This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 123 genes and 5 clinical features across 248 patients, 9 significant findings detected with Q value < 0.25.
-
PTEN mutation correlated to 'HISTOLOGICAL.TYPE'.
-
CTNNB1 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
KRAS mutation correlated to 'AGE'.
-
TP53 mutation correlated to 'AGE', 'HISTOLOGICAL.TYPE', and 'NEOADJUVANT.THERAPY'.
-
SAP30 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
ZNF69 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
ANKRD31 mutation correlated to 'HISTOLOGICAL.TYPE'.
Table 1. Get Full Table Overview of the association between mutation status of 123 genes and 5 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 9 significant findings detected.
|
Clinical Features |
Time to Death |
AGE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NEOADJUVANT THERAPY |
||
| nMutated (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | |
| TP53 | 69 (28%) | 179 |
0.325 (1.00) |
6.15e-06 (0.00376) |
3.98e-23 (2.45e-20) |
0.371 (1.00) |
6.08e-05 (0.037) |
| PTEN | 161 (65%) | 87 |
0.19 (1.00) |
0.0276 (1.00) |
5.44e-19 (3.34e-16) |
0.0503 (1.00) |
0.0016 (0.956) |
| CTNNB1 | 74 (30%) | 174 |
0.878 (1.00) |
0.0017 (1.00) |
1.04e-05 (0.00636) |
0.381 (1.00) |
0.0124 (1.00) |
| KRAS | 53 (21%) | 195 |
0.072 (1.00) |
0.000274 (0.166) |
0.00692 (1.00) |
0.253 (1.00) |
0.00892 (1.00) |
| SAP30 | 4 (2%) | 244 |
0.648 (1.00) |
0.57 (1.00) |
1.34e-08 (8.19e-06) |
1 (1.00) |
0.577 (1.00) |
| ZNF69 | 7 (3%) | 241 |
0.514 (1.00) |
0.0163 (1.00) |
0.000147 (0.0892) |
1 (1.00) |
0.396 (1.00) |
| ANKRD31 | 17 (7%) | 231 |
0.2 (1.00) |
0.964 (1.00) |
4.87e-05 (0.0297) |
0.432 (1.00) |
1 (1.00) |
| FBXW7 | 39 (16%) | 209 |
0.772 (1.00) |
0.904 (1.00) |
0.0473 (1.00) |
0.855 (1.00) |
0.117 (1.00) |
| SPOP | 21 (8%) | 227 |
0.65 (1.00) |
0.527 (1.00) |
0.332 (1.00) |
0.811 (1.00) |
0.452 (1.00) |
| CTCF | 45 (18%) | 203 |
0.405 (1.00) |
0.0198 (1.00) |
0.0021 (1.00) |
0.863 (1.00) |
1 (1.00) |
| PIK3CA | 132 (53%) | 116 |
0.055 (1.00) |
0.195 (1.00) |
0.555 (1.00) |
0.593 (1.00) |
0.887 (1.00) |
| PIK3R1 | 83 (33%) | 165 |
0.871 (1.00) |
0.806 (1.00) |
0.000827 (0.499) |
0.395 (1.00) |
0.293 (1.00) |
| PPP2R1A | 27 (11%) | 221 |
0.121 (1.00) |
0.0374 (1.00) |
0.00977 (1.00) |
0.52 (1.00) |
0.112 (1.00) |
| PRKAR1B | 4 (2%) | 244 |
0.702 (1.00) |
0.978 (1.00) |
0.961 (1.00) |
0.608 (1.00) |
1 (1.00) |
| FGFR2 | 31 (12%) | 217 |
0.9 (1.00) |
0.998 (1.00) |
0.719 (1.00) |
1 (1.00) |
0.39 (1.00) |
| ARID1A | 83 (33%) | 165 |
0.008 (1.00) |
0.00721 (1.00) |
0.00127 (0.759) |
0.673 (1.00) |
0.0234 (1.00) |
| CHD4 | 35 (14%) | 213 |
0.361 (1.00) |
0.418 (1.00) |
0.779 (1.00) |
0.565 (1.00) |
0.683 (1.00) |
| NFE2L2 | 15 (6%) | 233 |
0.903 (1.00) |
0.191 (1.00) |
0.447 (1.00) |
0.589 (1.00) |
1 (1.00) |
| P2RY11 | 9 (4%) | 239 |
0.395 (1.00) |
0.396 (1.00) |
0.987 (1.00) |
0.497 (1.00) |
0.709 (1.00) |
| CCND1 | 15 (6%) | 233 |
0.729 (1.00) |
0.0556 (1.00) |
0.413 (1.00) |
0.4 (1.00) |
0.13 (1.00) |
| SOX17 | 7 (3%) | 241 |
0.669 (1.00) |
0.848 (1.00) |
0.00567 (1.00) |
0.428 (1.00) |
0.677 (1.00) |
| FOXA2 | 12 (5%) | 236 |
0.799 (1.00) |
0.531 (1.00) |
0.972 (1.00) |
0.229 (1.00) |
1 (1.00) |
| FAM9A | 14 (6%) | 234 |
0.378 (1.00) |
0.913 (1.00) |
0.89 (1.00) |
1 (1.00) |
0.121 (1.00) |
| DNER | 18 (7%) | 230 |
0.746 (1.00) |
0.0414 (1.00) |
0.0324 (1.00) |
0.44 (1.00) |
0.277 (1.00) |
| SMTNL2 | 9 (4%) | 239 |
0.472 (1.00) |
0.53 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.451 (1.00) |
| RBMX | 13 (5%) | 235 |
0.336 (1.00) |
0.161 (1.00) |
0.4 (1.00) |
0.142 (1.00) |
0.756 (1.00) |
| PGR | 12 (5%) | 236 |
0.268 (1.00) |
0.228 (1.00) |
0.0105 (1.00) |
1 (1.00) |
0.52 (1.00) |
| TNFAIP6 | 12 (5%) | 236 |
0.819 (1.00) |
0.302 (1.00) |
0.6 (1.00) |
1 (1.00) |
0.741 (1.00) |
| SGK1 | 15 (6%) | 233 |
0.925 (1.00) |
0.427 (1.00) |
0.759 (1.00) |
0.158 (1.00) |
0.563 (1.00) |
| PDE8B | 16 (6%) | 232 |
0.196 (1.00) |
0.135 (1.00) |
0.0275 (1.00) |
1 (1.00) |
0.568 (1.00) |
| HPD | 7 (3%) | 241 |
0.43 (1.00) |
0.0538 (1.00) |
0.0585 (1.00) |
1 (1.00) |
1 (1.00) |
| RPL14 | 7 (3%) | 241 |
0.532 (1.00) |
0.677 (1.00) |
0.991 (1.00) |
0.428 (1.00) |
0.396 (1.00) |
| TAP1 | 8 (3%) | 240 |
0.588 (1.00) |
0.877 (1.00) |
0.343 (1.00) |
1 (1.00) |
0.452 (1.00) |
| MAX | 11 (4%) | 237 |
0.889 (1.00) |
0.336 (1.00) |
0.404 (1.00) |
0.753 (1.00) |
0.732 (1.00) |
| ZNF286A | 12 (5%) | 236 |
0.308 (1.00) |
0.518 (1.00) |
0.00262 (1.00) |
0.229 (1.00) |
1 (1.00) |
| RASA1 | 22 (9%) | 226 |
0.127 (1.00) |
0.466 (1.00) |
0.0211 (1.00) |
0.639 (1.00) |
0.803 (1.00) |
| ABI1 | 4 (2%) | 244 |
0.663 (1.00) |
0.0342 (1.00) |
0.961 (1.00) |
0.302 (1.00) |
0.303 (1.00) |
| NRAS | 9 (4%) | 239 |
0.354 (1.00) |
0.616 (1.00) |
0.0289 (1.00) |
0.722 (1.00) |
0.451 (1.00) |
| ZNF367 | 8 (3%) | 240 |
0.449 (1.00) |
0.365 (1.00) |
0.628 (1.00) |
0.127 (1.00) |
1 (1.00) |
| ING1 | 13 (5%) | 235 |
0.37 (1.00) |
0.694 (1.00) |
0.178 (1.00) |
0.142 (1.00) |
1 (1.00) |
| MFGE8 | 4 (2%) | 244 |
0.533 (1.00) |
0.127 (1.00) |
0.0702 (1.00) |
1 (1.00) |
0.303 (1.00) |
| ZNF267 | 16 (6%) | 232 |
0.565 (1.00) |
0.207 (1.00) |
0.0275 (1.00) |
0.79 (1.00) |
1 (1.00) |
| ARID5B | 29 (12%) | 219 |
0.642 (1.00) |
0.649 (1.00) |
0.00865 (1.00) |
1 (1.00) |
0.508 (1.00) |
| DYRK1A | 12 (5%) | 236 |
0.939 (1.00) |
0.386 (1.00) |
0.595 (1.00) |
0.552 (1.00) |
1 (1.00) |
| EMB | 8 (3%) | 240 |
0.443 (1.00) |
0.497 (1.00) |
0.000594 (0.359) |
0.719 (1.00) |
0.452 (1.00) |
| ESR1 | 11 (4%) | 237 |
0.329 (1.00) |
0.317 (1.00) |
0.653 (1.00) |
0.518 (1.00) |
0.179 (1.00) |
| NAA30 | 8 (3%) | 240 |
0.565 (1.00) |
0.358 (1.00) |
0.518 (1.00) |
0.719 (1.00) |
0.688 (1.00) |
| CHSY3 | 10 (4%) | 238 |
0.862 (1.00) |
0.00805 (1.00) |
0.62 (1.00) |
0.739 (1.00) |
0.468 (1.00) |
| SIN3A | 21 (8%) | 227 |
0.574 (1.00) |
0.256 (1.00) |
0.1 (1.00) |
0.811 (1.00) |
0.609 (1.00) |
| CYLC1 | 18 (7%) | 230 |
0.198 (1.00) |
0.765 (1.00) |
0.000601 (0.363) |
0.313 (1.00) |
0.413 (1.00) |
| METTL14 | 10 (4%) | 238 |
0.358 (1.00) |
0.833 (1.00) |
0.707 (1.00) |
1 (1.00) |
0.293 (1.00) |
| MORC4 | 20 (8%) | 228 |
0.152 (1.00) |
0.0204 (1.00) |
0.629 (1.00) |
1 (1.00) |
0.295 (1.00) |
| TAB3 | 18 (7%) | 230 |
0.22 (1.00) |
0.107 (1.00) |
0.00686 (1.00) |
0.616 (1.00) |
1 (1.00) |
| TPTE | 15 (6%) | 233 |
0.273 (1.00) |
0.167 (1.00) |
0.00648 (1.00) |
1 (1.00) |
0.369 (1.00) |
| UPF3B | 16 (6%) | 232 |
0.735 (1.00) |
0.81 (1.00) |
0.395 (1.00) |
0.588 (1.00) |
0.0775 (1.00) |
| C9ORF102 | 16 (6%) | 232 |
0.245 (1.00) |
0.35 (1.00) |
0.0343 (1.00) |
0.588 (1.00) |
0.568 (1.00) |
| RHBDD3 | 4 (2%) | 244 |
0.587 (1.00) |
0.206 (1.00) |
0.961 (1.00) |
0.608 (1.00) |
0.577 (1.00) |
| C12ORF34 | 6 (2%) | 242 |
0.542 (1.00) |
0.676 (1.00) |
0.897 (1.00) |
1 (1.00) |
0.193 (1.00) |
| FUT4 | 3 (1%) | 245 |
0.87 (1.00) |
0.837 (1.00) |
0.0165 (1.00) |
0.271 (1.00) |
0.564 (1.00) |
| C7ORF60 | 10 (4%) | 238 |
0.31 (1.00) |
0.136 (1.00) |
0.707 (1.00) |
0.318 (1.00) |
0.732 (1.00) |
| GYPB | 5 (2%) | 243 |
0.583 (1.00) |
0.843 (1.00) |
0.149 (1.00) |
0.168 (1.00) |
1 (1.00) |
| NHSL2 | 12 (5%) | 236 |
0.992 (1.00) |
0.506 (1.00) |
0.0105 (1.00) |
0.756 (1.00) |
1 (1.00) |
| OR4K2 | 11 (4%) | 237 |
0.304 (1.00) |
0.241 (1.00) |
0.00658 (1.00) |
1 (1.00) |
0.499 (1.00) |
| ZRANB3 | 8 (3%) | 240 |
0.325 (1.00) |
0.839 (1.00) |
0.000987 (0.593) |
0.451 (1.00) |
0.452 (1.00) |
| KIF26B | 19 (8%) | 229 |
0.768 (1.00) |
0.403 (1.00) |
0.054 (1.00) |
0.46 (1.00) |
0.294 (1.00) |
| ZNF263 | 8 (3%) | 240 |
0.452 (1.00) |
0.219 (1.00) |
0.809 (1.00) |
1 (1.00) |
0.22 (1.00) |
| DCAF4 | 4 (2%) | 244 |
0.611 (1.00) |
0.0779 (1.00) |
0.328 (1.00) |
1 (1.00) |
1 (1.00) |
| PSMG4 | 5 (2%) | 243 |
0.619 (1.00) |
0.778 (1.00) |
0.000441 (0.267) |
0.663 (1.00) |
0.327 (1.00) |
| TWF1 | 8 (3%) | 240 |
0.437 (1.00) |
0.888 (1.00) |
0.205 (1.00) |
0.27 (1.00) |
1 (1.00) |
| OR52I2 | 8 (3%) | 240 |
0.731 (1.00) |
0.559 (1.00) |
0.0802 (1.00) |
0.451 (1.00) |
0.452 (1.00) |
| SERHL2 | 6 (2%) | 242 |
0.464 (1.00) |
0.666 (1.00) |
0.897 (1.00) |
0.185 (1.00) |
0.667 (1.00) |
| UBE2QL1 | 5 (2%) | 243 |
0.753 (1.00) |
0.163 (1.00) |
0.933 (1.00) |
0.342 (1.00) |
1 (1.00) |
| ZNF649 | 14 (6%) | 234 |
0.246 (1.00) |
0.288 (1.00) |
0.182 (1.00) |
0.777 (1.00) |
1 (1.00) |
| CHEK2 | 13 (5%) | 235 |
0.891 (1.00) |
0.0163 (1.00) |
0.0307 (1.00) |
1 (1.00) |
0.352 (1.00) |
| IGFBP7 | 6 (2%) | 242 |
0.406 (1.00) |
0.659 (1.00) |
0.228 (1.00) |
0.667 (1.00) |
0.667 (1.00) |
| OR5D13 | 10 (4%) | 238 |
0.895 (1.00) |
0.741 (1.00) |
0.188 (1.00) |
0.318 (1.00) |
0.468 (1.00) |
| CSDE1 | 21 (8%) | 227 |
0.802 (1.00) |
0.294 (1.00) |
0.0435 (1.00) |
1 (1.00) |
0.452 (1.00) |
| HLA-B | 4 (2%) | 244 |
0.523 (1.00) |
0.52 (1.00) |
0.078 (1.00) |
0.302 (1.00) |
0.303 (1.00) |
| OR4D2 | 3 (1%) | 245 |
0.648 (1.00) |
0.693 (1.00) |
0.981 (1.00) |
0.271 (1.00) |
0.564 (1.00) |
| FMR1 | 16 (6%) | 232 |
0.304 (1.00) |
0.643 (1.00) |
0.0688 (1.00) |
0.588 (1.00) |
0.0775 (1.00) |
| CNPY1 | 7 (3%) | 241 |
0.449 (1.00) |
0.18 (1.00) |
0.294 (1.00) |
1 (1.00) |
0.677 (1.00) |
| HIST1H2AG | 7 (3%) | 241 |
0.542 (1.00) |
0.416 (1.00) |
0.991 (1.00) |
0.0485 (1.00) |
1 (1.00) |
| CTXN3 | 6 (2%) | 242 |
0.512 (1.00) |
0.794 (1.00) |
0.548 (1.00) |
1 (1.00) |
0.193 (1.00) |
| OR4A15 | 13 (5%) | 235 |
0.213 (1.00) |
0.167 (1.00) |
0.00219 (1.00) |
1 (1.00) |
0.756 (1.00) |
| CABP1 | 8 (3%) | 240 |
0.319 (1.00) |
0.285 (1.00) |
0.809 (1.00) |
0.719 (1.00) |
0.452 (1.00) |
| TXNDC8 | 6 (2%) | 242 |
0.439 (1.00) |
0.46 (1.00) |
0.32 (1.00) |
0.667 (1.00) |
1 (1.00) |
| FAM122A | 6 (2%) | 242 |
0.599 (1.00) |
0.936 (1.00) |
0.228 (1.00) |
0.415 (1.00) |
0.667 (1.00) |
| OR5AS1 | 10 (4%) | 238 |
0.675 (1.00) |
0.503 (1.00) |
0.396 (1.00) |
0.501 (1.00) |
0.732 (1.00) |
| ZNF334 | 17 (7%) | 231 |
0.95 (1.00) |
0.0232 (1.00) |
0.787 (1.00) |
1 (1.00) |
0.415 (1.00) |
| C12ORF4 | 13 (5%) | 235 |
0.287 (1.00) |
0.169 (1.00) |
0.00259 (1.00) |
1 (1.00) |
0.756 (1.00) |
| GNB2 | 6 (2%) | 242 |
0.556 (1.00) |
0.388 (1.00) |
0.228 (1.00) |
0.667 (1.00) |
1 (1.00) |
| CABLES1 | 6 (2%) | 242 |
0.425 (1.00) |
0.11 (1.00) |
0.897 (1.00) |
1 (1.00) |
1 (1.00) |
| KLHL8 | 12 (5%) | 236 |
0.362 (1.00) |
0.504 (1.00) |
0.404 (1.00) |
1 (1.00) |
1 (1.00) |
| LOC642587 | 7 (3%) | 241 |
0.679 (1.00) |
0.548 (1.00) |
0.294 (1.00) |
1 (1.00) |
0.677 (1.00) |
| RAB3GAP1 | 16 (6%) | 232 |
0.98 (1.00) |
0.596 (1.00) |
0.35 (1.00) |
1 (1.00) |
0.773 (1.00) |
| PAPD4 | 13 (5%) | 235 |
0.982 (1.00) |
0.181 (1.00) |
0.962 (1.00) |
0.378 (1.00) |
0.0492 (1.00) |
| DAPP1 | 8 (3%) | 240 |
0.568 (1.00) |
0.462 (1.00) |
0.343 (1.00) |
0.719 (1.00) |
0.688 (1.00) |
| DST | 39 (16%) | 209 |
0.467 (1.00) |
0.655 (1.00) |
0.301 (1.00) |
0.464 (1.00) |
0.563 (1.00) |
| HHIPL1 | 6 (2%) | 242 |
0.679 (1.00) |
0.892 (1.00) |
0.32 (1.00) |
0.415 (1.00) |
0.667 (1.00) |
| LUC7L2 | 8 (3%) | 240 |
0.332 (1.00) |
0.728 (1.00) |
0.343 (1.00) |
0.27 (1.00) |
0.452 (1.00) |
| MAP3K1 | 21 (8%) | 227 |
0.0962 (1.00) |
0.813 (1.00) |
0.2 (1.00) |
1 (1.00) |
0.452 (1.00) |
| PPM1N | 7 (3%) | 241 |
0.355 (1.00) |
0.79 (1.00) |
0.294 (1.00) |
1 (1.00) |
1 (1.00) |
| ZNF879 | 13 (5%) | 235 |
0.34 (1.00) |
0.0926 (1.00) |
0.4 (1.00) |
1 (1.00) |
1 (1.00) |
| TAF1 | 35 (14%) | 213 |
0.231 (1.00) |
0.837 (1.00) |
0.0158 (1.00) |
0.448 (1.00) |
0.841 (1.00) |
| ZNF645 | 10 (4%) | 238 |
0.353 (1.00) |
0.879 (1.00) |
0.0527 (1.00) |
1 (1.00) |
0.293 (1.00) |
| KCNH2 | 10 (4%) | 238 |
0.432 (1.00) |
0.597 (1.00) |
0.338 (1.00) |
0.0959 (1.00) |
0.143 (1.00) |
| XPA | 7 (3%) | 241 |
0.169 (1.00) |
0.9 (1.00) |
0.981 (1.00) |
0.236 (1.00) |
0.092 (1.00) |
| ZNF449 | 12 (5%) | 236 |
0.355 (1.00) |
0.95 (1.00) |
0.655 (1.00) |
0.552 (1.00) |
0.52 (1.00) |
| EDN1 | 4 (2%) | 244 |
0.729 (1.00) |
0.741 (1.00) |
0.961 (1.00) |
0.608 (1.00) |
1 (1.00) |
| GIPC2 | 9 (4%) | 239 |
0.851 (1.00) |
0.042 (1.00) |
0.376 (1.00) |
0.497 (1.00) |
0.709 (1.00) |
| C14ORF118 | 15 (6%) | 233 |
0.268 (1.00) |
0.0138 (1.00) |
0.369 (1.00) |
0.589 (1.00) |
0.766 (1.00) |
| IGFN1 | 13 (5%) | 235 |
0.713 (1.00) |
0.307 (1.00) |
0.296 (1.00) |
0.378 (1.00) |
0.756 (1.00) |
| BRS3 | 15 (6%) | 233 |
0.184 (1.00) |
0.133 (1.00) |
0.025 (1.00) |
0.4 (1.00) |
0.766 (1.00) |
| TBC1D12 | 9 (4%) | 239 |
0.479 (1.00) |
0.604 (1.00) |
0.759 (1.00) |
1 (1.00) |
1 (1.00) |
| NFE2L3 | 12 (5%) | 236 |
0.336 (1.00) |
0.656 (1.00) |
0.342 (1.00) |
0.115 (1.00) |
0.741 (1.00) |
| G3BP2 | 9 (4%) | 239 |
0.401 (1.00) |
0.101 (1.00) |
0.000879 (0.529) |
0.497 (1.00) |
0.709 (1.00) |
| RRAS2 | 4 (2%) | 244 |
0.752 (1.00) |
0.0717 (1.00) |
0.961 (1.00) |
0.608 (1.00) |
0.0639 (1.00) |
| CLIC2 | 10 (4%) | 238 |
0.294 (1.00) |
0.855 (1.00) |
0.00231 (1.00) |
1 (1.00) |
0.732 (1.00) |
| OPRK1 | 7 (3%) | 241 |
0.594 (1.00) |
0.542 (1.00) |
0.856 (1.00) |
0.694 (1.00) |
0.677 (1.00) |
| HIST1H2BD | 6 (2%) | 242 |
0.0836 (1.00) |
0.474 (1.00) |
0.897 (1.00) |
0.415 (1.00) |
1 (1.00) |
| OR8B8 | 7 (3%) | 241 |
0.524 (1.00) |
0.0339 (1.00) |
0.294 (1.00) |
0.428 (1.00) |
1 (1.00) |
| SHB | 6 (2%) | 242 |
0.484 (1.00) |
0.716 (1.00) |
0.996 (1.00) |
1 (1.00) |
0.667 (1.00) |
| SOS1 | 12 (5%) | 236 |
0.301 (1.00) |
0.0904 (1.00) |
0.6 (1.00) |
0.552 (1.00) |
0.52 (1.00) |
P value = 5.44e-19 (Chi-square test), Q value = 3.3e-16
Table S1. Gene #2: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
| nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|
| ALL | 182 | 3 | 8 | 2 | 5 | 4 | 44 |
| PTEN MUTATED | 146 | 2 | 6 | 1 | 4 | 1 | 1 |
| PTEN WILD-TYPE | 36 | 1 | 2 | 1 | 1 | 3 | 43 |
Figure S1. Get High-res Image Gene #2: 'PTEN MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
P value = 1.04e-05 (Chi-square test), Q value = 0.0064
Table S2. Gene #5: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
| nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|
| ALL | 182 | 3 | 8 | 2 | 5 | 4 | 44 |
| CTNNB1 MUTATED | 69 | 1 | 2 | 2 | 0 | 0 | 0 |
| CTNNB1 WILD-TYPE | 113 | 2 | 6 | 0 | 5 | 4 | 44 |
Figure S2. Get High-res Image Gene #5: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
P value = 0.000274 (t-test), Q value = 0.17
Table S3. Gene #6: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 248 | 63.1 (11.1) |
| KRAS MUTATED | 53 | 58.8 (8.7) |
| KRAS WILD-TYPE | 195 | 64.3 (11.4) |
Figure S3. Get High-res Image Gene #6: 'KRAS MUTATION STATUS' versus Clinical Feature #2: 'AGE'
P value = 6.15e-06 (t-test), Q value = 0.0038
Table S4. Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 248 | 63.1 (11.1) |
| TP53 MUTATED | 69 | 67.9 (9.4) |
| TP53 WILD-TYPE | 179 | 61.3 (11.2) |
Figure S4. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
P value = 3.98e-23 (Chi-square test), Q value = 2.4e-20
Table S5. Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
| nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|
| ALL | 182 | 3 | 8 | 2 | 5 | 4 | 44 |
| TP53 MUTATED | 23 | 0 | 0 | 0 | 4 | 3 | 39 |
| TP53 WILD-TYPE | 159 | 3 | 8 | 2 | 1 | 1 | 5 |
Figure S5. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
P value = 6.08e-05 (Fisher's exact test), Q value = 0.037
Table S6. Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'NEOADJUVANT.THERAPY'
| nPatients | NO | YES |
|---|---|---|
| ALL | 68 | 180 |
| TP53 MUTATED | 32 | 37 |
| TP53 WILD-TYPE | 36 | 143 |
Figure S6. Get High-res Image Gene #11: 'TP53 MUTATION STATUS' versus Clinical Feature #5: 'NEOADJUVANT.THERAPY'
P value = 1.34e-08 (Chi-square test), Q value = 8.2e-06
Table S7. Gene #55: 'SAP30 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
| nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|
| ALL | 182 | 3 | 8 | 2 | 5 | 4 | 44 |
| SAP30 MUTATED | 2 | 0 | 0 | 0 | 2 | 0 | 0 |
| SAP30 WILD-TYPE | 180 | 3 | 8 | 2 | 3 | 4 | 44 |
Figure S7. Get High-res Image Gene #55: 'SAP30 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
P value = 0.000147 (Chi-square test), Q value = 0.089
Table S8. Gene #89: 'ZNF69 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
| nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|
| ALL | 182 | 3 | 8 | 2 | 5 | 4 | 44 |
| ZNF69 MUTATED | 5 | 0 | 0 | 0 | 2 | 0 | 0 |
| ZNF69 WILD-TYPE | 177 | 3 | 8 | 2 | 3 | 4 | 44 |
Figure S8. Get High-res Image Gene #89: 'ZNF69 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
P value = 4.87e-05 (Chi-square test), Q value = 0.03
Table S9. Gene #96: 'ANKRD31 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
| nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1 OR 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 1) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 2) | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA (GRADE 3) | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
|---|---|---|---|---|---|---|---|
| ALL | 182 | 3 | 8 | 2 | 5 | 4 | 44 |
| ANKRD31 MUTATED | 12 | 1 | 1 | 0 | 3 | 0 | 0 |
| ANKRD31 WILD-TYPE | 170 | 2 | 7 | 2 | 2 | 4 | 44 |
Figure S9. Get High-res Image Gene #96: 'ANKRD31 MUTATION STATUS' versus Clinical Feature #3: 'HISTOLOGICAL.TYPE'
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Mutation data file = UCEC.mutsig.cluster.txt
-
Clinical data file = UCEC.clin.merged.picked.txt
-
Number of patients = 248
-
Number of significantly mutated genes = 123
-
Number of selected clinical features = 5
-
Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.