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'.
Table 1. Get Full Table Overview of the association between mutation status of 99 genes and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 12 significant findings detected.
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
Table S1. Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 252 |
TP53 MUTATED | 24 | 90 |
TP53 WILD-TYPE | 97 | 162 |
Figure S1. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
![](D1V7.png)
P value = 8e-05 (Fisher's exact test), Q value = 0.024
Table S2. Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'
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 |
Figure S2. Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'
![](D1V11.png)
P value = 7.84e-06 (Fisher's exact test), Q value = 0.0031
Table S3. Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 252 |
CTNNB1 MUTATED | 14 | 83 |
CTNNB1 WILD-TYPE | 107 | 169 |
Figure S3. Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
![](D2V7.png)
P value = 3.56e-06 (Fisher's exact test), Q value = 0.0031
Table S4. Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
nPatients | FEMALE | MALE |
---|---|---|
ALL | 121 | 252 |
BAP1 MUTATED | 17 | 4 |
BAP1 WILD-TYPE | 104 | 248 |
Figure S4. Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Clinical Feature #7: 'GENDER'
![](D6V7.png)
P value = 0.000659 (logrank test), Q value = 0.11
Table S5. Gene #18: 'MLL4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
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) |
Figure S5. Get High-res Image Gene #18: 'MLL4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D18V1.png)
P value = 0.00177 (Wilcoxon-test), Q value = 0.21
Table S6. Gene #19: 'ALB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
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) |
Figure S6. Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D19V2.png)
P value = 0.000221 (logrank test), Q value = 0.044
Table S7. Gene #47: 'BAZ2A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
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) |
Figure S7. Get High-res Image Gene #47: 'BAZ2A MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D47V1.png)
P value = 0.0021 (Fisher's exact test), Q value = 0.23
Table S8. Gene #59: 'PDZD4 MUTATION STATUS' versus Clinical Feature #11: 'RACE'
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 |
Figure S8. Get High-res Image Gene #59: 'PDZD4 MUTATION STATUS' versus Clinical Feature #11: 'RACE'
![](D59V11.png)
P value = 0.00247 (logrank test), Q value = 0.24
Table S9. Gene #78: 'SKA3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
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) |
Figure S9. Get High-res Image Gene #78: 'SKA3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D78V1.png)
P value = 0.00135 (logrank test), Q value = 0.2
Table S10. Gene #79: 'CBX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
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) |
Figure S10. Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D79V1.png)
P value = 7.93e-06 (logrank test), Q value = 0.0031
Table S11. Gene #82: 'NR4A2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
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) |
Figure S11. Get High-res Image Gene #82: 'NR4A2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D82V1.png)
P value = 0.000139 (logrank test), Q value = 0.033
Table S12. Gene #97: 'SWAP70 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
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) |
Figure S12. Get High-res Image Gene #97: 'SWAP70 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D97V1.png)
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Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
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Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/LIHC-TP/22623049/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LIHC-TP/22506983/LIHC-TP.merged_data.txt
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Number of patients = 373
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Number of significantly mutated genes = 99
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Number of selected clinical features = 12
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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.