This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 73 genes and 13 clinical features across 668 patients, 42 significant findings detected with Q value < 0.25.
-
TP53 mutation correlated to 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', and 'HISTOLOGICAL_TYPE'.
-
PBRM1 mutation correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
BAP1 mutation correlated to 'Time to Death', 'NEOPLASM_DISEASESTAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_M_STAGE', and 'HISTOLOGICAL_TYPE'.
-
SETD2 mutation correlated to 'Time to Death'.
-
KDM5C mutation correlated to 'YEARS_TO_BIRTH' and 'GENDER'.
-
NEFH mutation correlated to 'HISTOLOGICAL_TYPE'.
-
VHL mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
-
NF2 mutation correlated to 'PATHOLOGY_N_STAGE' and 'HISTOLOGICAL_TYPE'.
-
HNRNPM mutation correlated to 'HISTOLOGICAL_TYPE'.
-
MET mutation correlated to 'HISTOLOGICAL_TYPE'.
-
MUC5B mutation correlated to 'HISTOLOGICAL_TYPE'.
-
KDM6A mutation correlated to 'RACE'.
-
TDG mutation correlated to 'HISTOLOGICAL_TYPE'.
-
NFE2L2 mutation correlated to 'YEARS_TO_BIRTH'.
-
ATM mutation correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.
-
ZNF814 mutation correlated to 'HISTOLOGICAL_TYPE'.
-
CSGALNACT2 mutation correlated to 'HISTOLOGICAL_TYPE'.
-
ZNF598 mutation correlated to 'HISTOLOGICAL_TYPE'.
-
SKI mutation correlated to 'HISTOLOGICAL_TYPE'.
-
EGFR mutation correlated to 'Time to Death' and 'PATHOLOGY_T_STAGE'.
-
AHNAK2 mutation correlated to 'HISTOLOGICAL_TYPE' and 'RACE'.
-
STAM mutation correlated to 'NEOPLASM_DISEASESTAGE' and 'PATHOLOGY_T_STAGE'.
-
RTL1 mutation correlated to 'Time to Death' and 'NEOPLASM_DISEASESTAGE'.
-
IDUA mutation correlated to 'HISTOLOGICAL_TYPE'.
-
GFM1 mutation correlated to 'HISTOLOGICAL_TYPE'.
-
FAT1 mutation correlated to 'HISTOLOGICAL_TYPE'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
NEOPLASM DISEASESTAGE |
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 | |
BAP1 | 49 (7%) | 619 |
8.61e-05 (0.00681) |
0.649 (1.00) |
3e-05 (0.00316) |
8e-05 (0.00681) |
0.776 (1.00) |
0.00436 (0.129) |
0.0124 (0.262) |
0.0002 (0.0146) |
0.668 (1.00) |
0.735 (1.00) |
|||
TP53 | 38 (6%) | 630 |
0.369 (1.00) |
0.202 (1.00) |
0.00318 (0.103) |
0.00325 (0.103) |
0.0911 (0.9) |
0.569 (1.00) |
0.486 (1.00) |
0.28 (1.00) |
1e-05 (0.00158) |
0.386 (1.00) |
0.974 (1.00) |
0.23 (1.00) |
1 (1.00) |
PBRM1 | 146 (22%) | 522 |
0.29 (1.00) |
0.00663 (0.18) |
0.764 (1.00) |
0.37 (1.00) |
0.0222 (0.376) |
0.491 (1.00) |
0.622 (1.00) |
0.981 (1.00) |
1e-05 (0.00158) |
0.00695 (0.183) |
0.267 (1.00) |
||
KDM5C | 30 (4%) | 638 |
0.0162 (0.301) |
0.00965 (0.235) |
0.831 (1.00) |
0.816 (1.00) |
0.785 (1.00) |
1 (1.00) |
0.00286 (0.101) |
0.0129 (0.266) |
0.868 (1.00) |
0.385 (1.00) |
|||
VHL | 174 (26%) | 494 |
0.118 (0.904) |
0.182 (1.00) |
0.358 (1.00) |
0.264 (1.00) |
0.0689 (0.777) |
0.695 (1.00) |
0.353 (1.00) |
0.795 (1.00) |
1e-05 (0.00158) |
1e-05 (0.00158) |
0.681 (1.00) |
||
NF2 | 16 (2%) | 652 |
0.109 (0.904) |
0.228 (1.00) |
0.03 (0.474) |
0.118 (0.904) |
4e-05 (0.0038) |
0.0411 (0.571) |
0.794 (1.00) |
0.00254 (0.0927) |
0.0567 (0.681) |
0.217 (1.00) |
|||
ATM | 16 (2%) | 652 |
0.962 (1.00) |
0.101 (0.9) |
0.0103 (0.246) |
0.00141 (0.0669) |
0.449 (1.00) |
0.435 (1.00) |
0.432 (1.00) |
0.122 (0.904) |
0.562 (1.00) |
0.507 (1.00) |
|||
EGFR | 7 (1%) | 661 |
0.00499 (0.139) |
0.705 (1.00) |
0.0123 (0.262) |
0.0034 (0.104) |
0.44 (1.00) |
0.263 (1.00) |
0.432 (1.00) |
0.26 (1.00) |
1 (1.00) |
1 (1.00) |
|||
AHNAK2 | 33 (5%) | 635 |
0.773 (1.00) |
0.235 (1.00) |
0.171 (1.00) |
0.12 (0.904) |
0.122 (0.904) |
0.563 (1.00) |
0.574 (1.00) |
0.857 (1.00) |
0.00161 (0.0701) |
0.654 (1.00) |
0.145 (0.983) |
0.00455 (0.131) |
0.654 (1.00) |
STAM | 6 (1%) | 662 |
0.714 (1.00) |
0.44 (1.00) |
0.00049 (0.0291) |
0.00168 (0.0701) |
0.047 (0.602) |
0.0997 (0.9) |
0.67 (1.00) |
0.0743 (0.811) |
1 (1.00) |
0.039 (0.57) |
|||
RTL1 | 7 (1%) | 661 |
0.00825 (0.212) |
0.609 (1.00) |
0.0109 (0.25) |
0.0811 (0.855) |
1 (1.00) |
0.151 (0.989) |
0.102 (0.9) |
0.158 (1.00) |
1 (1.00) |
1 (1.00) |
|||
SETD2 | 58 (9%) | 610 |
0.00934 (0.233) |
0.0309 (0.48) |
0.0552 (0.68) |
0.066 (0.763) |
0.421 (1.00) |
0.216 (1.00) |
0.312 (1.00) |
0.628 (1.00) |
0.0684 (0.777) |
0.939 (1.00) |
0.501 (1.00) |
||
NEFH | 15 (2%) | 653 |
0.508 (1.00) |
0.419 (1.00) |
0.274 (1.00) |
0.239 (1.00) |
1 (1.00) |
0.596 (1.00) |
0.28 (1.00) |
0.00141 (0.0669) |
0.52 (1.00) |
0.106 (0.904) |
1 (1.00) |
||
HNRNPM | 12 (2%) | 656 |
0.322 (1.00) |
0.465 (1.00) |
0.443 (1.00) |
0.0601 (0.704) |
0.351 (1.00) |
0.601 (1.00) |
0.76 (1.00) |
0.836 (1.00) |
2e-05 (0.00237) |
0.217 (1.00) |
1 (1.00) |
||
MET | 19 (3%) | 649 |
0.782 (1.00) |
0.845 (1.00) |
0.458 (1.00) |
0.926 (1.00) |
0.102 (0.9) |
1 (1.00) |
1 (1.00) |
1e-05 (0.00158) |
0.35 (1.00) |
0.77 (1.00) |
0.145 (0.983) |
1 (1.00) |
|
MUC5B | 30 (4%) | 638 |
0.457 (1.00) |
0.688 (1.00) |
0.478 (1.00) |
0.58 (1.00) |
0.115 (0.904) |
0.51 (1.00) |
0.844 (1.00) |
0.44 (1.00) |
1e-05 (0.00158) |
0.989 (1.00) |
0.784 (1.00) |
0.386 (1.00) |
1 (1.00) |
KDM6A | 11 (2%) | 657 |
0.578 (1.00) |
0.0559 (0.68) |
0.371 (1.00) |
1 (1.00) |
0.609 (1.00) |
1 (1.00) |
0.0158 (0.301) |
0.00036 (0.0244) |
1 (1.00) |
||||
TDG | 5 (1%) | 663 |
0.237 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.116 (0.904) |
0.351 (1.00) |
1 (1.00) |
0.665 (1.00) |
0.0017 (0.0701) |
0.477 (1.00) |
1 (1.00) |
|||
NFE2L2 | 10 (1%) | 658 |
0.897 (1.00) |
0.0111 (0.25) |
0.764 (1.00) |
0.781 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.462 (1.00) |
0.408 (1.00) |
1 (1.00) |
|||
ZNF814 | 13 (2%) | 655 |
0.211 (1.00) |
0.242 (1.00) |
0.147 (0.986) |
0.264 (1.00) |
0.438 (1.00) |
1 (1.00) |
0.0421 (0.571) |
0.00045 (0.0285) |
0.339 (1.00) |
1 (1.00) |
|||
CSGALNACT2 | 8 (1%) | 660 |
0.103 (0.9) |
0.486 (1.00) |
0.751 (1.00) |
0.494 (1.00) |
1 (1.00) |
0.601 (1.00) |
0.456 (1.00) |
0.00297 (0.101) |
0.133 (0.951) |
1 (1.00) |
|||
ZNF598 | 11 (2%) | 657 |
0.741 (1.00) |
0.479 (1.00) |
0.603 (1.00) |
0.867 (1.00) |
0.0204 (0.352) |
0.0997 (0.9) |
0.347 (1.00) |
0.361 (1.00) |
2e-05 (0.00237) |
0.217 (1.00) |
0.507 (1.00) |
||
SKI | 9 (1%) | 659 |
0.579 (1.00) |
0.743 (1.00) |
0.63 (1.00) |
0.697 (1.00) |
0.443 (1.00) |
1 (1.00) |
0.726 (1.00) |
0.00187 (0.071) |
0.769 (1.00) |
0.268 (1.00) |
1 (1.00) |
||
IDUA | 5 (1%) | 663 |
0.691 (1.00) |
0.213 (1.00) |
0.841 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.665 (1.00) |
0.00184 (0.071) |
0.173 (1.00) |
1 (1.00) |
||||
GFM1 | 3 (0%) | 665 |
0.706 (1.00) |
0.0295 (0.474) |
0.689 (1.00) |
0.742 (1.00) |
0.266 (1.00) |
1 (1.00) |
0.00082 (0.0458) |
1 (1.00) |
1 (1.00) |
||||
FAT1 | 22 (3%) | 646 |
0.552 (1.00) |
0.231 (1.00) |
0.264 (1.00) |
0.294 (1.00) |
0.295 (1.00) |
1 (1.00) |
0.823 (1.00) |
0.00138 (0.0669) |
0.897 (1.00) |
0.0917 (0.9) |
0.624 (1.00) |
||
PTEN | 28 (4%) | 640 |
0.651 (1.00) |
0.665 (1.00) |
0.274 (1.00) |
0.475 (1.00) |
0.166 (1.00) |
0.23 (1.00) |
0.685 (1.00) |
0.28 (1.00) |
0.12 (0.904) |
1 (1.00) |
0.841 (1.00) |
0.549 (1.00) |
1 (1.00) |
DNMT3A | 10 (1%) | 658 |
0.129 (0.93) |
0.956 (1.00) |
0.329 (1.00) |
0.351 (1.00) |
0.513 (1.00) |
0.601 (1.00) |
0.323 (1.00) |
0.463 (1.00) |
0.408 (1.00) |
0.431 (1.00) |
|||
CDK12 | 9 (1%) | 659 |
0.912 (1.00) |
0.0421 (0.571) |
0.681 (1.00) |
0.696 (1.00) |
1 (1.00) |
0.623 (1.00) |
0.501 (1.00) |
0.668 (1.00) |
1 (1.00) |
1 (1.00) |
|||
PIK3CA | 14 (2%) | 654 |
0.83 (1.00) |
0.493 (1.00) |
0.589 (1.00) |
0.511 (1.00) |
1 (1.00) |
0.412 (1.00) |
0.0875 (0.9) |
0.392 (1.00) |
0.536 (1.00) |
0.573 (1.00) |
|||
KIAA1751 | 8 (1%) | 660 |
0.967 (1.00) |
0.101 (0.9) |
0.611 (1.00) |
0.81 (1.00) |
0.514 (1.00) |
0.601 (1.00) |
0.722 (1.00) |
0.533 (1.00) |
1 (1.00) |
0.645 (1.00) |
1 (1.00) |
||
MTOR | 32 (5%) | 636 |
0.0725 (0.8) |
0.0415 (0.571) |
0.326 (1.00) |
0.652 (1.00) |
1 (1.00) |
0.174 (1.00) |
0.0118 (0.261) |
0.0136 (0.276) |
0.0198 (0.352) |
0.773 (1.00) |
0.711 (1.00) |
||
RIMBP3 | 5 (1%) | 663 |
0.332 (1.00) |
0.308 (1.00) |
0.628 (1.00) |
0.0896 (0.9) |
1 (1.00) |
1 (1.00) |
0.345 (1.00) |
0.0802 (0.855) |
1 (1.00) |
1 (1.00) |
|||
GPR50 | 5 (1%) | 663 |
0.454 (1.00) |
0.311 (1.00) |
0.764 (1.00) |
0.855 (1.00) |
1 (1.00) |
0.345 (1.00) |
0.604 (1.00) |
0.474 (1.00) |
1 (1.00) |
||||
CCDC120 | 4 (1%) | 664 |
0.19 (1.00) |
0.751 (1.00) |
0.114 (0.904) |
0.149 (0.986) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.723 (1.00) |
1 (1.00) |
0.19 (1.00) |
|||
SLC6A14 | 5 (1%) | 663 |
0.728 (1.00) |
0.599 (1.00) |
0.218 (1.00) |
0.172 (1.00) |
0.093 (0.9) |
1 (1.00) |
0.345 (1.00) |
0.247 (1.00) |
1 (1.00) |
1 (1.00) |
|||
CYP4F11 | 5 (1%) | 663 |
0.828 (1.00) |
0.495 (1.00) |
0.141 (0.983) |
0.0453 (0.598) |
0.513 (1.00) |
0.461 (1.00) |
1 (1.00) |
0.342 (1.00) |
1 (1.00) |
1 (1.00) |
|||
STAG2 | 14 (2%) | 654 |
0.962 (1.00) |
0.0145 (0.282) |
0.161 (1.00) |
0.0918 (0.9) |
1 (1.00) |
0.662 (1.00) |
0.256 (1.00) |
0.165 (1.00) |
0.495 (1.00) |
1 (1.00) |
|||
ARID1A | 19 (3%) | 649 |
0.749 (1.00) |
0.776 (1.00) |
0.351 (1.00) |
0.67 (1.00) |
0.108 (0.904) |
0.713 (1.00) |
0.47 (1.00) |
0.587 (1.00) |
0.113 (0.904) |
0.0143 (0.282) |
0.243 (1.00) |
||
DPCR1 | 8 (1%) | 660 |
0.607 (1.00) |
0.226 (1.00) |
0.203 (1.00) |
0.674 (1.00) |
0.0407 (0.571) |
0.722 (1.00) |
0.74 (1.00) |
0.647 (1.00) |
1 (1.00) |
||||
GUSB | 4 (1%) | 664 |
0.593 (1.00) |
0.0578 (0.686) |
0.223 (1.00) |
0.332 (1.00) |
1 (1.00) |
1 (1.00) |
0.721 (1.00) |
1 (1.00) |
1 (1.00) |
||||
MED16 | 4 (1%) | 664 |
0.035 (0.519) |
0.828 (1.00) |
0.41 (1.00) |
0.328 (1.00) |
0.0913 (0.9) |
1 (1.00) |
0.61 (1.00) |
0.0958 (0.9) |
1 (1.00) |
1 (1.00) |
|||
PTCH1 | 8 (1%) | 660 |
0.0464 (0.602) |
0.295 (1.00) |
0.259 (1.00) |
0.077 (0.83) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.63 (1.00) |
0.642 (1.00) |
1 (1.00) |
|||
RLIM | 9 (1%) | 659 |
0.595 (1.00) |
0.129 (0.93) |
0.73 (1.00) |
0.764 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.249 (1.00) |
0.676 (1.00) |
1 (1.00) |
|||
SLC23A1 | 7 (1%) | 661 |
0.342 (1.00) |
0.308 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.206 (1.00) |
0.239 (1.00) |
1 (1.00) |
0.269 (1.00) |
1 (1.00) |
|||
RHEB | 4 (1%) | 664 |
0.835 (1.00) |
0.297 (1.00) |
0.877 (1.00) |
0.827 (1.00) |
0.371 (1.00) |
0.119 (0.904) |
1 (1.00) |
0.403 (1.00) |
1 (1.00) |
||||
SLC4A8 | 6 (1%) | 662 |
0.48 (1.00) |
0.382 (1.00) |
0.556 (1.00) |
0.665 (1.00) |
1 (1.00) |
0.67 (1.00) |
0.103 (0.9) |
1 (1.00) |
1 (1.00) |
||||
RUFY3 | 7 (1%) | 661 |
0.647 (1.00) |
0.564 (1.00) |
0.947 (1.00) |
0.888 (1.00) |
1 (1.00) |
0.539 (1.00) |
0.432 (1.00) |
0.312 (1.00) |
0.595 (1.00) |
0.345 (1.00) |
|||
PCK1 | 6 (1%) | 662 |
0.196 (1.00) |
0.426 (1.00) |
0.265 (1.00) |
0.148 (0.986) |
1 (1.00) |
0.601 (1.00) |
1 (1.00) |
1 (1.00) |
0.535 (1.00) |
1 (1.00) |
|||
TXNIP | 8 (1%) | 660 |
0.472 (1.00) |
0.61 (1.00) |
0.143 (0.983) |
0.3 (1.00) |
0.0201 (0.352) |
0.32 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.345 (1.00) |
|||
RNF128 | 5 (1%) | 663 |
0.595 (1.00) |
0.913 (1.00) |
0.469 (1.00) |
0.143 (0.983) |
1 (1.00) |
0.665 (1.00) |
0.171 (1.00) |
0.174 (1.00) |
0.245 (1.00) |
||||
ZFYVE26 | 9 (1%) | 659 |
0.485 (1.00) |
0.269 (1.00) |
0.678 (1.00) |
0.698 (1.00) |
0.263 (1.00) |
1 (1.00) |
0.879 (1.00) |
1 (1.00) |
1 (1.00) |
||||
FAM160B2 | 4 (1%) | 664 |
0.223 (1.00) |
0.746 (1.00) |
0.313 (1.00) |
0.658 (1.00) |
0.371 (1.00) |
0.61 (1.00) |
0.384 (1.00) |
1 (1.00) |
1 (1.00) |
||||
FAM47A | 6 (1%) | 662 |
0.023 (0.376) |
0.349 (1.00) |
0.599 (1.00) |
0.569 (1.00) |
0.461 (1.00) |
0.0198 (0.352) |
0.655 (1.00) |
1 (1.00) |
1 (1.00) |
||||
ATP1A1 | 10 (1%) | 658 |
0.232 (1.00) |
0.365 (1.00) |
0.292 (1.00) |
0.779 (1.00) |
0.0921 (0.9) |
0.507 (1.00) |
0.464 (1.00) |
0.406 (1.00) |
1 (1.00) |
||||
SH3BP2 | 4 (1%) | 664 |
0.533 (1.00) |
0.595 (1.00) |
1 (1.00) |
0.654 (1.00) |
1 (1.00) |
0.61 (1.00) |
0.0958 (0.9) |
0.404 (1.00) |
1 (1.00) |
||||
FAM200A | 5 (1%) | 663 |
0.67 (1.00) |
0.603 (1.00) |
0.84 (1.00) |
0.604 (1.00) |
1 (1.00) |
1 (1.00) |
0.0495 (0.626) |
0.465 (1.00) |
1 (1.00) |
1 (1.00) |
|||
NASP | 4 (1%) | 664 |
0.106 (0.904) |
0.343 (1.00) |
0.22 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.119 (0.904) |
0.0347 (0.519) |
1 (1.00) |
0.245 (1.00) |
||||
RPL7A | 3 (0%) | 665 |
0.753 (1.00) |
0.2 (1.00) |
0.591 (1.00) |
1 (1.00) |
0.143 (0.983) |
0.555 (1.00) |
0.0227 (0.376) |
0.319 (1.00) |
1 (1.00) |
||||
UIMC1 | 5 (1%) | 663 |
0.0555 (0.68) |
0.532 (1.00) |
0.295 (1.00) |
0.0448 (0.598) |
1 (1.00) |
0.539 (1.00) |
0.665 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|||
TCEB1 | 3 (0%) | 665 |
0.325 (1.00) |
0.199 (1.00) |
0.815 (1.00) |
0.43 (1.00) |
1 (1.00) |
1 (1.00) |
0.683 (1.00) |
0.319 (1.00) |
0.19 (1.00) |
||||
SFMBT1 | 3 (0%) | 665 |
0.115 (0.904) |
0.322 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.272 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||||
SLC16A1 | 3 (0%) | 665 |
0.416 (1.00) |
0.2 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.319 (1.00) |
0.19 (1.00) |
||||
PAM | 4 (1%) | 664 |
0.223 (1.00) |
0.961 (1.00) |
0.778 (1.00) |
1 (1.00) |
0.351 (1.00) |
1 (1.00) |
1 (1.00) |
0.0948 (0.9) |
0.399 (1.00) |
0.321 (1.00) |
1 (1.00) |
||
TMCO3 | 7 (1%) | 661 |
0.523 (1.00) |
0.565 (1.00) |
0.34 (1.00) |
0.626 (1.00) |
0.439 (1.00) |
1 (1.00) |
0.239 (1.00) |
1 (1.00) |
0.0315 (0.482) |
0.297 (1.00) |
|||
CCDC82 | 6 (1%) | 662 |
0.356 (1.00) |
0.514 (1.00) |
0.878 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.188 (1.00) |
0.254 (1.00) |
1 (1.00) |
1 (1.00) |
|||
NFAT5 | 8 (1%) | 660 |
0.772 (1.00) |
0.744 (1.00) |
0.348 (1.00) |
0.612 (1.00) |
1 (1.00) |
0.609 (1.00) |
0.722 (1.00) |
0.743 (1.00) |
0.643 (1.00) |
1 (1.00) |
|||
HNF1B | 3 (0%) | 665 |
0.109 (0.904) |
0.765 (1.00) |
0.123 (0.904) |
0.184 (1.00) |
0.266 (1.00) |
0.272 (1.00) |
0.4 (1.00) |
1 (1.00) |
|||||
OR2L8 | 7 (1%) | 661 |
0.214 (1.00) |
0.567 (1.00) |
0.568 (1.00) |
0.494 (1.00) |
0.151 (0.989) |
0.239 (1.00) |
0.124 (0.906) |
1 (1.00) |
1 (1.00) |
||||
ZC3H18 | 6 (1%) | 662 |
0.137 (0.969) |
0.777 (1.00) |
1 (1.00) |
0.763 (1.00) |
1 (1.00) |
0.418 (1.00) |
0.821 (1.00) |
0.54 (1.00) |
1 (1.00) |
||||
GAPDHS | 5 (1%) | 663 |
0.307 (1.00) |
0.396 (1.00) |
0.919 (1.00) |
0.604 (1.00) |
1 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.174 (1.00) |
1 (1.00) |
||||
GPR137 | 4 (1%) | 664 |
0.756 (1.00) |
0.388 (1.00) |
0.877 (1.00) |
0.824 (1.00) |
0.461 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||||
RRP12 | 9 (1%) | 659 |
0.792 (1.00) |
0.116 (0.904) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0696 (0.777) |
0.574 (1.00) |
1 (1.00) |
0.345 (1.00) |
P value = 0.00318 (Fisher's exact test), Q value = 0.1
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 327 | 79 | 165 | 86 |
TP53 MUTATED | 12 | 11 | 7 | 8 |
TP53 WILD-TYPE | 315 | 68 | 158 | 78 |
P value = 0.00325 (Fisher's exact test), Q value = 0.1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 340 | 97 | 221 | 10 |
TP53 MUTATED | 12 | 12 | 12 | 2 |
TP53 WILD-TYPE | 328 | 85 | 209 | 8 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
TP53 MUTATED | 22 | 12 | 4 |
TP53 WILD-TYPE | 44 | 429 | 157 |
P value = 0.00663 (Wilcoxon-test), Q value = 0.18
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 665 | 59.5 (12.6) |
PBRM1 MUTATED | 146 | 62.1 (10.9) |
PBRM1 WILD-TYPE | 519 | 58.7 (13.0) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
PBRM1 MUTATED | 1 | 139 | 6 |
PBRM1 WILD-TYPE | 65 | 302 | 155 |
P value = 0.00695 (Fisher's exact test), Q value = 0.18
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 65 | 569 |
PBRM1 MUTATED | 0 | 1 | 5 | 136 |
PBRM1 WILD-TYPE | 2 | 10 | 60 | 433 |
P value = 8.61e-05 (logrank test), Q value = 0.0068
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 661 | 175 | 0.1 - 194.8 (34.3) |
BAP1 MUTATED | 49 | 25 | 0.1 - 93.3 (27.6) |
BAP1 WILD-TYPE | 612 | 150 | 0.1 - 194.8 (35.1) |
P value = 3e-05 (Fisher's exact test), Q value = 0.0032
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 327 | 79 | 165 | 86 |
BAP1 MUTATED | 9 | 8 | 19 | 13 |
BAP1 WILD-TYPE | 318 | 71 | 146 | 73 |
P value = 8e-05 (Fisher's exact test), Q value = 0.0068
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 340 | 97 | 221 | 10 |
BAP1 MUTATED | 10 | 12 | 27 | 0 |
BAP1 WILD-TYPE | 330 | 85 | 194 | 10 |
P value = 0.00436 (Fisher's exact test), Q value = 0.13
nPatients | 0 | 1 |
---|---|---|
ALL | 468 | 78 |
BAP1 MUTATED | 34 | 14 |
BAP1 WILD-TYPE | 434 | 64 |
P value = 2e-04 (Fisher's exact test), Q value = 0.015
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
BAP1 MUTATED | 0 | 44 | 5 |
BAP1 WILD-TYPE | 66 | 397 | 156 |
P value = 0.00934 (logrank test), Q value = 0.23
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 661 | 175 | 0.1 - 194.8 (34.3) |
SETD2 MUTATED | 58 | 24 | 0.5 - 152.0 (33.0) |
SETD2 WILD-TYPE | 603 | 151 | 0.1 - 194.8 (34.3) |
P value = 0.00965 (Wilcoxon-test), Q value = 0.23
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 665 | 59.5 (12.6) |
KDM5C MUTATED | 30 | 65.4 (12.3) |
KDM5C WILD-TYPE | 635 | 59.2 (12.6) |
P value = 0.00286 (Fisher's exact test), Q value = 0.1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 229 | 439 |
KDM5C MUTATED | 3 | 27 |
KDM5C WILD-TYPE | 226 | 412 |
P value = 0.00141 (Fisher's exact test), Q value = 0.067
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
NEFH MUTATED | 0 | 5 | 10 |
NEFH WILD-TYPE | 66 | 436 | 151 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
VHL MUTATED | 1 | 171 | 2 |
VHL WILD-TYPE | 65 | 270 | 159 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 65 | 569 |
VHL MUTATED | 0 | 2 | 2 | 167 |
VHL WILD-TYPE | 2 | 9 | 63 | 402 |
P value = 4e-05 (Fisher's exact test), Q value = 0.0038
nPatients | N0 | N1 | N2 |
---|---|---|---|
ALL | 272 | 36 | 6 |
NF2 MUTATED | 1 | 6 | 0 |
NF2 WILD-TYPE | 271 | 30 | 6 |
P value = 0.00254 (Fisher's exact test), Q value = 0.093
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
NF2 MUTATED | 0 | 6 | 10 |
NF2 WILD-TYPE | 66 | 435 | 151 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0024
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
HNRNPM MUTATED | 1 | 1 | 10 |
HNRNPM WILD-TYPE | 65 | 440 | 151 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
MET MUTATED | 0 | 4 | 15 |
MET WILD-TYPE | 66 | 437 | 146 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
MUC5B MUTATED | 11 | 5 | 14 |
MUC5B WILD-TYPE | 55 | 436 | 147 |
P value = 0.00036 (Fisher's exact test), Q value = 0.024
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 65 | 569 |
KDM6A MUTATED | 1 | 0 | 4 | 3 |
KDM6A WILD-TYPE | 1 | 11 | 61 | 566 |
P value = 0.0017 (Fisher's exact test), Q value = 0.07
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
TDG MUTATED | 0 | 0 | 5 |
TDG WILD-TYPE | 66 | 441 | 156 |
P value = 0.0111 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 665 | 59.5 (12.6) |
NFE2L2 MUTATED | 10 | 68.9 (7.0) |
NFE2L2 WILD-TYPE | 655 | 59.3 (12.7) |
P value = 0.0103 (Fisher's exact test), Q value = 0.25
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 327 | 79 | 165 | 86 |
ATM MUTATED | 6 | 6 | 1 | 3 |
ATM WILD-TYPE | 321 | 73 | 164 | 83 |
P value = 0.00141 (Fisher's exact test), Q value = 0.067
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 340 | 97 | 221 | 10 |
ATM MUTATED | 6 | 6 | 2 | 2 |
ATM WILD-TYPE | 334 | 91 | 219 | 8 |
P value = 0.00045 (Fisher's exact test), Q value = 0.028
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
ZNF814 MUTATED | 3 | 2 | 8 |
ZNF814 WILD-TYPE | 63 | 439 | 153 |
P value = 0.00297 (Fisher's exact test), Q value = 0.1
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
CSGALNACT2 MUTATED | 2 | 1 | 5 |
CSGALNACT2 WILD-TYPE | 64 | 440 | 156 |
P value = 2e-05 (Fisher's exact test), Q value = 0.0024
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
ZNF598 MUTATED | 1 | 0 | 10 |
ZNF598 WILD-TYPE | 65 | 441 | 151 |
P value = 0.00187 (Fisher's exact test), Q value = 0.071
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
SKI MUTATED | 2 | 1 | 6 |
SKI WILD-TYPE | 64 | 440 | 155 |
P value = 0.00499 (logrank test), Q value = 0.14
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 661 | 175 | 0.1 - 194.8 (34.3) |
EGFR MUTATED | 7 | 5 | 2.3 - 61.3 (34.0) |
EGFR WILD-TYPE | 654 | 170 | 0.1 - 194.8 (34.3) |
P value = 0.0034 (Fisher's exact test), Q value = 0.1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 340 | 97 | 221 | 10 |
EGFR MUTATED | 0 | 1 | 5 | 1 |
EGFR WILD-TYPE | 340 | 96 | 216 | 9 |
P value = 0.00161 (Fisher's exact test), Q value = 0.07
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
AHNAK2 MUTATED | 10 | 16 | 7 |
AHNAK2 WILD-TYPE | 56 | 425 | 154 |
P value = 0.00455 (Fisher's exact test), Q value = 0.13
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 2 | 11 | 65 | 569 |
AHNAK2 MUTATED | 1 | 2 | 6 | 22 |
AHNAK2 WILD-TYPE | 1 | 9 | 59 | 547 |
P value = 0.00049 (Fisher's exact test), Q value = 0.029
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 327 | 79 | 165 | 86 |
STAM MUTATED | 0 | 3 | 0 | 3 |
STAM WILD-TYPE | 327 | 76 | 165 | 83 |
P value = 0.00168 (Fisher's exact test), Q value = 0.07
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 340 | 97 | 221 | 10 |
STAM MUTATED | 0 | 3 | 2 | 1 |
STAM WILD-TYPE | 340 | 94 | 219 | 9 |
P value = 0.00825 (logrank test), Q value = 0.21
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 661 | 175 | 0.1 - 194.8 (34.3) |
RTL1 MUTATED | 7 | 5 | 8.1 - 115.0 (21.6) |
RTL1 WILD-TYPE | 654 | 170 | 0.1 - 194.8 (34.3) |
P value = 0.0109 (Fisher's exact test), Q value = 0.25
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV |
---|---|---|---|---|
ALL | 327 | 79 | 165 | 86 |
RTL1 MUTATED | 0 | 2 | 3 | 2 |
RTL1 WILD-TYPE | 327 | 77 | 162 | 84 |
P value = 0.00184 (Fisher's exact test), Q value = 0.071
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
IDUA MUTATED | 0 | 0 | 5 |
IDUA WILD-TYPE | 66 | 441 | 156 |
P value = 0.00082 (Fisher's exact test), Q value = 0.046
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
GFM1 MUTATED | 3 | 0 | 0 |
GFM1 WILD-TYPE | 63 | 441 | 161 |
P value = 0.00138 (Fisher's exact test), Q value = 0.067
nPatients | KIDNEY CHROMOPHOBE | KIDNEY CLEAR CELL RENAL CARCINOMA | KIDNEY PAPILLARY RENAL CELL CARCINOMA |
---|---|---|---|
ALL | 66 | 441 | 161 |
FAT1 MUTATED | 1 | 8 | 13 |
FAT1 WILD-TYPE | 65 | 433 | 148 |
-
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/15639742/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/15081103/KIPAN-TP.merged_data.txt
-
Number of patients = 668
-
Number of significantly mutated genes = 73
-
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.