This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 70 genes and 13 clinical features across 784 patients, 21 significant findings detected with Q value < 0.25.
-
TP53 mutation correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
-
PBRM1 mutation correlated to 'HISTOLOGICAL_TYPE'.
-
VHL mutation correlated to 'Time to Death', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
NF2 mutation correlated to 'PATHOLOGY_N_STAGE'.
-
MET mutation correlated to 'HISTOLOGICAL_TYPE'.
-
KDM5C mutation correlated to 'HISTOLOGICAL_TYPE'.
-
MTOR mutation correlated to 'GENDER' and 'HISTOLOGICAL_TYPE'.
-
ZNF814 mutation correlated to 'HISTOLOGICAL_TYPE'.
-
AR mutation correlated to 'HISTOLOGICAL_TYPE'.
-
CACNA1C mutation correlated to 'PATHOLOGY_M_STAGE'.
-
PCF11 mutation correlated to 'HISTOLOGICAL_TYPE'.
-
KDM6A mutation correlated to 'YEARS_TO_BIRTH'.
-
FAM178A mutation correlated to 'Time to Death'.
-
FAM47A mutation correlated to 'Time to Death'.
-
MLL3 mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
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 | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
TP53 | 38 (5%) | 746 |
0.605 (1.00) |
0.268 (1.00) |
0.0031 (0.166) |
0.00241 (0.166) |
0.0223 (0.422) |
0.768 (1.00) |
0.38 (1.00) |
0.464 (1.00) |
1e-05 (0.00152) |
0.378 (1.00) |
0.802 (1.00) |
0.204 (1.00) |
1 (1.00) |
VHL | 196 (25%) | 588 |
0.0045 (0.214) |
0.282 (1.00) |
0.409 (1.00) |
0.205 (1.00) |
0.0262 (0.461) |
0.704 (1.00) |
0.0964 (0.794) |
0.651 (1.00) |
1e-05 (0.00152) |
1e-05 (0.00152) |
1 (1.00) |
||
MTOR | 34 (4%) | 750 |
0.0745 (0.77) |
0.117 (0.853) |
0.323 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.181 (1.00) |
0.00493 (0.214) |
0.0109 (0.337) |
0.00253 (0.166) |
0.795 (1.00) |
0.713 (1.00) |
||
MLL3 | 42 (5%) | 742 |
0.791 (1.00) |
0.982 (1.00) |
0.0931 (0.794) |
0.0825 (0.794) |
1 (1.00) |
1 (1.00) |
0.177 (1.00) |
0.655 (1.00) |
0.00301 (0.166) |
0.489 (1.00) |
0.327 (1.00) |
0.00464 (0.214) |
0.713 (1.00) |
PBRM1 | 143 (18%) | 641 |
0.094 (0.794) |
0.023 (0.428) |
0.222 (1.00) |
0.225 (1.00) |
0.055 (0.659) |
0.482 (1.00) |
0.768 (1.00) |
0.298 (1.00) |
1e-05 (0.00152) |
0.26 (1.00) |
0.0139 (0.337) |
0.819 (1.00) |
|
NF2 | 16 (2%) | 768 |
0.0783 (0.778) |
0.341 (1.00) |
0.0137 (0.337) |
0.0672 (0.71) |
0.00025 (0.0253) |
0.155 (0.967) |
0.789 (1.00) |
0.896 (1.00) |
0.09 (0.794) |
0.394 (1.00) |
0.796 (1.00) |
0.202 (1.00) |
0.533 (1.00) |
MET | 25 (3%) | 759 |
0.78 (1.00) |
0.497 (1.00) |
0.514 (1.00) |
0.633 (1.00) |
0.14 (0.912) |
1 (1.00) |
0.671 (1.00) |
0.0918 (0.794) |
1e-05 (0.00152) |
0.416 (1.00) |
0.184 (1.00) |
0.822 (1.00) |
1 (1.00) |
KDM5C | 27 (3%) | 757 |
0.0171 (0.362) |
0.0574 (0.67) |
0.536 (1.00) |
0.6 (1.00) |
0.769 (1.00) |
0.775 (1.00) |
0.0583 (0.67) |
8e-05 (0.0104) |
0.636 (1.00) |
0.631 (1.00) |
|||
ZNF814 | 14 (2%) | 770 |
0.346 (1.00) |
0.439 (1.00) |
0.135 (0.912) |
0.455 (1.00) |
0.434 (1.00) |
1 (1.00) |
0.567 (1.00) |
0.00301 (0.166) |
0.185 (1.00) |
0.75 (1.00) |
1 (1.00) |
||
AR | 15 (2%) | 769 |
0.599 (1.00) |
0.373 (1.00) |
0.534 (1.00) |
0.542 (1.00) |
0.579 (1.00) |
1 (1.00) |
0.584 (1.00) |
0.464 (1.00) |
0.00014 (0.0159) |
0.993 (1.00) |
0.943 (1.00) |
1 (1.00) |
1 (1.00) |
CACNA1C | 15 (2%) | 769 |
0.482 (1.00) |
0.51 (1.00) |
0.0154 (0.359) |
0.249 (1.00) |
0.0169 (0.362) |
0.00494 (0.214) |
1 (1.00) |
0.139 (0.912) |
1 (1.00) |
0.469 (1.00) |
|||
PCF11 | 13 (2%) | 771 |
0.848 (1.00) |
0.2 (1.00) |
0.501 (1.00) |
0.407 (1.00) |
0.621 (1.00) |
0.562 (1.00) |
0.0015 (0.124) |
0.651 (1.00) |
0.731 (1.00) |
0.469 (1.00) |
|||
KDM6A | 13 (2%) | 771 |
0.406 (1.00) |
0.000542 (0.0493) |
0.567 (1.00) |
0.94 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.767 (1.00) |
0.481 (1.00) |
0.0125 (0.337) |
0.164 (0.997) |
0.0515 (0.633) |
1 (1.00) |
|
FAM178A | 8 (1%) | 776 |
1.48e-09 (1.35e-06) |
0.089 (0.794) |
0.373 (1.00) |
0.597 (1.00) |
0.6 (1.00) |
0.123 (0.858) |
0.748 (1.00) |
1 (1.00) |
0.315 (1.00) |
||||
FAM47A | 6 (1%) | 778 |
0.00299 (0.166) |
0.406 (1.00) |
0.576 (1.00) |
0.474 (1.00) |
0.456 (1.00) |
0.0165 (0.362) |
0.426 (1.00) |
1 (1.00) |
1 (1.00) |
||||
PTEN | 28 (4%) | 756 |
0.727 (1.00) |
0.578 (1.00) |
0.268 (1.00) |
0.278 (1.00) |
0.16 (0.99) |
0.343 (1.00) |
0.539 (1.00) |
0.787 (1.00) |
0.0443 (0.601) |
0.434 (1.00) |
0.731 (1.00) |
0.324 (1.00) |
1 (1.00) |
SETD2 | 61 (8%) | 723 |
0.0347 (0.535) |
0.0537 (0.652) |
0.00619 (0.256) |
0.00845 (0.31) |
1 (1.00) |
0.142 (0.915) |
0.478 (1.00) |
0.91 (1.00) |
0.0414 (0.601) |
0.918 (1.00) |
0.509 (1.00) |
0.507 (1.00) |
|
NEFH | 12 (2%) | 772 |
0.525 (1.00) |
0.695 (1.00) |
0.283 (1.00) |
0.624 (1.00) |
1 (1.00) |
0.639 (1.00) |
0.117 (0.853) |
0.733 (1.00) |
0.598 (1.00) |
1 (1.00) |
1 (1.00) |
||
STAG2 | 15 (2%) | 769 |
0.906 (1.00) |
0.0132 (0.337) |
0.0279 (0.462) |
0.0181 (0.366) |
0.514 (1.00) |
0.659 (1.00) |
0.273 (1.00) |
0.474 (1.00) |
0.733 (1.00) |
1 (1.00) |
|||
KRAS | 6 (1%) | 778 |
0.296 (1.00) |
0.649 (1.00) |
0.689 (1.00) |
0.559 (1.00) |
1 (1.00) |
0.0165 (0.362) |
0.0589 (0.67) |
0.00713 (0.282) |
1 (1.00) |
||||
SLC6A14 | 4 (1%) | 780 |
0.359 (1.00) |
0.203 (1.00) |
0.0478 (0.613) |
0.0419 (0.601) |
0.0459 (0.612) |
1 (1.00) |
0.602 (1.00) |
0.512 (1.00) |
1 (1.00) |
1 (1.00) |
|||
SMARCA4 | 20 (3%) | 764 |
0.719 (1.00) |
0.494 (1.00) |
0.832 (1.00) |
0.964 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.334 (1.00) |
0.469 (1.00) |
0.422 (1.00) |
0.663 (1.00) |
0.616 (1.00) |
||
NFE2L2 | 12 (2%) | 772 |
0.924 (1.00) |
0.0131 (0.337) |
0.768 (1.00) |
0.669 (1.00) |
0.633 (1.00) |
1 (1.00) |
0.76 (1.00) |
0.598 (1.00) |
0.138 (0.912) |
1 (1.00) |
|||
ARID1A | 18 (2%) | 766 |
0.633 (1.00) |
0.942 (1.00) |
0.0951 (0.794) |
0.343 (1.00) |
0.279 (1.00) |
0.704 (1.00) |
0.616 (1.00) |
0.553 (1.00) |
0.506 (1.00) |
0.0122 (0.337) |
0.207 (1.00) |
||
BCLAF1 | 10 (1%) | 774 |
0.357 (1.00) |
0.353 (1.00) |
0.0432 (0.601) |
0.14 (0.912) |
0.175 (1.00) |
1 (1.00) |
1 (1.00) |
0.0386 (0.585) |
0.688 (1.00) |
1 (1.00) |
|||
ATM | 20 (3%) | 764 |
0.386 (1.00) |
0.228 (1.00) |
0.0821 (0.794) |
0.0764 (0.778) |
1 (1.00) |
0.455 (1.00) |
0.48 (1.00) |
0.464 (1.00) |
0.341 (1.00) |
0.98 (1.00) |
0.313 (1.00) |
0.589 (1.00) |
|
PARD6B | 8 (1%) | 776 |
0.482 (1.00) |
0.0091 (0.31) |
0.618 (1.00) |
0.803 (1.00) |
1 (1.00) |
0.0582 (0.67) |
0.0968 (0.794) |
0.0922 (0.794) |
1 (1.00) |
||||
CUL3 | 16 (2%) | 768 |
0.0996 (0.803) |
0.964 (1.00) |
0.978 (1.00) |
0.655 (1.00) |
0.0656 (0.705) |
1 (1.00) |
0.106 (0.803) |
0.464 (1.00) |
0.0887 (0.794) |
0.0105 (0.337) |
0.218 (1.00) |
0.785 (1.00) |
0.589 (1.00) |
PIK3CA | 15 (2%) | 769 |
0.745 (1.00) |
0.195 (1.00) |
0.15 (0.953) |
0.0965 (0.794) |
1 (1.00) |
0.192 (1.00) |
0.273 (1.00) |
0.624 (1.00) |
1 (1.00) |
0.562 (1.00) |
|||
SMARCB1 | 9 (1%) | 775 |
0.764 (1.00) |
0.0613 (0.683) |
0.203 (1.00) |
0.0965 (0.794) |
0.51 (1.00) |
1 (1.00) |
0.725 (1.00) |
0.0874 (0.794) |
1 (1.00) |
1 (1.00) |
|||
WASL | 8 (1%) | 776 |
0.971 (1.00) |
0.251 (1.00) |
0.51 (1.00) |
0.729 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.535 (1.00) |
0.672 (1.00) |
1 (1.00) |
|||
DNMT3A | 11 (1%) | 773 |
0.282 (1.00) |
0.603 (1.00) |
0.305 (1.00) |
0.33 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.757 (1.00) |
0.723 (1.00) |
1 (1.00) |
0.469 (1.00) |
|||
KIAA0922 | 7 (1%) | 777 |
0.895 (1.00) |
0.163 (0.997) |
0.182 (1.00) |
0.155 (0.967) |
1 (1.00) |
0.103 (0.803) |
0.206 (1.00) |
0.566 (1.00) |
1 (1.00) |
||||
GPR50 | 5 (1%) | 779 |
0.37 (1.00) |
0.366 (1.00) |
0.825 (1.00) |
0.855 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.46 (1.00) |
0.502 (1.00) |
1 (1.00) |
||||
ACSF2 | 11 (1%) | 773 |
0.00919 (0.31) |
0.727 (1.00) |
0.254 (1.00) |
0.459 (1.00) |
0.435 (1.00) |
0.089 (0.794) |
1 (1.00) |
0.787 (1.00) |
0.725 (1.00) |
0.0616 (0.683) |
1 (1.00) |
||
WDR52 | 9 (1%) | 775 |
0.749 (1.00) |
0.102 (0.803) |
0.319 (1.00) |
0.282 (1.00) |
1 (1.00) |
0.202 (1.00) |
1 (1.00) |
0.772 (1.00) |
0.391 (1.00) |
0.434 (1.00) |
|||
ALMS1 | 14 (2%) | 770 |
0.363 (1.00) |
0.242 (1.00) |
0.81 (1.00) |
1 (1.00) |
1 (1.00) |
0.314 (1.00) |
0.0436 (0.601) |
0.265 (1.00) |
0.281 (1.00) |
0.162 (0.997) |
|||
TXNIP | 8 (1%) | 776 |
0.763 (1.00) |
0.743 (1.00) |
0.034 (0.535) |
0.0343 (0.535) |
0.00912 (0.31) |
0.258 (1.00) |
0.723 (1.00) |
1 (1.00) |
1 (1.00) |
0.357 (1.00) |
|||
NUDT11 | 5 (1%) | 779 |
0.521 (1.00) |
0.221 (1.00) |
0.608 (1.00) |
0.473 (1.00) |
1 (1.00) |
1 (1.00) |
0.778 (1.00) |
1 (1.00) |
1 (1.00) |
||||
PCK1 | 9 (1%) | 775 |
0.626 (1.00) |
0.479 (1.00) |
0.949 (1.00) |
0.261 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.419 (1.00) |
1 (1.00) |
1 (1.00) |
|||
RAI1 | 11 (1%) | 773 |
0.808 (1.00) |
0.379 (1.00) |
0.279 (1.00) |
0.107 (0.803) |
0.366 (1.00) |
0.355 (1.00) |
0.102 (0.803) |
0.689 (1.00) |
1 (1.00) |
||||
PAM | 4 (1%) | 780 |
0.236 (1.00) |
0.896 (1.00) |
0.677 (1.00) |
1 (1.00) |
0.351 (1.00) |
1 (1.00) |
1 (1.00) |
0.402 (1.00) |
0.448 (1.00) |
0.342 (1.00) |
1 (1.00) |
||
GLS | 9 (1%) | 775 |
0.829 (1.00) |
0.931 (1.00) |
0.948 (1.00) |
0.0658 (0.705) |
0.6 (1.00) |
1 (1.00) |
0.349 (1.00) |
1 (1.00) |
1 (1.00) |
||||
EPS15L1 | 10 (1%) | 774 |
0.961 (1.00) |
0.0265 (0.461) |
0.0268 (0.461) |
0.119 (0.856) |
1 (1.00) |
0.601 (1.00) |
0.511 (1.00) |
0.796 (1.00) |
0.204 (1.00) |
0.0464 (0.612) |
|||
NOM1 | 6 (1%) | 778 |
0.327 (1.00) |
0.464 (1.00) |
1 (1.00) |
0.0948 (0.794) |
0.437 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.537 (1.00) |
0.567 (1.00) |
1 (1.00) |
|||
CDK12 | 8 (1%) | 776 |
0.995 (1.00) |
0.0498 (0.621) |
0.592 (1.00) |
0.727 (1.00) |
1 (1.00) |
0.314 (1.00) |
0.45 (1.00) |
0.313 (1.00) |
1 (1.00) |
1 (1.00) |
|||
ARHGAP35 | 7 (1%) | 777 |
0.123 (0.858) |
0.745 (1.00) |
0.104 (0.803) |
0.206 (1.00) |
1 (1.00) |
0.202 (1.00) |
0.69 (1.00) |
0.395 (1.00) |
0.0428 (0.601) |
1 (1.00) |
|||
RIMBP3 | 5 (1%) | 779 |
0.277 (1.00) |
0.358 (1.00) |
0.667 (1.00) |
0.0786 (0.778) |
1 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.0336 (0.535) |
1 (1.00) |
1 (1.00) |
|||
FAT1 | 20 (3%) | 764 |
0.775 (1.00) |
0.337 (1.00) |
0.303 (1.00) |
0.38 (1.00) |
0.23 (1.00) |
0.659 (1.00) |
1 (1.00) |
0.896 (1.00) |
0.0779 (0.778) |
0.687 (1.00) |
0.403 (1.00) |
0.523 (1.00) |
0.616 (1.00) |
TCEB1 | 4 (1%) | 780 |
0.195 (1.00) |
0.0887 (0.794) |
0.806 (1.00) |
0.406 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.427 (1.00) |
0.223 (1.00) |
||||
PODXL | 6 (1%) | 778 |
0.247 (1.00) |
0.0406 (0.601) |
0.322 (1.00) |
0.476 (1.00) |
1 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.539 (1.00) |
0.568 (1.00) |
0.172 (1.00) |
0.11 (0.815) |
1 (1.00) |
|
DNAJA3 | 3 (0%) | 781 |
0.391 (1.00) |
0.874 (1.00) |
0.558 (1.00) |
0.288 (1.00) |
1 (1.00) |
0.253 (1.00) |
0.667 (1.00) |
1 (1.00) |
|||||
NASP | 5 (1%) | 779 |
0.434 (1.00) |
0.317 (1.00) |
0.326 (1.00) |
0.473 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.0492 (0.621) |
1 (1.00) |
0.27 (1.00) |
||||
SLC23A1 | 6 (1%) | 778 |
0.123 (0.858) |
0.963 (1.00) |
0.435 (1.00) |
0.297 (1.00) |
1 (1.00) |
0.533 (1.00) |
0.401 (1.00) |
1 (1.00) |
0.239 (1.00) |
1 (1.00) |
|||
RILPL1 | 5 (1%) | 779 |
0.572 (1.00) |
0.99 (1.00) |
0.122 (0.858) |
0.33 (1.00) |
0.348 (1.00) |
0.456 (1.00) |
1 (1.00) |
0.0478 (0.613) |
0.189 (1.00) |
1 (1.00) |
|||
NIPBL | 15 (2%) | 769 |
0.875 (1.00) |
0.617 (1.00) |
0.139 (0.912) |
0.0636 (0.697) |
0.513 (1.00) |
0.371 (1.00) |
0.408 (1.00) |
0.787 (1.00) |
0.153 (0.967) |
0.179 (1.00) |
0.302 (1.00) |
1 (1.00) |
1 (1.00) |
RHEB | 3 (0%) | 781 |
0.745 (1.00) |
0.951 (1.00) |
0.455 (1.00) |
0.574 (1.00) |
0.262 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.341 (1.00) |
1 (1.00) |
||||
BRAF | 5 (1%) | 779 |
0.667 (1.00) |
0.601 (1.00) |
0.865 (1.00) |
1 (1.00) |
0.366 (1.00) |
0.666 (1.00) |
0.201 (1.00) |
1 (1.00) |
1 (1.00) |
||||
ANK3 | 22 (3%) | 762 |
0.128 (0.883) |
0.638 (1.00) |
0.462 (1.00) |
0.567 (1.00) |
0.579 (1.00) |
0.712 (1.00) |
0.106 (0.803) |
0.32 (1.00) |
0.846 (1.00) |
0.136 (0.912) |
0.389 (1.00) |
0.54 (1.00) |
1 (1.00) |
EMG1 | 4 (1%) | 780 |
0.212 (1.00) |
0.829 (1.00) |
0.589 (1.00) |
0.402 (1.00) |
1 (1.00) |
1 (1.00) |
0.295 (1.00) |
1 (1.00) |
1 (1.00) |
||||
LHX1 | 4 (1%) | 780 |
0.729 (1.00) |
0.812 (1.00) |
0.0241 (0.438) |
0.175 (1.00) |
1 (1.00) |
0.107 (0.803) |
0.511 (1.00) |
1 (1.00) |
0.172 (1.00) |
||||
SCARB2 | 4 (1%) | 780 |
0.192 (1.00) |
0.0274 (0.461) |
0.146 (0.933) |
0.136 (0.912) |
1 (1.00) |
1 (1.00) |
0.295 (1.00) |
1 (1.00) |
1 (1.00) |
||||
C1ORF25 | 6 (1%) | 778 |
0.0679 (0.71) |
0.0141 (0.337) |
0.576 (1.00) |
0.0833 (0.794) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.541 (1.00) |
1 (1.00) |
1 (1.00) |
|||
KDELR3 | 7 (1%) | 777 |
0.249 (1.00) |
0.495 (1.00) |
0.236 (1.00) |
0.0126 (0.337) |
1 (1.00) |
1 (1.00) |
0.436 (1.00) |
0.108 (0.803) |
0.622 (1.00) |
1 (1.00) |
|||
TTLL6 | 4 (1%) | 780 |
0.813 (1.00) |
0.517 (1.00) |
0.0123 (0.337) |
0.0176 (0.364) |
1 (1.00) |
0.107 (0.803) |
0.0204 (0.403) |
1 (1.00) |
1 (1.00) |
||||
STXBP3 | 5 (1%) | 779 |
0.727 (1.00) |
0.789 (1.00) |
0.41 (1.00) |
0.189 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.605 (1.00) |
1 (1.00) |
0.27 (1.00) |
||||
FAM20C | 5 (1%) | 779 |
0.446 (1.00) |
0.526 (1.00) |
0.453 (1.00) |
0.389 (1.00) |
1 (1.00) |
1 (1.00) |
0.338 (1.00) |
0.0208 (0.403) |
1 (1.00) |
1 (1.00) |
|||
CCBL2 | 3 (0%) | 781 |
0.196 (1.00) |
0.313 (1.00) |
0.557 (1.00) |
0.289 (1.00) |
1 (1.00) |
0.253 (1.00) |
0.667 (1.00) |
0.34 (1.00) |
1 (1.00) |
||||
B3GNT6 | 3 (0%) | 781 |
0.736 (1.00) |
0.511 (1.00) |
0.805 (1.00) |
0.733 (1.00) |
1 (1.00) |
0.555 (1.00) |
0.669 (1.00) |
0.341 (1.00) |
0.118 (0.854) |
||||
HNF1B | 4 (1%) | 780 |
0.173 (1.00) |
0.704 (1.00) |
0.322 (1.00) |
0.322 (1.00) |
0.262 (1.00) |
0.602 (1.00) |
0.511 (1.00) |
1 (1.00) |
1 (1.00) |
P value = 0.0031 (Fisher's exact test), Q value = 0.17
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 399 | 89 | 175 | 93 |
TP53 MUTATED | 12 | 10 | 6 | 8 |
TP53 WILD-TYPE | 387 | 79 | 169 | 85 |
P value = 0.00241 (Fisher's exact test), Q value = 0.17
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 423 | 111 | 237 | 11 |
TP53 MUTATED | 13 | 12 | 11 | 2 |
TP53 WILD-TYPE | 410 | 99 | 226 | 9 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0015
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
TP53 MUTATED | 22 | 9 | 7 |
TP53 WILD-TYPE | 44 | 427 | 275 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0015
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
PBRM1 MUTATED | 1 | 131 | 11 |
PBRM1 WILD-TYPE | 65 | 305 | 271 |
P value = 0.0045 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 780 | 202 | 0.1 - 194.8 (37.0) |
VHL MUTATED | 196 | 69 | 0.4 - 149.2 (41.7) |
VHL WILD-TYPE | 584 | 133 | 0.1 - 194.8 (36.0) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0015
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
VHL MUTATED | 1 | 192 | 3 |
VHL WILD-TYPE | 65 | 244 | 279 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0015
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 14 | 83 | 663 |
VHL MUTATED | 0 | 2 | 2 | 190 |
VHL WILD-TYPE | 2 | 12 | 81 | 473 |
P value = 0.00025 (Fisher's exact test), Q value = 0.025
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 293 | 40 | 5 |
NF2 MUTATED | 1 | 5 | 0 |
NF2 WILD-TYPE | 292 | 35 | 5 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0015
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
MET MUTATED | 0 | 4 | 21 |
MET WILD-TYPE | 66 | 432 | 261 |
P value = 8e-05 (Fisher's exact test), Q value = 0.01
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
KDM5C MUTATED | 1 | 25 | 1 |
KDM5C WILD-TYPE | 65 | 411 | 281 |
P value = 0.00493 (Fisher's exact test), Q value = 0.21
nPatients | FEMALE | MALE |
---|---|---|
ALL | 258 | 526 |
MTOR MUTATED | 19 | 15 |
MTOR WILD-TYPE | 239 | 511 |
P value = 0.00253 (Fisher's exact test), Q value = 0.17
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
MTOR MUTATED | 2 | 28 | 4 |
MTOR WILD-TYPE | 64 | 408 | 278 |
P value = 0.00301 (Fisher's exact test), Q value = 0.17
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
ZNF814 MUTATED | 3 | 2 | 9 |
ZNF814 WILD-TYPE | 63 | 434 | 273 |
P value = 0.00014 (Fisher's exact test), Q value = 0.016
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
AR MUTATED | 1 | 1 | 13 |
AR WILD-TYPE | 65 | 435 | 269 |
P value = 0.00494 (Fisher's exact test), Q value = 0.21
nPatients | 0 | 1 |
---|---|---|
ALL | 494 | 81 |
CACNA1C MUTATED | 7 | 6 |
CACNA1C WILD-TYPE | 487 | 75 |
P value = 0.0015 (Fisher's exact test), Q value = 0.12
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
PCF11 MUTATED | 0 | 2 | 11 |
PCF11 WILD-TYPE | 66 | 434 | 271 |
P value = 0.000542 (Wilcoxon-test), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 779 | 60.1 (12.6) |
KDM6A MUTATED | 11 | 72.4 (6.7) |
KDM6A WILD-TYPE | 768 | 59.9 (12.5) |
P value = 1.48e-09 (logrank test), Q value = 1.3e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 780 | 202 | 0.1 - 194.8 (37.0) |
FAM178A MUTATED | 8 | 6 | 0.5 - 52.1 (10.4) |
FAM178A WILD-TYPE | 772 | 196 | 0.1 - 194.8 (37.2) |
P value = 0.00299 (logrank test), Q value = 0.17
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 780 | 202 | 0.1 - 194.8 (37.0) |
FAM47A MUTATED | 6 | 4 | 2.5 - 84.3 (22.3) |
FAM47A WILD-TYPE | 774 | 198 | 0.1 - 194.8 (37.2) |
P value = 0.00301 (Fisher's exact test), Q value = 0.17
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 436 | 282 |
MLL3 MUTATED | 9 | 15 | 18 |
MLL3 WILD-TYPE | 57 | 421 | 264 |
P value = 0.00464 (Fisher's exact test), Q value = 0.21
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 14 | 83 | 663 |
MLL3 MUTATED | 0 | 1 | 12 | 28 |
MLL3 WILD-TYPE | 2 | 13 | 71 | 635 |
-
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/KIPAN-TP/22815577/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/22506733/KIPAN-TP.merged_data.txt
-
Number of patients = 784
-
Number of significantly mutated genes = 70
-
Number of selected clinical features = 13
-
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.