Table 2.
Cox regression for survival analysis of the 42 genes’ mRNA expression in meta-cohort (Affymetrix U133A, n = 1820; or U133Plus2, n = 1436) for overall survival (OS), and disease-free survival (DFS). A negative regression coefficient implies a better prognosis for patients if they retain the function of a given gene (worse prognosis when the cancer underexpresses the gene). Conversely, a positive regression coefficient means that the hazard is higher for a given gene’s overexpression and, thus, the prognosis worse.
| Gene | Gene ID | aCGH CNA Event | %CNA Overlap with Normal | Cox’s OS (p-Value) | Cox’s DFS (p-Value) |
|---|---|---|---|---|---|
| ADRA1A | 148 | Loss | 0.42 | −0.40185, (0.152322) | −1.67582, (0.001948) |
| ADRA1D | 146 | Loss | 1.15 | −0.5968, (0.020507) | 0.066504, (0.880385) |
| ADRB3 | 155 | Loss | 0 | −1.21809, (0.002366) | −1.12818, (0.08601) |
| APOBEC3D | 140564 | Loss | 0 | −0.45803, (0.24853) | −1.56085, (0.0224) |
| BRF2 | 55290 | Loss | 0 | −0.45526, (0.02013) | 0.061887, (0.8515) |
| C20orf202 | 400831 | Loss | 0.89 | −0.80141, (0.000481) | −0.19907, (0.628292) |
| CABIN1 | 23523 | Loss | 4.02 | −0.47782, (0.0210) | −0.51601, (0.14935) |
| CACNA1I | 8911 | Loss | 0 | −0.69524, (0.00404) | −0.73386, (0.082677) |
| CSMD1 | 64478 | Loss | 0 | −0.01578, (0.956357) | −1.30789, (0.01948) |
| DIO3 | 1735 | Loss | 1.76 | −0.32561, (0.041777) | −0.00829, (0.973719) |
| EPHX2 | 2053 | Loss | 0.42 | 0.036582, (0.61411) | −0.30515, (0.0099) |
| FAM83F | 113828 | Loss | 0 | −0.13746, (0.287004) | −0.72925, (0.00085) |
| GP1BB | 2812 | Loss | 0 | −0.56827, (0.000246) | −0.19289, (0.495577) |
| KIAA1656 | 85371 | Loss | 0 | −0.60241, (0.01922) | −1.02118, (0.032326) |
| LOC339593 | 339593 | Loss | 0.17 | 0.29021, (0.385267) | −1.12678, (0.047789) |
| MCM8 | 84515 | Loss | 0 | 0.043419, (0.614947) | −0.31948, (0.034203) |
| NAT1 | 9 | Loss | 0 | 0.028159, (0.713606) | −0.36337, (0.007197) |
| NAT2 | 10 | Loss | 0 | −0.09059, (0.160865) | −0.30169, (0.003804) |
| HNF6 | 3175 | Loss | 0 | −0.66924, (0.017955) | −0.51152, (0.31) |
| PCDHGA11 | 56105 | Loss | 0 | −0.85799, (0.001447) | −0.577, (0.33928) |
| RAB11FIP1 | 80223 | Loss | 0 | −0.38036, (5.55× 10−05) | −0.02196, (0.87) |
| SPAG11A | 653423 | Loss | 68.65 | −0.81665, (0.001447) | −0.13298, (0.57) |
| SIRPD | 128646 | Loss | 0.89 | −0.89166, (0.014166) | −0.13392, (0.82) |
| TEX43 | 389320 | Loss | 0 | −0.46611, (0.175471) | −0.19907, (0.01162) |
| TOP1P2 | 7152 | Loss | 0 | −1.13965, (0.005692) | 0.599602, (0.32) |
| WDR5 | 11091 | Loss | 0 | −0.0007, (0.995962) | −0.52505, (0.024307) |
| ZNF366 | 167465 | Loss | 0.07 | −0.76274, (0.01779) | −0.93429, (0.09208) |
| ZNF703 | 80139 | Loss | 0 | −0.32601, (0.000744) | −0.14954, (0.366064) |
| ZNRF3 | 84133 | Loss | 0 | −0.03445, (0.605797) | −0.33884, (0.002065) |
| ANXA2P2 | 304 | Gain | 0 | 0.478663, (0.003259) | 0.997702, (0.000504) |
| CDC42BPA | 8476 | Gain | 0 | 0.032966, (0.690294) | 0.401718, (0.005473) |
| DOK5 | 55816 | Gain | 0.57 | 0.105512, (0.1) | 0.577502, (0.002218) |
| DUSP14 | 11072 | Gain | 0.70 | 0.207902, (0.047604) | 0.709569, (0.000159) |
| GLIS3 | 169792 | Gain | 1.25 | 0.0916, (0.210004) | 0.397791, (0.000566) |
| ING1 | 3621 | Gain | 0 | 0.461934, (0.020587) | 0.127394, (0.710857) |
| MPDZ | 8777 | Gain | 0 | 0.079568, (0.406857) | 0.657405, (3.98 × 10−5) |
| PITPNC1 | 26207 | Gain | 0 | 0.257758, (0.029048) | 0.418362, (0.026674) |
| SCEL | 8796 | Gain | 0 | 0.081094, (0.202236) | 0.301113, (0.000357) |
| SEMG1 | 6406 | Gain | 0 | 0.098826, (0.043099) | 0.153704, (0.061048) |
| SMU1 | 55234 | Gain | 0.73 | 0.36857, (0.008896) | 0.016381, (0.942047) |
| USP32 | 84669 | Gain | 0 | 0.162429, (0.221638) | 0.586012, (0.01236) |
| VLDLR | 7436 | Gain | 0.14 | −0.00629, (0.92868) | 0.323607, (0.004972) |