Table 1.
List of deregulated genes associated with bad prognosis
| Probe ID | Transcript ID | Gene symbol | AFFYMETRIX | ONCOMINE | KMPLOTTER | |||
|---|---|---|---|---|---|---|---|---|
| PFS | ||||||||
| Fold change | P‐Value ANOVA | Fold change | P‐Value | HR | P‐Value | |||
| 211767_at | g13543688 | GINS4 | 4.01 | 0.002866 | 2.404 | 1.11E‐05 | 2.87 (1.54–5.35) | 0.0005 |
| 228729_at | Hs.23960.0 | CCNB1 | 4.03 | 8.24E‐07 | 6.152 | 5.33E‐06 | 2.85 (1.3–6.22) | 0.0062 |
| 1569241_a_at | Hs2.149839.1 | ZNF93 | 4.06 | 0.004685 | 2.296 | 6.40E‐06 | 2.41 (1.14–5.08) | 0.0176 |
| 205869_at | g4506144 | PRSS1 | 4.06 | 0.000394 | 2.008 | 2.12E‐07 | 1.91 (1.06–3.45) | 0.0296 |
| 213100_at | Hs.13350.0 | UNC5B | 4.07 | 0.000451 | 1.351 | 0.006 | 1.82 (1.01–3.3) | 0.0432 |
| 216615_s_at | Hs.2142.1 | HTR3A | 4.11 | 0.001305 | 3.505 | 4.76E‐16 | 2.23 (1.19–4.15) | 0.0098 |
| 40020_at | 4858618_RC | CELSR3 | 4.13 | 9.48E‐08 | 1.502 | 7.89E‐07 | 3.86 (1.98–7.54) | 0 |
| 219306_at | g9910265 | KIF15 | 4.17 | 0.000147 | 3.696 | 2.29E‐08 | 2.88 (1.54–5.38) | 0.0005 |
| 209342_s_at | g4185274 | IKBKB | 4.17 | 0.007424 | 1.31 | 2.12E‐04 | 2.44 (1.31–4.56) | 0.0038 |
| 213759_at | Hs.111554.1 | ARL4C | 4.21 | 0.008012 | 3.624 | 8.81E‐06 | 1.89 (1.06–3.39) | 0.0289 |
| 206134_at | g7657318 | ADAMDEC1 | 4.21 | 0.003324 | 1.87 | 0.012 | 1.88 (1.04–3.39) | 0.0337 |
| 219787_s_at | g8922431 | ECT2 | 4.23 | 0.000033 | 10.209 | 2.81E‐08 | 2.62 (1.42–4.83) | 0.0014 |
| 210559_s_at | g3126638 | CDK1 | 4.23 | 0.000803 | 7.317 | 4.85E‐07 | 1.8 (1.01–3.23) | 0.0447 |
| 204444_at | g13699823 | KIF11 | 4.25 | 0.000272 | 5.467 | 7.52E‐07 | 2.73 (1.48–5.03) | 0.0008 |
| 209053_s_at | Hs.110457.3 | WHSC1 | 4.25 | 0.000004 | 3.805 | 3.67E‐10 | 3.03 (1.57–5.84) | 0.0005 |
| 209198_s_at | g13279139 | SYT11 | 4.27 | 0.000005 | 2.974 | 1.43E‐07 | 3.4 (1.81–6.39) | 0.0001 |
| 207156_at | g10800131 | HIST1H2AG | 4.3 | 0.006192 | 1.554 | 5.81E‐06 | 1.96 (1.1–3.5) | 0.0201 |
| 205544_s_at | g4503026 | CR2 | 4.34 | 0.027892 | 1.428 | 6.37E‐06 | 3.37 (1.74–6.53) | 0.0001 |
| 203046_s_at | g4507506 | TIMELESS | 4.36 | 4.84E‐07 | 3.434 | 2.30E‐09 | 1.86 (1.03–3.37) | 0.0365 |
| 202870_s_at | g4557436 | CDC20 | 4.41 | 0.000004 | 11.259 | 2.44E‐06 | 3.87 (2.01–7.46) | 0 |
| 202860_at | g7662151 | DENND4B | 4.43 | 0.000019 | 1.563 | 3.19E‐04 | 3.3 (1.71–6.37) | 0.0002 |
| 214933_at | Hs.96253.2 | CACNA1A | 4.45 | 0.000001 | 2.563 | 1.47E‐05 | 2.6 (1.39–4.85) | 0.0018 |
| 210587_at | g13477368 | INHBE | 4.47 | 0.042977 | 1.32 | 7.38E‐05 | 2.22 (1.2–4.09) | 0.0089 |
| 214005_at | Hs.77719.1 | GGCX | 4.5 | 2.02E‐08 | 1.837 | 2.04E‐04 | 2.45 (1.35–4.46) | 0.0025 |
| 205660_at | g11321576 | OASL | 4.53 | 0.006553 | 2.449 | 9.95E‐05 | 2.06 (1.13–3.78) | 0.0165 |
| 219454_at | g13124887 | EGFL6 | 4.54 | 0.000439 | 2.582 | 5.00E‐03 | 2.34 (1.27–4.31) | 0.0049 |
| 212816_s_at | Hs.84152.2 | CBS | 4.55 | 0.000561 | 2.658 | 1.00E‐03 | 2.06 (1.14–3.74) | 0.0146 |
| 205394_at | g4502802 | CHEK1 | 4.6 | 0.000004 | 4.147 | 2.43E‐07 | 2.04 (1.13–3.66) | 0.015 |
| 221436_s_at | g13876383 | CDCA3 | 4.65 | 0.001047 | 4.847 | 1.30E‐09 | 2.09 (1.15–3.77) | 0.0128 |
| 207109_at | g7657408 | POU2F3 | 4.66 | 0.024312 | 1.741 | 4.43E‐04 | 2.81 (1.53–5.18) | 0.0005 |
| 202219_at | g5032096 | SLC6A8 | 4.68 | 0.000195 | 1.94 | 1.76E‐07 | 2.17 (1.18–4) | 0.0108 |
| 217025_s_at | Hs.89434.1 | DBN1 | 4.69 | 0.007175 | 2.141 | 1.84E‐06 | 2.11 (1.13–3.93) | 0.0163 |
| 202338_at | g4507518 | TK1 | 4.73 | 0.00005 | 4.968 | 1.55E‐08 | 2.07 (1.13–3.77) | 0.0156 |
| 222251_s_at | Hs.28906.1 | GMEB2 | 4.81 | 0.004936 | 1.339 | 3.27E‐04 | 5.5 (2.57–11.76) | 0 |
| 210697_at | g4454677 | ZNF257 | 4.82 | 0.001284 | 1.673 | 1.66E‐05 | 2.06 (1.15–3.7) | 0.0135 |
| 214339_s_at | Hs.86575.2 | MAP4K1 | 4.87 | 0.000074 | 1.866 | 1.13E‐05 | 2.07 (1.13–3.79) | 0.0154 |
| 203022_at | g5454009 | RNASEH2A | 4.94 | 0.000147 | 2.785 | 1.11E‐06 | 2.06 (1.13–3.76) | 0.016 |
| 206280_at | g4826670 | CDH18 | 4.96 | 0.006096 | 1.396 | 0.004 | 2.05 (1.14–3.7) | 0.0143 |
| 211343_s_at | g180828 | COL13A1 | 5 | 0.000822 | 1.318 | 3.17E‐04 | 2.05 (1.13–3.75) | 0.0165 |
| 206513_at | g4757733 | AIM2 | 5.02 | 0.007612 | 1.547 | 6.09E‐04 | 2.73 (1.46–5.11) | 0.0011 |
| 204994_at | g11342663 | MX2 | 5.03 | 0.001647 | 3.916 | 3.32E‐04 | 2.2 (1.19–4.06) | 0.0098 |
| 205163_at | g7019426 | MYLPF | 5.04 | 0.000789 | 1.397 | 4.94E‐06 | 1.97 (1.1–3.54) | 0.0201 |
| 218726_at | g8922180 | HJURP | 5.07 | 0.010918 | 5.547 | 2.20E‐09 | 1.95 (1.08–3.5) | 0.023 |
| 239219_at | Hs.221197.0 | AURKB | 5.1 | 0.001028 | 2.818 | 2.34E‐05 | 2.22 (1.04–4.76) | 0.0353 |
| 202575_at | g6382069 | CRABP2 | 5.27 | 0.000004 | 3.216 | 9.08E‐05 | 2.08 (1.16–3.74) | 0.0124 |
| 35160_at | 4870487_RC | LDB1 | 5.29 | 0.00032 | 1.5 | 1.00E‐03 | 2.35 (1.27–4.32) | 0.0048 |
| 212556_at | Hs.239784.0 | SCRIB | 5.31 | 5.24E‐07 | 2.578 | 8.65E‐07 | 2 (1.1–3.65) | 0.021 |
| 203439_s_at | g12653744 | STC2 | 5.31 | 0.001003 | 2.509 | 1.53E‐06 | 1.85 (1.03–3.35) | 0.0379 |
| 234040_at | Hs.287543.0 | HELLS | 5.35 | 0.004925 | 2.352 | 3.86E‐05 | 2.39 (1.11–5.11) | 0.0209 |
| 221125_s_at | g7657250 | KCNMB3 | 5.47 | 0.000016 | 1.637 | 2.06E‐06 | 2.03 (1.11–3.71) | 0.0183 |
| 205569_at | g7657660 | LAMP3 | 5.48 | 0.040774 | 3.979 | 3.15E‐04 | 3.56 (1.85–6.85) | 0.0001 |
| 213520_at | Hs.31442.0 | RECQL4 | 5.48 | 0.00012 | 1.358 | 0.002 | 2.61 (1.4–4.87) | 0.0018 |
| 205034_at | g4757931 | CCNE2 | 5.49 | 0.00002 | 1.344 | 2.00E‐03 | 2.29 (1.27–4.11) | 0.0046 |
| 222037_at | Hs.154443.1 | MCM4 | 5.52 | 0.013214 | 4.726 | 8.00E‐08 | 2.9 (1.55–5.41) | 0.0005 |
| 218494_s_at | g13236503 | SLC2A4RG | 5.64 | 0.000878 | 2.118 | 5.86E‐06 | 2.48 (1.33–4.62) | 0.0031 |
| 212235_at | Hs.301685.0 | PLXND1 | 5.64 | 0.000117 | 1.496 | 4.67E‐04 | 2.05 (1.13–3.71) | 0.0152 |
| 218296_x_at | g8922469 | MSTO1 | 5.72 | 0.000026 | 1.381 | 0.018 | 1.83 (1–3.33) | 0.0458 |
| 218009_s_at | g4506038 | PRC1 | 5.74 | 9.19E‐07 | 7.214 | 5.32E‐08 | 2.85 (1.53–5.32) | 0.0006 |
| 209680_s_at | g12653842 | KIFC1 | 5.78 | 0.000129 | 3.845 | 3.64E‐08 | 2.33 (1.28–4.24) | 0.0046 |
| 202954_at | g5902145 | UBE2C | 5.81 | 2.13E‐08 | 10.184 | 2.24E‐07 | 3.03 (1.62–5.66) | 0.0003 |
| 205240_at | g9558734 | GPSM2 | 6.01 | 0.000545 | 3.965 | 2.97E‐08 | 1.81 (1.01–3.25) | 0.0435 |
| 209262_s_at | g12803666 | NR2F6 | 6.05 | 2.41E‐07 | 1.61 | 2.18E‐05 | 2.26 (1.23–4.17) | 0.0071 |
| 203632_s_at | g7706450 | GPRC5B | 6.12 | 0.000022 | 1.672 | 0.004 | 2.22 (1.21–4.04) | 0.0078 |
| 207165_at | g7108350 | HMMR | 6.14 | 0.000011 | 3.819 | 1.48E‐10 | 2.35 (1.3–4.25) | 0.0037 |
| 205046_at | g4502780 | CENPE | 6.16 | 0.00057 | 2.711 | 1.59E‐07 | 2.55 (1.36–4.75) | 0.0024 |
| 208394_x_at | g13259505 | ESM1 | 6.2 | 0.000021 | 1.496 | 0.009 | 2.05 (1.13–3.71) | 0.0152 |
| 216237_s_at | Hs.77171.1 | MCM5 | 6.22 | 0.001843 | 1.795 | 7.33E‐05 | 2.33 (1.25–4.34) | 0.0063 |
| 205449_at | g9558738 | SAC3D1 | 6.31 | 0.000029 | 1.891 | 3.53E‐05 | 2.19 (1.2–4) | 0.0086 |
| 203099_s_at | g4558755 | CDYL | 6.33 | 0.000004 | 1.889 | 4.26E‐05 | 2.1 (1.15–3.83) | 0.013 |
| 210983_s_at | g12751125 | MCM7 | 6.48 | 0.008102 | 3.523 | 2.31E‐07 | 2.23 (1.21–4.1) | 0.0084 |
| 210052_s_at | g6073830 | TPX2 | 6.5 | 2.90E‐08 | 13.887 | 1.65E‐07 | 2.55 (1.38–4.69) | 0.0019 |
| 225846_at | Hs.24743.1 | ESRP1 | 6.53 | 0.000005 | 2.135 | 2.68E‐04 | 2.3 (1.04–5.06) | 0.0335 |
| 218308_at | g5454101 | TACC3 | 6.54 | 0.000462 | 4.047 | 9.61E‐06 | 4.1 (2.04–8.24) | 0 |
| 239570_at | Hs.144137.0 | RAB1A | 6.76 | 0.000581 | 1.31 | 3.07E‐04 | 2.48 (1.1–5.6) | 0.0242 |
| 203358_s_at | g4758323 | EZH2 | 6.84 | 0.000002 | 6.584 | 1.44E‐06 | 3.63 (1.93–6.8) | 0 |
| 203806_s_at | g4503654 | FANCA | 6.87 | 0.00001 | 1.793 | 7.55E‐05 | 2.69 (1.42–5.08) | 0.0016 |
| 219502_at | g8922721 | NEIL3 | 6.91 | 0.000004 | 1.519 | 1.08E‐05 | 2.36 (1.3–4.28) | 0.0035 |
| 208079_s_at | g4507278 | AURKA | 7 | 3.64E‐08 | 6.504 | 6.53E‐08 | 2.95 (1.6–5.45) | 0.0003 |
| 204709_s_at | g13699831 | KIF23 | 7 | 0.000061 | 4.68 | 2.17E‐06 | 2.7 (1.48–4.95) | 0.0008 |
| 203755_at | g5729749 | BUB1B | 7.09 | 6.83E‐10 | 8.04 | 2.56E‐07 | 2.86 (1.55–5.29) | 0.0004 |
| 222039_at | Hs.274448.1 | KIF18B | 7.2 | 6.26E‐09 | 2.135 | 4.91E‐06 | 2.4 (1.31–4.37) | 0.0032 |
| 204822_at | g4507718 | TTK | 7.21 | 7.51E‐07 | 15.153 | 2.06E‐09 | 2.52 (1.38–4.61) | 0.0019 |
| 212023_s_at | Hs.80976.1 | MKI67 | 7.25 | 1.04E‐07 | 4.023 | 5.17E‐10 | 1.94 (1.07–3.51) | 0.0256 |
| 204170_s_at | g4502858 | CKS2 | 7.39 | 6.82E‐08 | 5.956 | 3.85E‐05 | 2.06 (1.14–3.73) | 0.0147 |
| 207183_at | g5453665 | GPR19 | 7.43 | 0.000063 | 2.901 | 8.95E‐09 | 3.07 (1.64–5.72) | 0.0002 |
| 207828_s_at | g4885132 | CENPF | 7.52 | 0.000002 | 3.811 | 1.75E‐06 | 2.64 (1.43–4.87) | 0.0013 |
| 206157_at | g4506332 | PTX3 | 7.56 | 0.000006 | 2.79 | 0.004 | 2.93 (1.6–5.37) | 0.0003 |
| 218039_at | g7705950 | NUSAP1 | 7.63 | 5.89E‐09 | 9.731 | 7.45E‐07 | 2.08 (1.16–3.75) | 0.0123 |
| 203554_x_at | g11038651 | PTTG1 | 7.68 | 0.000002 | 5.99 | 1.80E‐05 | 3.34 (1.76–6.34) | 0.0001 |
| 209891_at | g9963834 | SPC25 | 7.73 | 0.000027 | 2.928 | 9.73E‐24 | 2.45 (1.34–4.47) | 0.0026 |
| 221520_s_at | g12804484 | CDCA8 | 7.78 | 0.000076 | 3.705 | 5.44E‐07 | 2.63 (1.41–4.91) | 0.0016 |
| 218755_at | g5032012 | KIF20A | 7.9 | 1.87E‐08 | 9.021 | 9.21E‐08 | 2.56 (1.37–4.78) | 0.0021 |
| 201761_at | g13699869 | MTHFD2 | 7.92 | 0.000004 | 3.82 | 1.20E‐04 | 2.68 (1.45–4.94) | 0.001 |
| 204649_at | g4885624 | TROAP | 7.95 | 0.000014 | 3.096 | 5.11E‐08 | 2.83 (1.49–5.35) | 0.0008 |
| 209408_at | g1695881 | KIF2C | 8.01 | 2.31E‐08 | 2.834 | 6.75E‐11 | 2.43 (1.33–4.44) | 0.003 |
| 201663_s_at | g4885112 | SMC4 | 8.12 | 0.008518 | 7.44 | 9.32E‐09 | 2.55 (1.38–4.71) | 0.0019 |
| 218542_at | g8922501 | CEP55 | 8.28 | 0.000158 | 8.075 | 1.50E‐08 | 1.89 (1.05–3.4) | 0.0304 |
| 222958_s_at | Hs.133260.0 | DEPDC1 | 8.47 | 0.000182 | 3.833 | 2.12E‐07 | 2.61 (1.19–5.7) | 0.0127 |
| 222008_at | Hs.154850.0 | COL9A1 | 8.48 | 0.000545 | 1.946 | 2.30E‐16 | 1.93 (1.08–3.47) | 0.0249 |
| 210512_s_at | g3719220 | VEGFA | 8.51 | 6.97E‐09 | 2.741 | 1.17E‐07 | 3.37 (1.75–6.48) | 0.0001 |
| 205733_at | g4557364 | BLM | 8.53 | 0.000002 | 2.88 | 3.59E‐06 | 1.99 (1.1–3.59) | 0.0205 |
| 236641_at | Hs.116649.0 | KIF14 | 8.88 | 0.000311 | 3.139 | 5.27E‐06 | 2.28 (1.01–5.13) | 0.0414 |
| 204962_s_at | g4585861 | CENPA | 8.9 | 0.000014 | 11.775 | 2.63E‐09 | 2.48 (1.35–4.57) | 0.0026 |
| 202705_at | g10938017 | CCNB2 | 9.15 | 1.13E‐07 | 10.154 | 1.59E‐06 | 1.87 (1.04–3.37) | 0.0329 |
| 218585_s_at | g7705575 | DTL | 9.2 | 2.49E‐10 | 6.089 | 1.58E‐07 | 1.89 (1.06–3.38) | 0.0289 |
| 38158_at | 4852842_RC | ESPL1 | 9.2 | 8.96E‐09 | 4.341 | 6.11E‐07 | 3.19 (1.69–6.04) | 0.0002 |
| 213523_at | Hs.9700.0 | CCNE1 | 9.36 | 2.03E‐07 | 7.062 | 8.28E‐09 | 1.84 (1.02–3.33) | 0.0407 |
| 222946_s_at | g12652906 | AUNIP | 9.41 | 0.00175 | 2.956 | 7.47E‐08 | 2.11 (0.99–4.52) | 0.0485 |
| 213075_at | Hs.94795.0 | OLFML2A | 9.44 | 0.000481 | 1.423 | 3.00E‐03 | 1.86 (1.04–3.34) | 0.0348 |
| 204825_at | g7661973 | MELK | 9.59 | 0.000007 | 10.6 | 2.98E‐07 | 1.95 (1.08–3.5) | 0.0233 |
| 212563_at | Hs.30736.0 | BOP1 | 9.61 | 0.000165 | 1.669 | 3.35E‐06 | 2.03 (1.11–3.69) | 0.0186 |
| 204026_s_at | g6857828 | ZWINT | 9.92 | 1.65E‐09 | 7.001 | 1.71E‐05 | 2.05 (1.14–3.7) | 0.015 |
| 202580_x_at | g11386144 | FOXM1 | 10.06 | 0.000022 | 5.982 | 8.64E‐09 | 3.03 (1.6–5.73) | 0.0003 |
| 205694_at | g4507756 | TYRP1 | 10.15 | 0.000772 | 1.624 | 2.09E‐34 | 1.79 (1–3.23) | 0.0486 |
| 204584_at | Hs.1757.0 | L1CAM | 10.27 | 0.000008 | 3.985 | 7.02E‐15 | 3.02 (1.63–5.58) | 0.0002 |
| 218662_s_at | g11641252 | NCAPG | 10.35 | 4.18E‐08 | 3.207 | 2.13E‐10 | 3.28 (1.76–6.14) | 0.0001 |
| 204695_at | Hs.1634.0 | CDC25A | 10.39 | 0.000002 | 2.633 | 2.49E‐05 | 2.39 (1.31–4.34) | 0.0033 |
| 212807_s_at | Hs.281706.1 | SORT1 | 10.54 | 4.63E‐07 | 1.977 | 9.60E‐06 | 2.05 (1.12–3.75) | 0.0172 |
| 202094_at | Hs.1578.0 | BIRC5 | 10.82 | 0.000018 | 4.83 | 2.20E‐10 | 2.85 (1.53–5.31) | 0.0006 |
| 204558_at | g4506396 | RAD54L | 11.24 | 0.000856 | 2.09 | 6.38E‐06 | 2.85 (1.53–5.32) | 0.0006 |
| 218355_at | g7305204 | KIF4A | 11.53 | 5.42E‐08 | 2.359 | 1.00E‐03 | 2.82 (1.51–5.27) | 0.0007 |
| 219650_at | g8923111 | ERCC6L | 12.29 | 6.30E‐07 | 2.245 | 8.13E‐06 | 2.24 (1.24–4.04) | 0.0063 |
| 204437_s_at | g9257206 | FOLR1 | 12.72 | 0.000017 | 1.696 | 2.00E‐03 | 2.05 (1.13–3.7) | 0.0155 |
| 203418_at | g4502612 | CCNA2 | 13.14 | 0.00196 | 4.795 | 2.28E‐07 | 1.82 (1.02–3.26) | 0.0403 |
| 205242_at | g5453576 | CXCL13 | 16.29 | 0.0001 | 2.091 | 2.94E‐08 | 1.83 (1.02–3.28) | 0.0411 |
| 205572_at | g4557314 | ANGPT2 | 19.81 | 0.000006 | 1.312 | 0.029 | 2.02 (1.12–3.63) | 0.0164 |
| 212949_at | Hs.1192.0 | NCAPH | 19.94 | 7.17E‐07 | 2.497 | 1.51E‐06 | 3.06 (1.62–5.78) | 0.0003 |
| 206772_at | g4826953 | PTH2R | 21.94 | 0.000027 | 5.579 | 8.58E‐10 | 3.14 (1.66–5.97) | 0.0002 |
| 222962_s_at | g11527601 | MCM10 | 29.44 | 6.72E‐09 | 2.718 | 1.28E‐07 | 2.33 (1.06–5.1) | 0.0296 |
| 207039_at | g4502748 | CDKN2A | 45.1 | 0.000022 | 6.481 | 5.60E‐14 | 2.01 (1.11–3.63) | 0.0186 |
| 206373_at | g4507970 | ZIC1 | 99.77 | 2.13E‐08 | 3.712 | 8.24E‐07 | 2.19 (1.22–3.93) | 0.0073 |