This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 99 genes and 12 clinical features across 373 patients, 12 significant findings detected with Q value < 0.25.
-
TP53 mutation correlated to 'GENDER' and 'RACE'.
-
CTNNB1 mutation correlated to 'GENDER'.
-
BAP1 mutation correlated to 'GENDER'.
-
MLL4 mutation correlated to 'Time to Death'.
-
ALB mutation correlated to 'YEARS_TO_BIRTH'.
-
BAZ2A mutation correlated to 'Time to Death'.
-
PDZD4 mutation correlated to 'RACE'.
-
SKA3 mutation correlated to 'Time to Death'.
-
CBX4 mutation correlated to 'Time to Death'.
-
NR4A2 mutation correlated to 'Time to Death'.
-
SWAP70 mutation correlated to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
RACE | ETHNICITY | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
TP53 | 114 (31%) | 259 |
0.0264 (0.666) |
0.138 (0.935) |
0.748 (1.00) |
0.225 (1.00) |
0.581 (1.00) |
0.314 (1.00) |
0.00178 (0.212) |
1 (1.00) |
0.86 (1.00) |
0.682 (1.00) |
8e-05 (0.0238) |
0.602 (1.00) |
CTNNB1 | 97 (26%) | 276 |
0.898 (1.00) |
0.0215 (0.637) |
0.979 (1.00) |
0.864 (1.00) |
1 (1.00) |
1 (1.00) |
7.84e-06 (0.00314) |
0.0572 (0.736) |
0.232 (1.00) |
0.182 (0.975) |
0.579 (1.00) |
0.789 (1.00) |
BAP1 | 21 (6%) | 352 |
0.144 (0.935) |
0.424 (1.00) |
0.0827 (0.819) |
0.152 (0.953) |
0.174 (0.975) |
0.178 (0.975) |
3.56e-06 (0.00314) |
1 (1.00) |
0.104 (0.891) |
1 (1.00) |
0.128 (0.935) |
1 (1.00) |
MLL4 | 19 (5%) | 354 |
0.000659 (0.112) |
0.42 (1.00) |
0.535 (1.00) |
1 (1.00) |
1 (1.00) |
0.228 (1.00) |
0.135 (0.935) |
1 (1.00) |
1 (1.00) |
0.0091 (0.541) |
0.137 (0.935) |
0.612 (1.00) |
ALB | 43 (12%) | 330 |
0.229 (1.00) |
0.00177 (0.212) |
0.476 (1.00) |
0.119 (0.922) |
1 (1.00) |
1 (1.00) |
0.0154 (0.599) |
1 (1.00) |
0.712 (1.00) |
0.855 (1.00) |
0.295 (1.00) |
1 (1.00) |
BAZ2A | 11 (3%) | 362 |
0.000221 (0.0438) |
0.447 (1.00) |
0.746 (1.00) |
0.772 (1.00) |
1 (1.00) |
1 (1.00) |
0.514 (1.00) |
1 (1.00) |
1 (1.00) |
0.717 (1.00) |
0.0437 (0.709) |
0.441 (1.00) |
PDZD4 | 4 (1%) | 369 |
0.784 (1.00) |
0.795 (1.00) |
0.157 (0.962) |
0.513 (1.00) |
1 (1.00) |
1 (1.00) |
0.309 (1.00) |
1 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.0021 (0.227) |
1 (1.00) |
SKA3 | 4 (1%) | 369 |
0.00247 (0.245) |
0.426 (1.00) |
0.0679 (0.761) |
0.713 (1.00) |
1 (1.00) |
0.0576 (0.736) |
0.598 (1.00) |
1 (1.00) |
1 (1.00) |
0.0149 (0.599) |
0.11 (0.902) |
1 (1.00) |
CBX4 | 6 (2%) | 367 |
0.00135 (0.201) |
0.147 (0.935) |
0.336 (1.00) |
0.796 (1.00) |
1 (1.00) |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.776 (1.00) |
1 (1.00) |
NR4A2 | 6 (2%) | 367 |
7.93e-06 (0.00314) |
0.34 (1.00) |
0.184 (0.975) |
0.0628 (0.747) |
1 (1.00) |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.135 (0.935) |
0.778 (1.00) |
1 (1.00) |
SWAP70 | 5 (1%) | 368 |
0.000139 (0.033) |
0.156 (0.961) |
0.679 (1.00) |
0.76 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.232 (1.00) |
1 (1.00) |
AXIN1 | 24 (6%) | 349 |
0.982 (1.00) |
0.113 (0.917) |
0.226 (1.00) |
0.923 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.824 (1.00) |
1 (1.00) |
1 (1.00) |
0.671 (1.00) |
0.045 (0.709) |
0.102 (0.891) |
RB1 | 21 (6%) | 352 |
0.0349 (0.695) |
0.0223 (0.637) |
0.176 (0.975) |
0.0423 (0.709) |
1 (1.00) |
1 (1.00) |
0.339 (1.00) |
0.431 (1.00) |
0.444 (1.00) |
0.863 (1.00) |
0.135 (0.935) |
0.289 (1.00) |
ARID1A | 32 (9%) | 341 |
0.00585 (0.431) |
0.923 (1.00) |
0.147 (0.935) |
0.498 (1.00) |
1 (1.00) |
1 (1.00) |
0.432 (1.00) |
0.166 (0.975) |
1 (1.00) |
0.445 (1.00) |
0.156 (0.961) |
1 (1.00) |
CDC27 | 15 (4%) | 358 |
0.466 (1.00) |
0.207 (1.00) |
0.792 (1.00) |
0.964 (1.00) |
0.133 (0.935) |
1 (1.00) |
0.782 (1.00) |
0.252 (1.00) |
1 (1.00) |
0.218 (1.00) |
0.0214 (0.637) |
1 (1.00) |
CDKN2A | 11 (3%) | 362 |
0.169 (0.975) |
0.621 (1.00) |
0.965 (1.00) |
0.855 (1.00) |
1 (1.00) |
1 (1.00) |
0.514 (1.00) |
0.252 (1.00) |
1 (1.00) |
1 (1.00) |
0.0145 (0.599) |
0.441 (1.00) |
KRT2 | 12 (3%) | 361 |
0.418 (1.00) |
0.689 (1.00) |
0.222 (1.00) |
0.706 (1.00) |
1 (1.00) |
1 (1.00) |
0.215 (1.00) |
1 (1.00) |
0.281 (1.00) |
1 (1.00) |
0.884 (1.00) |
1 (1.00) |
NFE2L2 | 13 (3%) | 360 |
0.96 (1.00) |
0.118 (0.922) |
0.7 (1.00) |
0.435 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.292 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
PTEN | 11 (3%) | 362 |
0.516 (1.00) |
0.133 (0.935) |
0.517 (1.00) |
0.674 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.715 (1.00) |
0.573 (1.00) |
0.377 (1.00) |
ARID2 | 22 (6%) | 351 |
0.0661 (0.758) |
0.167 (0.975) |
0.594 (1.00) |
0.866 (1.00) |
1 (1.00) |
1 (1.00) |
0.359 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.308 (1.00) |
RBM10 | 8 (2%) | 365 |
0.61 (1.00) |
0.675 (1.00) |
0.889 (1.00) |
0.851 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0568 (0.736) |
ZNF512B | 8 (2%) | 365 |
0.531 (1.00) |
0.0218 (0.637) |
0.943 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.119 (0.922) |
1 (1.00) |
1 (1.00) |
0.214 (1.00) |
0.142 (0.935) |
0.343 (1.00) |
KCNN3 | 12 (3%) | 361 |
0.307 (1.00) |
0.911 (1.00) |
0.743 (1.00) |
0.411 (1.00) |
1 (1.00) |
1 (1.00) |
0.758 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.47 (1.00) |
KRT10 | 9 (2%) | 364 |
0.0496 (0.736) |
0.0393 (0.709) |
0.472 (1.00) |
0.229 (1.00) |
1 (1.00) |
1 (1.00) |
0.282 (1.00) |
1 (1.00) |
0.218 (1.00) |
1 (1.00) |
0.0551 (0.736) |
1 (1.00) |
APOB | 39 (10%) | 334 |
0.122 (0.923) |
0.031 (0.695) |
0.297 (1.00) |
0.504 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.859 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.783 (1.00) |
0.328 (1.00) |
0.702 (1.00) |
TSC2 | 12 (3%) | 361 |
0.00657 (0.434) |
0.701 (1.00) |
0.0564 (0.736) |
0.00747 (0.467) |
1 (1.00) |
1 (1.00) |
0.758 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.117 (0.922) |
0.41 (1.00) |
IL6ST | 12 (3%) | 361 |
0.106 (0.891) |
0.14 (0.935) |
1 (1.00) |
0.953 (1.00) |
1 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.0238 (0.643) |
1 (1.00) |
0.747 (1.00) |
0.605 (1.00) |
1 (1.00) |
C19ORF55 | 6 (2%) | 367 |
0.0612 (0.741) |
0.75 (1.00) |
0.52 (1.00) |
0.487 (1.00) |
1 (1.00) |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.495 (1.00) |
1 (1.00) |
1 (1.00) |
PIK3CA | 13 (3%) | 360 |
0.83 (1.00) |
0.195 (0.992) |
0.691 (1.00) |
0.587 (1.00) |
1 (1.00) |
1 (1.00) |
0.129 (0.935) |
1 (1.00) |
1 (1.00) |
0.776 (1.00) |
0.271 (1.00) |
1 (1.00) |
CELA1 | 6 (2%) | 367 |
0.477 (1.00) |
0.889 (1.00) |
0.164 (0.975) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.498 (1.00) |
0.351 (1.00) |
1 (1.00) |
RPS6KA3 | 14 (4%) | 359 |
0.668 (1.00) |
0.465 (1.00) |
0.0388 (0.709) |
0.306 (1.00) |
1 (1.00) |
1 (1.00) |
0.396 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.524 (1.00) |
NRD1 | 13 (3%) | 360 |
0.0939 (0.858) |
0.805 (1.00) |
0.162 (0.97) |
1 (1.00) |
0.133 (0.935) |
1 (1.00) |
0.56 (1.00) |
1 (1.00) |
0.121 (0.923) |
0.381 (1.00) |
0.07 (0.774) |
1 (1.00) |
EEF1A1 | 9 (2%) | 364 |
0.0663 (0.758) |
0.0446 (0.709) |
0.437 (1.00) |
0.139 (0.935) |
1 (1.00) |
1 (1.00) |
0.724 (1.00) |
1 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.242 (1.00) |
0.343 (1.00) |
TCHH | 17 (5%) | 356 |
0.972 (1.00) |
0.16 (0.966) |
0.144 (0.935) |
0.0175 (0.63) |
1 (1.00) |
0.191 (0.984) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.552 (1.00) |
0.394 (1.00) |
0.21 (1.00) |
COG2 | 4 (1%) | 369 |
0.138 (0.935) |
0.227 (1.00) |
0.864 (1.00) |
0.838 (1.00) |
1 (1.00) |
1 (1.00) |
0.309 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0346 (0.695) |
1 (1.00) |
ATXN1 | 10 (3%) | 363 |
0.272 (1.00) |
0.302 (1.00) |
0.197 (0.994) |
0.197 (0.994) |
0.0903 (0.838) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.076 (0.796) |
1 (1.00) |
KCTD20 | 5 (1%) | 368 |
0.158 (0.962) |
0.266 (1.00) |
0.0249 (0.657) |
0.15 (0.949) |
0.0757 (0.796) |
0.0717 (0.774) |
0.661 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.525 (1.00) |
1 (1.00) |
GPR110 | 6 (2%) | 367 |
0.641 (1.00) |
0.616 (1.00) |
0.109 (0.9) |
0.0613 (0.741) |
1 (1.00) |
1 (1.00) |
0.183 (0.975) |
0.146 (0.935) |
1 (1.00) |
1 (1.00) |
0.582 (1.00) |
1 (1.00) |
CEP164 | 9 (2%) | 364 |
0.427 (1.00) |
0.983 (1.00) |
0.0522 (0.736) |
0.546 (1.00) |
0.105 (0.891) |
0.126 (0.935) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0263 (0.666) |
0.0559 (0.736) |
1 (1.00) |
TCEAL6 | 4 (1%) | 369 |
0.138 (0.935) |
0.227 (1.00) |
0.866 (1.00) |
0.837 (1.00) |
1 (1.00) |
1 (1.00) |
0.309 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0327 (0.695) |
1 (1.00) |
DNAJC28 | 4 (1%) | 369 |
0.0332 (0.695) |
0.0848 (0.819) |
0.817 (1.00) |
0.36 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0655 (0.758) |
0.698 (1.00) |
1 (1.00) |
FOXI1 | 5 (1%) | 368 |
0.0857 (0.821) |
0.941 (1.00) |
0.887 (1.00) |
0.866 (1.00) |
1 (1.00) |
1 (1.00) |
0.179 (0.975) |
1 (1.00) |
1 (1.00) |
0.433 (1.00) |
0.0455 (0.709) |
1 (1.00) |
KRTAP5-7 | 4 (1%) | 369 |
0.339 (1.00) |
0.264 (1.00) |
0.0121 (0.598) |
0.0156 (0.599) |
1 (1.00) |
0.0576 (0.736) |
0.102 (0.891) |
1 (1.00) |
1 (1.00) |
0.363 (1.00) |
0.0736 (0.788) |
0.189 (0.984) |
JAK1 | 14 (4%) | 359 |
0.913 (1.00) |
0.285 (1.00) |
0.341 (1.00) |
0.832 (1.00) |
1 (1.00) |
0.165 (0.975) |
0.562 (1.00) |
0.272 (1.00) |
1 (1.00) |
0.0656 (0.758) |
0.00295 (0.27) |
0.498 (1.00) |
DENND4B | 12 (3%) | 361 |
0.00617 (0.431) |
0.18 (0.975) |
0.805 (1.00) |
0.795 (1.00) |
1 (1.00) |
1 (1.00) |
0.536 (1.00) |
1 (1.00) |
1 (1.00) |
0.381 (1.00) |
0.0798 (0.811) |
1 (1.00) |
BRD7 | 10 (3%) | 363 |
0.178 (0.975) |
0.0439 (0.709) |
0.385 (1.00) |
0.886 (1.00) |
1 (1.00) |
1 (1.00) |
0.304 (1.00) |
1 (1.00) |
1 (1.00) |
0.46 (1.00) |
0.203 (1.00) |
1 (1.00) |
IDH1 | 8 (2%) | 365 |
0.55 (1.00) |
0.18 (0.975) |
0.105 (0.891) |
0.108 (0.895) |
0.0903 (0.838) |
1 (1.00) |
0.718 (1.00) |
1 (1.00) |
1 (1.00) |
0.0466 (0.71) |
0.826 (1.00) |
1 (1.00) |
CNGA3 | 11 (3%) | 362 |
0.411 (1.00) |
0.254 (1.00) |
0.713 (1.00) |
0.507 (1.00) |
1 (1.00) |
1 (1.00) |
0.514 (1.00) |
1 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.869 (1.00) |
0.41 (1.00) |
PLA2G3 | 6 (2%) | 367 |
0.0346 (0.695) |
0.265 (1.00) |
0.716 (1.00) |
0.709 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.352 (1.00) |
1 (1.00) |
HLA-DPB1 | 5 (1%) | 368 |
0.792 (1.00) |
0.0868 (0.825) |
0.259 (1.00) |
0.133 (0.935) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0542 (0.736) |
1 (1.00) |
ALMS1 | 24 (6%) | 349 |
0.265 (1.00) |
0.944 (1.00) |
0.503 (1.00) |
0.26 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.586 (1.00) |
1 (1.00) |
1 (1.00) |
NUCB2 | 3 (1%) | 370 |
0.00367 (0.311) |
0.843 (1.00) |
0.0442 (0.709) |
0.272 (1.00) |
1 (1.00) |
0.0435 (0.709) |
0.554 (1.00) |
1 (1.00) |
1 (1.00) |
0.0146 (0.599) |
0.66 (1.00) |
1 (1.00) |
TAF1B | 6 (2%) | 367 |
0.106 (0.891) |
0.195 (0.992) |
1 (1.00) |
0.897 (1.00) |
1 (1.00) |
1 (1.00) |
0.183 (0.975) |
1 (1.00) |
0.151 (0.952) |
1 (1.00) |
0.0305 (0.695) |
1 (1.00) |
C1ORF125 | 11 (3%) | 362 |
0.412 (1.00) |
0.428 (1.00) |
0.467 (1.00) |
0.467 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
1 (1.00) |
1 (1.00) |
0.496 (1.00) |
0.458 (1.00) |
1 (1.00) |
AR | 10 (3%) | 363 |
0.0778 (0.796) |
0.878 (1.00) |
0.736 (1.00) |
0.64 (1.00) |
1 (1.00) |
1 (1.00) |
0.0838 (0.819) |
1 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.536 (1.00) |
0.41 (1.00) |
SPHK1 | 6 (2%) | 367 |
0.104 (0.891) |
0.39 (1.00) |
0.283 (1.00) |
0.368 (1.00) |
1 (1.00) |
1 (1.00) |
0.183 (0.975) |
0.146 (0.935) |
1 (1.00) |
1 (1.00) |
0.0613 (0.741) |
1 (1.00) |
CREB3L3 | 5 (1%) | 368 |
0.551 (1.00) |
0.894 (1.00) |
0.504 (1.00) |
0.355 (1.00) |
1 (1.00) |
1 (1.00) |
0.661 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.746 (1.00) |
1 (1.00) |
LFNG | 7 (2%) | 366 |
0.0421 (0.709) |
0.614 (1.00) |
0.571 (1.00) |
0.439 (1.00) |
1 (1.00) |
1 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.0617 (0.741) |
1 (1.00) |
0.28 (1.00) |
0.307 (1.00) |
FZR1 | 6 (2%) | 367 |
0.525 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.898 (1.00) |
1 (1.00) |
1 (1.00) |
0.183 (0.975) |
0.146 (0.935) |
1 (1.00) |
0.0847 (0.819) |
0.215 (1.00) |
1 (1.00) |
TRIOBP | 11 (3%) | 362 |
0.784 (1.00) |
0.113 (0.917) |
1 (1.00) |
0.901 (1.00) |
1 (1.00) |
1 (1.00) |
0.514 (1.00) |
1 (1.00) |
1 (1.00) |
0.68 (1.00) |
0.859 (1.00) |
0.41 (1.00) |
GJB1 | 3 (1%) | 370 |
0.0351 (0.695) |
0.402 (1.00) |
0.136 (0.935) |
0.649 (1.00) |
0.046 (0.709) |
1 (1.00) |
0.247 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
DYRK1A | 7 (2%) | 366 |
0.0283 (0.695) |
0.03 (0.695) |
0.929 (1.00) |
0.759 (1.00) |
1 (1.00) |
1 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.174 (0.975) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
TNPO1 | 9 (2%) | 364 |
0.872 (1.00) |
0.246 (1.00) |
0.426 (1.00) |
0.673 (1.00) |
1 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.211 (1.00) |
1 (1.00) |
0.0586 (0.741) |
0.498 (1.00) |
1 (1.00) |
CCNA2 | 5 (1%) | 368 |
0.057 (0.736) |
0.75 (1.00) |
0.0213 (0.637) |
0.454 (1.00) |
1 (1.00) |
0.0717 (0.774) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0225 (0.637) |
1 (1.00) |
0.23 (1.00) |
AHCTF1 | 8 (2%) | 365 |
0.812 (1.00) |
0.456 (1.00) |
0.715 (1.00) |
0.923 (1.00) |
1 (1.00) |
1 (1.00) |
0.28 (1.00) |
0.19 (0.984) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
RXRB | 8 (2%) | 365 |
0.0403 (0.709) |
0.0875 (0.825) |
0.405 (1.00) |
0.589 (1.00) |
0.0609 (0.741) |
1 (1.00) |
0.28 (1.00) |
0.19 (0.984) |
1 (1.00) |
1 (1.00) |
0.17 (0.975) |
1 (1.00) |
PARP1 | 5 (1%) | 368 |
0.535 (1.00) |
0.305 (1.00) |
0.341 (1.00) |
0.314 (1.00) |
1 (1.00) |
1 (1.00) |
0.661 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0112 (0.576) |
1 (1.00) |
NBEA | 21 (6%) | 352 |
0.226 (1.00) |
0.489 (1.00) |
0.8 (1.00) |
0.597 (1.00) |
1 (1.00) |
1 (1.00) |
0.813 (1.00) |
1 (1.00) |
1 (1.00) |
0.547 (1.00) |
0.938 (1.00) |
0.613 (1.00) |
H6PD | 5 (1%) | 368 |
0.568 (1.00) |
0.0775 (0.796) |
0.193 (0.989) |
0.397 (1.00) |
1 (1.00) |
1 (1.00) |
0.661 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
VPS4B | 5 (1%) | 368 |
0.428 (1.00) |
0.132 (0.935) |
0.888 (1.00) |
0.866 (1.00) |
1 (1.00) |
1 (1.00) |
0.179 (0.975) |
0.123 (0.923) |
1 (1.00) |
1 (1.00) |
0.524 (1.00) |
0.23 (1.00) |
HNRNPL | 8 (2%) | 365 |
0.0399 (0.709) |
0.378 (1.00) |
0.703 (1.00) |
0.634 (1.00) |
1 (1.00) |
1 (1.00) |
0.718 (1.00) |
1 (1.00) |
1 (1.00) |
0.377 (1.00) |
0.45 (1.00) |
1 (1.00) |
FILIP1 | 13 (3%) | 360 |
0.022 (0.637) |
0.392 (1.00) |
0.599 (1.00) |
0.394 (1.00) |
1 (1.00) |
1 (1.00) |
0.56 (1.00) |
0.292 (1.00) |
1 (1.00) |
0.298 (1.00) |
0.185 (0.976) |
0.498 (1.00) |
FAM22F | 4 (1%) | 369 |
0.0843 (0.819) |
0.944 (1.00) |
0.0768 (0.796) |
0.426 (1.00) |
1 (1.00) |
0.0576 (0.736) |
0.598 (1.00) |
1 (1.00) |
1 (1.00) |
0.0142 (0.599) |
1 (1.00) |
1 (1.00) |
GPSM2 | 4 (1%) | 369 |
0.0537 (0.736) |
0.0294 (0.695) |
0.547 (1.00) |
0.713 (1.00) |
1 (1.00) |
1 (1.00) |
0.598 (1.00) |
1 (1.00) |
1 (1.00) |
0.364 (1.00) |
0.295 (1.00) |
1 (1.00) |
RCCD1 | 5 (1%) | 368 |
0.423 (1.00) |
0.807 (1.00) |
0.593 (1.00) |
0.519 (1.00) |
1 (1.00) |
1 (1.00) |
0.179 (0.975) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.746 (1.00) |
1 (1.00) |
PTGR1 | 5 (1%) | 368 |
0.656 (1.00) |
0.566 (1.00) |
0.433 (1.00) |
0.278 (1.00) |
1 (1.00) |
1 (1.00) |
0.179 (0.975) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.746 (1.00) |
1 (1.00) |
SAMM50 | 3 (1%) | 370 |
0.26 (1.00) |
0.43 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.554 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0224 (0.637) |
1 (1.00) |
PBRM1 | 9 (2%) | 364 |
0.804 (1.00) |
0.337 (1.00) |
0.587 (1.00) |
0.762 (1.00) |
1 (1.00) |
1 (1.00) |
0.724 (1.00) |
0.211 (1.00) |
0.219 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
SGK269 | 8 (2%) | 365 |
0.331 (1.00) |
0.443 (1.00) |
0.531 (1.00) |
0.354 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.597 (1.00) |
0.628 (1.00) |
1 (1.00) |
LEO1 | 5 (1%) | 368 |
0.0381 (0.709) |
0.486 (1.00) |
0.156 (0.961) |
0.0558 (0.736) |
1 (1.00) |
1 (1.00) |
0.179 (0.975) |
0.123 (0.923) |
1 (1.00) |
0.431 (1.00) |
0.379 (1.00) |
1 (1.00) |
CD97 | 5 (1%) | 368 |
0.559 (1.00) |
0.884 (1.00) |
0.889 (1.00) |
0.865 (1.00) |
1 (1.00) |
1 (1.00) |
0.334 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0454 (0.709) |
1 (1.00) |
MTA1 | 6 (2%) | 367 |
0.0163 (0.606) |
0.629 (1.00) |
0.656 (1.00) |
0.71 (1.00) |
1 (1.00) |
1 (1.00) |
0.183 (0.975) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.159 (0.964) |
1 (1.00) |
CRIP3 | 6 (2%) | 367 |
0.66 (1.00) |
0.556 (1.00) |
0.916 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
0.286 (1.00) |
1 (1.00) |
1 (1.00) |
HNF1A | 8 (2%) | 365 |
0.697 (1.00) |
0.293 (1.00) |
0.0932 (0.858) |
0.14 (0.935) |
1 (1.00) |
1 (1.00) |
0.119 (0.922) |
1 (1.00) |
1 (1.00) |
0.597 (1.00) |
0.264 (1.00) |
1 (1.00) |
KRAS | 6 (2%) | 367 |
1 (1.00) |
0.974 (1.00) |
0.552 (1.00) |
0.406 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0522 (0.736) |
1 (1.00) |
0.775 (1.00) |
1 (1.00) |
PGBD1 | 3 (1%) | 370 |
0.138 (0.935) |
0.929 (1.00) |
0.82 (1.00) |
0.649 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.66 (1.00) |
1 (1.00) |
LATS1 | 7 (2%) | 366 |
0.404 (1.00) |
0.249 (1.00) |
0.871 (1.00) |
0.835 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0676 (0.761) |
1 (1.00) |
1 (1.00) |
KEAP1 | 17 (5%) | 356 |
0.213 (1.00) |
0.583 (1.00) |
0.45 (1.00) |
0.0984 (0.891) |
1 (1.00) |
1 (1.00) |
0.597 (1.00) |
1 (1.00) |
1 (1.00) |
0.55 (1.00) |
0.28 (1.00) |
0.21 (1.00) |
SENP6 | 11 (3%) | 362 |
0.00981 (0.555) |
0.651 (1.00) |
0.617 (1.00) |
0.9 (1.00) |
1 (1.00) |
1 (1.00) |
0.019 (0.637) |
1 (1.00) |
1 (1.00) |
0.34 (1.00) |
0.0714 (0.774) |
1 (1.00) |
FKBP4 | 4 (1%) | 369 |
0.893 (1.00) |
0.919 (1.00) |
0.339 (1.00) |
0.229 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0103 (0.555) |
1 (1.00) |
FOXK2 | 6 (2%) | 367 |
0.0132 (0.599) |
0.0411 (0.709) |
0.63 (1.00) |
0.586 (1.00) |
1 (1.00) |
1 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.527 (1.00) |
1 (1.00) |
DSPP | 21 (6%) | 352 |
0.492 (1.00) |
0.103 (0.891) |
0.183 (0.975) |
0.843 (1.00) |
1 (1.00) |
1 (1.00) |
0.813 (1.00) |
1 (1.00) |
1 (1.00) |
0.461 (1.00) |
0.12 (0.922) |
1 (1.00) |
C10ORF28 | 4 (1%) | 369 |
0.621 (1.00) |
0.242 (1.00) |
0.565 (1.00) |
0.513 (1.00) |
1 (1.00) |
1 (1.00) |
0.309 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.47 (1.00) |
1 (1.00) |
PRAMEF4 | 4 (1%) | 369 |
0.00576 (0.431) |
0.797 (1.00) |
0.191 (0.984) |
0.107 (0.895) |
1 (1.00) |
1 (1.00) |
0.598 (1.00) |
1 (1.00) |
1 (1.00) |
0.365 (1.00) |
1 (1.00) |
0.145 (0.935) |
RPS6KA5 | 5 (1%) | 368 |
0.51 (1.00) |
0.115 (0.922) |
0.539 (1.00) |
0.451 (1.00) |
1 (1.00) |
1 (1.00) |
0.661 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
DDX42 | 6 (2%) | 367 |
0.0819 (0.819) |
0.234 (1.00) |
0.835 (1.00) |
0.798 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.775 (1.00) |
1 (1.00) |
RHCG | 4 (1%) | 369 |
0.0232 (0.642) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.309 (1.00) |
1 (1.00) |
1 (1.00) |
0.191 (0.984) |
0.231 (1.00) |
1 (1.00) |
BIN1 | 4 (1%) | 369 |
0.72 (1.00) |
0.297 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0994 (0.891) |
1 (1.00) |
1 (1.00) |
0.0333 (0.695) |
1 (1.00) |
SMARCA4 | 11 (3%) | 362 |
0.0296 (0.695) |
0.442 (1.00) |
0.485 (1.00) |
0.382 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
1 (1.00) |
1 (1.00) |
0.501 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 0.00178 (Fisher's exact test), Q value = 0.21
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 252 |
TP53 MUTATED | 24 | 90 |
TP53 WILD-TYPE | 97 | 162 |
P value = 8e-05 (Fisher's exact test), Q value = 0.024
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 160 | 17 | 184 |
TP53 MUTATED | 1 | 58 | 12 | 41 |
TP53 WILD-TYPE | 1 | 102 | 5 | 143 |
P value = 7.84e-06 (Fisher's exact test), Q value = 0.0031
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 252 |
CTNNB1 MUTATED | 14 | 83 |
CTNNB1 WILD-TYPE | 107 | 169 |
P value = 3.56e-06 (Fisher's exact test), Q value = 0.0031
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 252 |
BAP1 MUTATED | 17 | 4 |
BAP1 WILD-TYPE | 104 | 248 |
P value = 0.000659 (logrank test), Q value = 0.11
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 130 | 0.0 - 120.8 (19.8) |
MLL4 MUTATED | 19 | 10 | 0.2 - 45.1 (8.6) |
MLL4 WILD-TYPE | 348 | 120 | 0.0 - 120.8 (20.2) |
P value = 0.00177 (Wilcoxon-test), Q value = 0.21
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 369 | 59.1 (13.4) |
ALB MUTATED | 42 | 64.9 (11.5) |
ALB WILD-TYPE | 327 | 58.4 (13.5) |
P value = 0.000221 (logrank test), Q value = 0.044
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 130 | 0.0 - 120.8 (19.8) |
BAZ2A MUTATED | 11 | 9 | 5.6 - 25.1 (19.1) |
BAZ2A WILD-TYPE | 356 | 121 | 0.0 - 120.8 (20.0) |
P value = 0.0021 (Fisher's exact test), Q value = 0.23
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 160 | 17 | 184 |
PDZD4 MUTATED | 1 | 0 | 1 | 2 |
PDZD4 WILD-TYPE | 1 | 160 | 16 | 182 |
P value = 0.00247 (logrank test), Q value = 0.24
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 130 | 0.0 - 120.8 (19.8) |
SKA3 MUTATED | 4 | 3 | 0.5 - 18.2 (11.1) |
SKA3 WILD-TYPE | 363 | 127 | 0.0 - 120.8 (20.0) |
P value = 0.00135 (logrank test), Q value = 0.2
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 130 | 0.0 - 120.8 (19.8) |
CBX4 MUTATED | 6 | 4 | 1.8 - 20.8 (8.1) |
CBX4 WILD-TYPE | 361 | 126 | 0.0 - 120.8 (20.0) |
P value = 7.93e-06 (logrank test), Q value = 0.0031
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 130 | 0.0 - 120.8 (19.8) |
NR4A2 MUTATED | 6 | 5 | 0.7 - 25.8 (6.3) |
NR4A2 WILD-TYPE | 361 | 125 | 0.0 - 120.8 (20.0) |
P value = 0.000139 (logrank test), Q value = 0.033
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 367 | 130 | 0.0 - 120.8 (19.8) |
SWAP70 MUTATED | 5 | 4 | 0.2 - 20.8 (7.7) |
SWAP70 WILD-TYPE | 362 | 126 | 0.0 - 120.8 (19.9) |
-
Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
-
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22623049/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/22506983/LIHC-TP.merged_data.txt
-
Number of patients = 373
-
Number of significantly mutated genes = 99
-
Number of selected clinical features = 12
-
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 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.
In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.