Table 1.
Gene signatures that best predicted the responses of TCGA patients
| Gene signature ID | Cancer type tested | GI50 threshold | Signature (C; σ) |
|---|---|---|---|
| Cis1 (Cisplatin) | Bladder | 5.11 | BARD1, BCL2, BCL2L1, CDKN2C, FAAP24, FEN1, MAP3K1, MAPK13, MAPK3, NFKB1, NFKB2, SLC22A5, SLC31A2, TLR4, TWIST1 (100,000; 100) |
| Cis2 (Cisplatin) | Bladder | 5.12 | BARD1, BCL2L1, CFLAR, FAAP24, MAP3K1, MAPK3, NFKB1, POLQ, PRKAA2, SLC22A5, SLC31A2, TLR4, TWIST1 (10,000; 100) |
| Cis3 (Cisplatin) | Bladder | 5.60 | BCL2, CFLAR, ERCC2, ERCC6, FAAP24, FEN1, MAP3K1, NFKB1, NFKB2, PNKP, POLQ, PRKCB, SLC22A5, SNAI1, TLR4 (100,000; 100) |
| Cis12 (Cisplatin) | Bladder | 5.40 | ATP7B, BCL2, BCL2L1, CDKN2C, ERCC2, FAAP24, GSTO1, MAP3K1, MAPK3, MT2A, NFKB1, NFKB2, POLD1, POLQ, PRKCB, SNAI1, TLR4, TP63 (10,000; 100) |
| Cis14 (Cisplatin) | Bladder | 5.16 | BARD1, BCL2, BCL2L1, CDKN2C, FAAP24, FEN1, FOS, GSTP1, MAP3K1, MAPK13, MAPK3, MSH2, NFKB1, POLD1, POLQ, PRKAA2, PRKCB, SLC22A5, SLC31A2, SNAI1, TWIST1 (10,000; 100) |
| Cis17 (Cisplatin) | Bladder | 5.10 | ATP7B, BCL2, BCL2L1, FEN1, GSTP1, MAP3K1, MAPK3, MT2A, NFKB1, PNKP, POLQ, PRKAA2, PRKCB, SLC31A2, TLR4, TP63 (100,000; 100) |
| Car1 (Carboplatin) | Ovarian | 4.22 | AKT1, EIF3K, ERCC1, GNGT1, GSR, MTHFR, NEDD4L, NLRP1, NRAS, RAF1, SGK1, TIGD1, TP53, VEGFB, VEGFC (100,000; 100) |
| Car9 (Carboplatin) | Ovarian | 4.32 | AKT1, ATP7B, EIF3I, ETS2, GNGT1, HRAS, KRAS, LIG3, MTHFR, MTR, NRAS, RAD50, SCN10A, TIGD1, TP53, VEGFB (10,000; 100) |
| Car51 (Carboplatin) | Ovarian | 4.34 | AKT1, EGF, EIF3I, ERCC1, ETS2, GNGT1, KRAS, MTHFR, MTR, NEDD4L, NLRP1, NRAS, RAD50, RAF1, SGK1, TIGD1, TP53, VEGFB, VEGFC (10,000; 100) |
| Car73 (Carboplatin) | Ovarian | 4.09 | AKT1, ATP7B, ETS2, GNGT1, HRAS, NLRP1, SCN10A, VEGFB (100,000; 1000) |
| Oxa1 (Oxaliplatin) | Colorectal | 5.10 | BRAF, FCGR2A, IGF1, MSH2, NAGK, NFE2L2, NQO1, PANK3, SLC47A1, SLCO1B1, UGT1A1 (10; 10) |
| Oxa21 (Oxaliplatin) | Colorectal | 5.10 | BRAF, IGF1, IGF1R, KLF3, MSH2, NAT2, NFE2L2, NQO1, PANK3, PRSS1, SIAE, SLC47A1, SLCO1B1, UGT1A1 (1000; 100) |
C—the box-constraint; σ—the kernel-scale (sigma)
Bolded gene signatures are those that exhibited the best overall performance in discriminating among TCGA patient outcomes