOX5, ADAMS, and ABCC2;

(h) a set of genes consisting of one or more genes selected from: YBX1, XIAP, WWOX, WISP1, VWF, VHL, VEGFA, VCAM1, USP34, UMOD, UGCG, UBB, UBA3, TYMS, TUSC4, TUSC2, TSPAN7, TSC2, TSC1, TP53, TOP2B, TNFSF12, TNFSF10, TNFRSF11B, TNFRSF10D, TNFRSF10B, TNFAIP6, TMEM47, TMEM27, TLR3, TIMP3, TIMP2, THBS1, TGFBR2, TGFBR1, TGFB2, IGF2, IGF1R, ID3, ID2, ID1, ICAM2, HYAL2, HYAL1, HSPG2, HSP90AB1, HSD11B2, HPN, HPCAL1, HMGB1, HLA-DPB1, HIF1AN, HDAC1, HAVCR1, HADH, GSTT1, GSTP1, GSTM3, GSTM1, GRB7, GPX3, GPC3, GJA1, GFRA1, GCLC, GATM, GATA3, GADD45B, FOS, FOLR1, FLT4, FLT3LG, TGFB1, TGFA, TEK, TCF4, TAGLN, TACSTD2, SUCLG1, STK11, STAT5B, STAT5A, STATS, SPRY1, SPAST, SPARCL1, SOD1, SNRK, SNAI1, SMAD4, SMAD2, SLC34A1, SLC22A6, SKIL, SHANKS, SGK1, SFRP1, SEMA3F, SELENBP1, SDPR, SDHA, SCNN1A, SCN4B, S100A2, RPTOR, RPS6KB1, FLT1, FILIP1, FIGF, FHL1, FHIT, FH, FGFR2, FGFR1, FGF2, FGF1, FDPS, FBXW7, FAS, ESRRG, ERG, ERCC4, ERCC1, ERBB4, ERBB3, ERBB2, EPHB4, EPHA2, EPAS1, ENPP2, ENPEP, ENG, EMP1, EMCN, ELTD1, EIF2C1, EGR1, EGLN3, EGFR, EFNB2, EFNB1, RPS6KA1, RPS23, ROCK2, ROCK1, RIPK1, RHOC, RHOB, RHOA, RHEB, RGS5, RERGL, RELA, RB1, RASSF1, BARB, RALBP1, RAF1, RAC1, PTPRG, PTPRB, PTN, PTK2, PTH1R, PTEN, PSMA7, PRSS8, PRKCH, PRKCD, PPP2CA, PPARG, PPAP2B, PMP22, PLG, PLAT, PLA2G4C, EEF1A1, EDNRB, EDN2, EDN1, EBAG9, DUSP1, DPYS, DPEP1, DLL4, DLC1, DKFZP56400823, DICER1, DIAPH1, DIABLO, DHPS, DET1, DEFB1, DDC, DCXR, DAPK1, CYR61, CYP3A4, CYP2C8_21, CXCL12, CX3CR1, CX3CL1, CUL1, CUBN, CTSH, CTNNB1, CTNNA1, CTGF, CSF1R, CSF1, CRADD, PIK3CA, PIK3C2B, PGF, PFKP, PECAM1, PDZK3, PDZK1, PDGFRB, PDGFD, PDGFC, PDGFB, PDGFA, PCK1, PCCA, PARD6A, PAK1, PAH, OGG1, NUDT6, NRG1, NPR1, NPM1, NOTCH3, NOTCH2, NOTCH1, NOS3, NOS2, NOL3, NFX1, NFKB1, NFATC2, NFAT5, MYRIP, MYH11, MYC, MVP, COL4A1, COL18A1, CLU, CLDN7, CLDN10, CLCNKB, CFLAR, CEACAM1, CDKN1B, CDKN1A, CDH6, CDH5, CDH2, CDH16, CDH13, CD36, CD34, CD24, CCND1, CCL2, CAT, CASP10, CALD1, CACNA2D1, CA2, C7, C2 orf40, C13 orf15, BUB3, BTRC, BNIP3, BIRC2, BIN1, BGN, BCL2L12, MTOR, MSH3, MSH2, MMP2, MMP11, MLST8, MIF, MICA, MGMT, MCM3, MCAM, MARCKS, MAP2K3, MAP2K1, MAL2, MAL, LTF, LRP2, LMO2, LDB2, LDB1, LAMA 4, KRT7, KRAS, KL, KITLG, KIT, KDR, KCNJ15, KAT5, JUP, JUN, BCL2L1, BCL2, BAG1, BAD, AXL, ATP6V1B1, ASS1, ARRB1, ARHGFIB, ARF1, AQP1, APOLD1, APC, APAF1, ANXA4, ANXA1, ANTXR1, ANGPTL4, ANGPTL3, ANGPTL2, ANGPT2, ANGPT1, ALDOB, ALDH6A1, ALDH4A1, AKT3, AKT2, AKT1, AHR, AGTR1, AGT, ADH6, ADH1B, ADFP, JAG1, ITGB5, ITGB3, ITGB1, ITGA7, ITGA6, ITGA5, ITGA4, ITGA3, IQGAP2, INSR, IMPS, IL6ST, IL15, IGFBP6, ADD1, ADAMTS9, ADMATS5, ADAMTS1, ADAM17, ACE2, ACADSB, ABCG2, ABCC4, ABCC3, ABCC1, ABCB1, ABAT, AAMP, and A2M;

(i) a set of genes consisting of one or more genes selected from: TUBB2A, TPX2, TK1, SPHK1, SLC7A5, SILV, SELE, PLAU, MMP9, MMP7, MMP14, LAMB1, IL8, IL6, HSP1A1, GSTP1, GRB14, GMNN, ENO2, CCNB1, BUB1, BAG2, and ADAMTS1; and

(j) a set of genes consisting of one or more genes selected from: VWF, VCAM1, UBA3, TUSC4, TSPAN7, TSC1, TSMB10, TMEM47, TMEM27, TLR3, TIMP3, TGFBR2, TGFB2, TGFA, TEK, TCF4, STAT5A, SPRY1, SPARCL1, SOD1, SNRK, SMAD2, SLC22A6, SIRPA, SHANKS, SGK1, SELENBP1, SCN4B, ROCK1, RHOB, RGS5, RERGL, RB1, RASSF1, HMGB1, HLA-DPB1, HADH, GSTM1, GPX2, GJA1, GATM, GATA3, FOLR1, FLT4, FLT1, FHL1, FHIT, FAS, ERBB3, EPHA2, EPAS1, ENPEP, ENG, EMCN, EIF2C1, EGLN3, EFNB2, EFNB1, EDNRB, EDN1, DPYS, DKFZP56200823, DHPS, DAPK1, CYP2C8_21, CYP2C8_2, CX3CR1, CUBN, PTPRB, PTK2, PTHR1, PRSS8, PRKCH, PPAP2B, PLA2G4C, PIK3C2B, PFKP, PECAM1, PDGFD, PDGFC, PDFGB, PCSK6, PCK1, PCCA, PARD6A, NUDT6, NRG1, NOS3, NOS2, NFX1, MYH11, MYC, MUC1, MIF, MICA, MGMT, MAP2K1, LMO2, LDB2, KITLG, KDR, ITGB1, ITGA7, CRADD, CLDN10, CFLAR, CEACAM1, CDKN2A, CDKN1B, CDH5, CDH13, CD99, CD36, CD34, CD247, CCND1, CAT, CASP6, CALD1, CA9, C13 orf15, BUB3, BIN1, BCL2L1, BCL2, AXL, ATP6V1B1, ARRB1, ARHGDIB, AQP1, APOLD1, APC, ANXA5, ANXA4, ANXA1, ANGPTL7, ANGPTL4, ANGPT1, ITGA6, ITGA4, INSR, IMPS, IL6ST, IL15, IFI27, HYAL2, HYAL1, HPN, HPCAL1, ALDOB, ALDH4A1, AGTR1, ADH6, ADFP, ADD1, ABCG2, ABCC3, ABCC1, ABAT, and A2M;

wherein the gene(s) of the sets do not overlap.

9. The method of claim 8 , wherein the renal cancer is renal cell carcinoma (RCC).

10. The method of claim 9 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).

11. The method of claim 8 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.

12. The method of claim 8 , wherein the renal tumor sample is obtained from a biopsy.

13. The method of claim 8 , wherein the renal tumor sample is paraffin-embedded and fixed.

14. The method of claim 8 , wherein one or more of AAMP, ARF1, ATP5E, EEF1A1, GPX1, RPS23, SDHA, UBB, and RPLP1 is a member of the panel.

15. The method of claim 8 , wherein one or more angiogenesis genes selected from: ADD1, ANGPTL3, APOLD1, CEACAM1, EDNRB, EMCN, ENG, EPAS1, FLT1, JAG1, KDR, KL, LDB2, NOS3, NUDT6, PPAP2B, PRKCH, PTPRB, RGS5, SHANK3, SNRK, TEK, ICAM2, and VCAM1;

one or more immune response genes selected from: CCL5, CCR7, CD8A, CX3CL1, CXCL10, CXCL9, HLA-DPB1, IL6, IL8, and SPP1;

a transport gene selected from: AQP1, SGK1, and both AQP1 and SGK1;

one or more cell adhesion/extracellular matrix genes selected from: ITGB1, A2M, ITGB5, LAMB1, LOX, MMP14, TGFBR2, TIMP3, and TSPAN7;

one or more cell cycle genes selected from: BUB1, C13 orf15, CCNB1, PTTG1, TPX2, LMNB1, and TUBB2A; and/or CASP10 is a member of the panel.

16. A method of analyzing the expression of RNA transcripts of genes in a human renal cancer patient, comprising:

measuring a level of an RNA transcript, in a renal tumor sample from the patient, of a panel of genes consisting of:

(a) a set of genes consisting of one or more genes selected from: YBX1, XIAP, WWOX, VWF, VEGFA, VCAM1, USP34, UMOD, UGCG, UBB, UBA3, TYMS, TUSC4, TSPAN7, TSC2, TSC1, TP53, TOP2B, TNFSF12, TNFSF10, TNFRSF11B, TNFRSF10D, TNFRSF10B, TNFAIP6, TMEM47, TM2M27, TLR3, TIMP3, TIMP2, THBS1, TGFBR2, IGF1R, IFI27, ID3, ID2, ID1, ICAM2, HYAL2, HYAL1, HSPG2, HSD11B2, HPN, HPCAL1, HMGB1, HLA-DPB1, HIF1AN, HDAC1, HAVCR1, HADH, GZMA, GSTP1, GSTM3, GSTM1, GRB7, GPX3, GJA1, GFRA1, GCLC, GBP2, GATM, GATA3, FOS, TGFBR1, TGFB2, TGFA, TEK, TCF4, TAP1, TAGLN, TACSTD2, SUCLG1, STK11, STAT5B, STAT5A, STATS, SPRY1, SPARCL1, SPARC, SOD1, SNRK, SNAI1, SMAD4, SMAD2, SLC34A1, SLC22A6, SKIL, SHANKS, SGK1, SFRP1, SEMA3F, SELENBP1, SDPR, SDHA, SCNN1A, FOLR1, FLT4, FLT3LG, FLT1, FILIP1, FIGF, FHL1, FHIT, FH, FGFR2, FGFR1, FGF2, FGF1, FDPS, FBXW7, FAS, FABP1, ESRRG, ERG, ERCC1, ERBB3, ERBB2, EPHB4, EPHA2, EPAS1, ENPP2, ENPEP, ENG, EMP1, EMCN, ELTD1, EIF2C1, SCN4B, RPTOR, RPS6KB1, RPS6KA1, RPS23, ROCK2, ROCK1, RIPK1, RHOC, RHOB, RHOA, RGS5, RERGL, RELA, RB1, RASSF1, BARB, RALBP1, RAF1, PTPRG, PTPRB, PTN, PTK2, PTH1R, PTEN, PSMB9, PSMB8, PRSS8, PRPS2, PRKCH, PPP2CA, EGR1, EGLN3, EGFR, EFNB2, EFNB1, EEF1A1, EDNRB, EDN2, EDN1, EBAG9, DUSP1, DPYS, DPEP1, DLL4, DLC1, DKFZP56400823, DICER1, DIAPH1, DIABLO, DHPS, DET1, DEFB1, DDC, DCXR, DAPK1, CYR61, CYP3A4, CXCL9, CXCL12, CX3CR1, CX3CL1, PPARG, PPAP2B, PLG, PLAT, PLA2G4C, PIK3CA, PIK3C2B, PFKP, PECAM1, PDZK3, PDZK1, PDGFRB, PDGFD, PDGFC, PDGFB, PDGFA, PCK1, PCCA, PARD6A, PAK1, PAH, OGG1, NUDT6, NRG1, NPR1, NPM1, NOTCH3, NOTCH2, NOTCH1, NOS3, NOS2, NOL3, NFX1, CUL1, CUBN, CTSS, CTSH, CTNNB1, CTNNA1, CTGF, CSF1R, CSF1, CRADD, COL4A2, COL18A1, CLU, CLDN7, CLDN10, CLCNKB, CFLAR, CEACAM1, CDKN1B, CDKN1A, CDH6, CDH5, CDH16, CDH13, CD4, CD36, CD34, CCR7, CCR4, CCND1, CCL4, CCL2, CAT, NFKB1, NFATC2, NFAT5, MYRIP, MYH11, MYC, MVP, MUC1, MTOR, MSH3, MSH2, MLST8, MIF, MICA, MGMT, MCM3, MCAM, MARCKS, MAPK3, MAPK1, MAP4, MAP2K3, MAP2K1, MAL2, MAL, LYZ, LTF, LRP2, LMO2, LDB2, LDB1, LAMA 4, KRT7, CASP6, CASP10, CALD1, CA9, CA2, C7, C2 orf40, C13 orf15, BUB3, BTRC, BIRC2, BIN1, BGN, BCL2L12, BCL2L1, BCL2, BBC3, BAG1, BAD, ATP6V1B1, ASS1, ARRB1, ARHGDIB, AQP1, APOLD1, APC, ANXA4, ANXA1, ANTXR1, ANGPTL4, ANGPTL3, ANGPT1, ALDOB, KRAS, KL, KITLG, KIT, KDR, KCNJ15, KAT5, JUP, JUN, JAG1, ITGB1, ITGA7, ITGA6, ITGA4, ITGA3, IQGAP2, INSR, IMPS, IL6ST, IL15, IGFBP6, IGFBP3, IGFBP2, ALDH6A1, ALDH4A1, AKT3, AKT2, AKT1, AIF1, AHR, AGTR1, ADH1B, ADFP, ADD1, ADAMTS5, ADAMTS1, ACE2, ACADSB, ABCG2, ABCC4, ABCC3, ABCC1, ABCB1, ABAT, AAMP, and A2M;

(b) a set of genes consisting of one or more genes selected from: WT1, VTN, VDR, VCAN, UBE2T, TPX2, TOP2A, TK1, TIMP1, TGFBI, SQSTM1, SPP1, SPHK1, SLC7A5, SLC2A1, SLC16A3, SLC13A3, SHC1, SFN, SERPINA5, SEMA3C, SAA2, S100A1, RRM2, RPLP1, PTTG1, PTGS2, PLAUR, PF4, PCSK6, MYBL2, MT1X, MMP9, LGALS1, LAMBS, LAMB1, L1CAM, IL8, IL6, ICAM1, HIST1H1D, FN1, F3, F2, ESPL1, EPHB2, EPHB1, ENO2, EIF4EBP1, CXCR4, CXCL1, CTSB, CRP, CP, COL7A1, COL1A1, CHEK1, CENPF, CD82, CD44_s, CCNE1, CCNB1, CCL20, CA12, C3, BUB1, MMP7, MMP14, MKI67, MGST1, MDK, LOX, LMNB1, LIMK1, BIRC5, BIRC3, BCL2A1, AURKA, ANXA2, ALOX5, ADAM8, and ABCC2;

(c) a set of genes consisting of one or more genes selected from: ACE2, ADD1, ALDOB, ANGPTL3, APOLD1, AQP1, NUDT6, CASP10, CAV2, CCL4, CCL5, CCR2, CCR4, CCR7, CD4, CD8A, CEACAM1, CFLAR, CTSS, CX3CL1, CXCL10, CXCL9, CXCR6, DAPK1, DDC, DLC1, C2 orf40, EDNRB, EMCN, EPAS1, FAS, FH, GATA3, GZMA, HLA-DPB1, HSPG2, ICAM2, ICAM3, ID1, IGF1R, IL15, IQGAP2, KL, KLRK1, LDB2, LRP2, LTF, MAP4, ABCC1, NOS3, PIK3C2B, PLA2G4C, PPAP2B, PRCC, PRKCB, PRKCH, PRSS8, PSMB9, PTPRB, RGS5, SDPR, SELE, SGK1, SHANKS, SNRK, TEK, TGFBR2, TIMP3, TMEM27, TSPAN7, UBB, and WWOX; and

(d) a set of genes consisting of one or more genes selected from: BIRC2, BUB1, CCNB1, ENO2, ITGB1, ITGB5, LAMB1, MMP14, MMP9, PSMA7, RUNX1, SPHK1, SPP1, SQSTM1, TPX2, TUBB2A, and VCAN; and

(e) a set of genes consisting of one or more reference genes wherein the set of reference genes is GAPDH, beta-actin, or both of GAPDH and beta-actin;

wherein the gene(s) of the sets do not overlap.

17. The method of claim 16 , wherein the renal cancer is renal cell carcinoma (RCC).

18. The method of claim 17 , wherein the RCC is clear cell renal cell carcinoma (ccRCC).

19. The method of claim 16 , wherein the level of the RNA transcripts is measured by quantitative RT-PCR.

20. The method of claim 16 , wherein the renal tumor sample is obtained from a biopsy.

21. The method of claim 16 , wherein the renal tumor sample is paraffin-embedded and fixed.

22. The method of claim 16 , wherein one or more angiogenesis genes selected from: ADD1, ANGPTL3, APOLD1, CEACAM1, EDNRB, EMCN, ENG, EPAS1, FLT1, JAG1, KDR, KT, LDB2, NOS3, NUDT6, PPAP2B, PRKCH, PTPRB, RGS5, SHANK3, SNRK, TEK, ICAM2, and VCAM1;

one or more immune response genes selected from: CCL5, CCR7, CD8A, CX3CL1, CXCL10, CXCL9, HLA-DPB1, IL6, IL8, and SPP1;

a transport gene selected from: AQP1, SGK1, and both AQP1 and SGK1;

one or more cell adhesion/extracellular matrix genes selected from: ITGB1, A2M, ITGB5, LAMB1, LOX, MMP14, TGFBR2, TIMP3, and TSPAN7;

one or more cell cycle genes selected from: BUB1, C13 orf15, CCNB1, PTTG1, ‘1 PX2, LMNB1, and TUBB2A; and/or

CASP10 is a member of the panel.