This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 73 genes and 10 clinical features across 943 patients, 20 significant findings detected with Q value < 0.25.
-
TP53 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
CDH1 mutation correlated to 'PATHOLOGY.T.STAGE' and 'HISTOLOGICAL.TYPE'.
-
MLL3 mutation correlated to 'AGE'.
-
FAM86B1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
CASP8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
ASXL2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
GPRIN2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
TRPM5 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
PRICKLE3 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
WDR52 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
ERBB3 mutation correlated to 'Time to Death'.
-
PTHLH mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
HLA-DRB5 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
GYG2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
HRNR mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
DMXL2 mutation correlated to 'HISTOLOGICAL.TYPE' and 'NUMBER.OF.LYMPH.NODES'.
-
MUC5B mutation correlated to 'HISTOLOGICAL.TYPE'.
-
XBP1 mutation correlated to 'Time to Death'.
Table 1. Get Full Table Overview of the association between mutation status of 73 genes and 10 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 20 significant findings detected.
|
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBER OF LYMPH NODES |
||
| nMutated (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | t-test | |
| CDH1 | 96 (10%) | 847 |
0.151 (1.00) |
0.00934 (1.00) |
0.0261 (1.00) |
1.44e-06 (0.00104) |
0.00644 (1.00) |
0.00397 (1.00) |
0.61 (1.00) |
1.24e-69 (9.04e-67) |
0.00898 (1.00) |
0.197 (1.00) |
| DMXL2 | 18 (2%) | 925 |
0.745 (1.00) |
0.212 (1.00) |
0.357 (1.00) |
0.0774 (1.00) |
0.0598 (1.00) |
0.792 (1.00) |
0.16 (1.00) |
1.76e-28 (1.28e-25) |
0.303 (1.00) |
3.56e-29 (2.59e-26) |
| TP53 | 282 (30%) | 661 |
0.128 (1.00) |
0.00533 (1.00) |
0.19 (1.00) |
0.0169 (1.00) |
0.153 (1.00) |
0.0444 (1.00) |
0.0645 (1.00) |
3.9e-12 (2.82e-09) |
0.0606 (1.00) |
0.887 (1.00) |
| MLL3 | 66 (7%) | 877 |
0.157 (1.00) |
3.16e-05 (0.0225) |
0.704 (1.00) |
0.633 (1.00) |
0.0924 (1.00) |
0.538 (1.00) |
1 (1.00) |
0.86 (1.00) |
0.577 (1.00) |
0.789 (1.00) |
| FAM86B1 | 8 (1%) | 935 |
0.696 (1.00) |
0.0828 (1.00) |
0.894 (1.00) |
0.908 (1.00) |
0.824 (1.00) |
0.338 (1.00) |
1 (1.00) |
0.915 (1.00) |
0.45 (1.00) |
2.1e-07 (0.000152) |
| CASP8 | 10 (1%) | 933 |
0.838 (1.00) |
0.586 (1.00) |
0.785 (1.00) |
0.929 (1.00) |
0.354 (1.00) |
1 (1.00) |
1 (1.00) |
0.616 (1.00) |
1 (1.00) |
1.43e-06 (0.00103) |
| ASXL2 | 16 (2%) | 927 |
0.0063 (1.00) |
0.255 (1.00) |
0.809 (1.00) |
0.964 (1.00) |
0.136 (1.00) |
0.781 (1.00) |
1 (1.00) |
0.888 (1.00) |
1 (1.00) |
0.000195 (0.138) |
| GPRIN2 | 10 (1%) | 933 |
0.964 (1.00) |
0.357 (1.00) |
0.885 (1.00) |
0.929 (1.00) |
0.354 (1.00) |
0.68 (1.00) |
1 (1.00) |
0.407 (1.00) |
0.488 (1.00) |
1.73e-14 (1.25e-11) |
| TRPM5 | 11 (1%) | 932 |
0.591 (1.00) |
0.734 (1.00) |
0.426 (1.00) |
0.743 (1.00) |
0.709 (1.00) |
0.694 (1.00) |
0.00426 (1.00) |
0.0118 (1.00) |
0.192 (1.00) |
4.55e-06 (0.00325) |
| PRICKLE3 | 11 (1%) | 932 |
0.909 (1.00) |
0.293 (1.00) |
0.0622 (1.00) |
0.0212 (1.00) |
0.952 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.847 (1.00) |
0.192 (1.00) |
0.000181 (0.129) |
| WDR52 | 16 (2%) | 927 |
0.348 (1.00) |
0.383 (1.00) |
0.677 (1.00) |
0.617 (1.00) |
0.189 (1.00) |
0.434 (1.00) |
0.143 (1.00) |
0.758 (1.00) |
1 (1.00) |
8.56e-08 (6.19e-05) |
| ERBB3 | 18 (2%) | 925 |
1.72e-05 (0.0123) |
0.148 (1.00) |
0.433 (1.00) |
0.0651 (1.00) |
0.462 (1.00) |
1 (1.00) |
1 (1.00) |
0.859 (1.00) |
0.00287 (1.00) |
0.724 (1.00) |
| PTHLH | 7 (1%) | 936 |
0.5 (1.00) |
0.244 (1.00) |
0.833 (1.00) |
1 (1.00) |
0.129 (1.00) |
1 (1.00) |
1 (1.00) |
0.992 (1.00) |
0.68 (1.00) |
3.34e-41 (2.43e-38) |
| HLA-DRB5 | 6 (1%) | 937 |
0.548 (1.00) |
0.236 (1.00) |
0.977 (1.00) |
0.672 (1.00) |
0.467 (1.00) |
1 (1.00) |
1 (1.00) |
0.944 (1.00) |
1 (1.00) |
3.68e-06 (0.00264) |
| GYG2 | 8 (1%) | 935 |
0.59 (1.00) |
0.457 (1.00) |
0.434 (1.00) |
0.834 (1.00) |
0.788 (1.00) |
0.66 (1.00) |
1 (1.00) |
0.954 (1.00) |
0.24 (1.00) |
3.98e-06 (0.00285) |
| HRNR | 31 (3%) | 912 |
0.149 (1.00) |
0.285 (1.00) |
0.352 (1.00) |
0.125 (1.00) |
0.127 (1.00) |
0.756 (1.00) |
1 (1.00) |
0.929 (1.00) |
0.112 (1.00) |
1.09e-05 (0.00778) |
| MUC5B | 32 (3%) | 911 |
0.825 (1.00) |
0.787 (1.00) |
0.067 (1.00) |
0.55 (1.00) |
0.788 (1.00) |
0.405 (1.00) |
1 (1.00) |
3.9e-06 (0.0028) |
1 (1.00) |
0.94 (1.00) |
| XBP1 | 4 (0%) | 939 |
1.92e-05 (0.0137) |
0.0265 (1.00) |
0.986 (1.00) |
0.794 (1.00) |
0.381 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.329 (1.00) |
|
| PIK3CA | 302 (32%) | 641 |
0.389 (1.00) |
0.028 (1.00) |
0.77 (1.00) |
0.804 (1.00) |
0.878 (1.00) |
0.575 (1.00) |
1 (1.00) |
0.00264 (1.00) |
0.939 (1.00) |
0.572 (1.00) |
| CBFB | 23 (2%) | 920 |
0.884 (1.00) |
0.973 (1.00) |
0.782 (1.00) |
0.183 (1.00) |
0.0786 (1.00) |
0.392 (1.00) |
0.2 (1.00) |
0.944 (1.00) |
1 (1.00) |
0.444 (1.00) |
| GATA3 | 76 (8%) | 867 |
0.181 (1.00) |
0.00132 (0.93) |
0.24 (1.00) |
0.0305 (1.00) |
0.718 (1.00) |
0.0682 (1.00) |
0.532 (1.00) |
0.0793 (1.00) |
0.51 (1.00) |
0.00802 (1.00) |
| FOXA1 | 22 (2%) | 921 |
0.000486 (0.344) |
0.00054 (0.382) |
0.922 (1.00) |
0.317 (1.00) |
0.917 (1.00) |
0.539 (1.00) |
1 (1.00) |
0.00873 (1.00) |
0.152 (1.00) |
0.444 (1.00) |
| SF3B1 | 16 (2%) | 927 |
0.308 (1.00) |
0.37 (1.00) |
0.422 (1.00) |
0.638 (1.00) |
0.835 (1.00) |
0.434 (1.00) |
1 (1.00) |
0.937 (1.00) |
1 (1.00) |
0.649 (1.00) |
| RUNX1 | 29 (3%) | 914 |
0.855 (1.00) |
0.718 (1.00) |
0.571 (1.00) |
0.428 (1.00) |
0.365 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.00152 (1.00) |
0.68 (1.00) |
0.176 (1.00) |
| PTEN | 34 (4%) | 909 |
0.981 (1.00) |
0.0732 (1.00) |
0.0579 (1.00) |
0.262 (1.00) |
0.525 (1.00) |
0.0449 (1.00) |
1 (1.00) |
0.12 (1.00) |
0.338 (1.00) |
0.435 (1.00) |
| TBX3 | 26 (3%) | 917 |
0.342 (1.00) |
0.0279 (1.00) |
0.607 (1.00) |
0.855 (1.00) |
0.596 (1.00) |
0.85 (1.00) |
1 (1.00) |
0.277 (1.00) |
1 (1.00) |
0.5 (1.00) |
| MAP2K4 | 32 (3%) | 911 |
0.724 (1.00) |
0.411 (1.00) |
0.949 (1.00) |
0.303 (1.00) |
0.483 (1.00) |
0.586 (1.00) |
1 (1.00) |
0.22 (1.00) |
0.695 (1.00) |
0.548 (1.00) |
| MAP3K1 | 68 (7%) | 875 |
0.956 (1.00) |
0.0047 (1.00) |
0.713 (1.00) |
0.461 (1.00) |
0.919 (1.00) |
0.369 (1.00) |
1 (1.00) |
0.765 (1.00) |
0.782 (1.00) |
0.0171 (1.00) |
| NCOR1 | 41 (4%) | 902 |
0.666 (1.00) |
0.342 (1.00) |
0.938 (1.00) |
0.567 (1.00) |
0.942 (1.00) |
0.309 (1.00) |
1 (1.00) |
0.663 (1.00) |
0.861 (1.00) |
0.453 (1.00) |
| RB1 | 19 (2%) | 924 |
0.569 (1.00) |
0.165 (1.00) |
0.465 (1.00) |
0.35 (1.00) |
0.757 (1.00) |
0.402 (1.00) |
0.168 (1.00) |
0.886 (1.00) |
0.306 (1.00) |
0.468 (1.00) |
| CTCF | 17 (2%) | 926 |
0.12 (1.00) |
0.831 (1.00) |
0.537 (1.00) |
0.186 (1.00) |
0.619 (1.00) |
1 (1.00) |
1 (1.00) |
0.488 (1.00) |
0.421 (1.00) |
0.0327 (1.00) |
| THEM5 | 11 (1%) | 932 |
0.537 (1.00) |
0.208 (1.00) |
0.651 (1.00) |
0.0365 (1.00) |
0.386 (1.00) |
1 (1.00) |
1 (1.00) |
0.00801 (1.00) |
0.739 (1.00) |
0.364 (1.00) |
| GPS2 | 10 (1%) | 933 |
0.467 (1.00) |
0.141 (1.00) |
0.998 (1.00) |
0.0806 (1.00) |
0.29 (1.00) |
1 (1.00) |
1 (1.00) |
0.856 (1.00) |
0.488 (1.00) |
0.519 (1.00) |
| RPGR | 17 (2%) | 926 |
0.469 (1.00) |
0.29 (1.00) |
0.903 (1.00) |
0.795 (1.00) |
0.205 (1.00) |
0.586 (1.00) |
1 (1.00) |
0.984 (1.00) |
0.79 (1.00) |
0.000628 (0.442) |
| DNAH12 | 17 (2%) | 926 |
0.676 (1.00) |
0.512 (1.00) |
0.916 (1.00) |
0.718 (1.00) |
0.176 (1.00) |
1 (1.00) |
1 (1.00) |
0.644 (1.00) |
0.593 (1.00) |
0.284 (1.00) |
| CDKN1B | 9 (1%) | 934 |
0.992 (1.00) |
0.92 (1.00) |
0.186 (1.00) |
0.0345 (1.00) |
0.0138 (1.00) |
0.0674 (1.00) |
1 (1.00) |
0.982 (1.00) |
1 (1.00) |
0.114 (1.00) |
| ZFP36L1 | 9 (1%) | 934 |
0.37 (1.00) |
0.372 (1.00) |
0.953 (1.00) |
0.788 (1.00) |
0.894 (1.00) |
1 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.46 (1.00) |
0.0535 (1.00) |
| ASB10 | 8 (1%) | 935 |
0.0785 (1.00) |
0.517 (1.00) |
0.928 (1.00) |
0.764 (1.00) |
0.175 (1.00) |
1 (1.00) |
1 (1.00) |
0.168 (1.00) |
1 (1.00) |
0.382 (1.00) |
| HIST1H3B | 10 (1%) | 933 |
0.896 (1.00) |
0.0519 (1.00) |
0.536 (1.00) |
0.561 (1.00) |
0.678 (1.00) |
1 (1.00) |
1 (1.00) |
0.956 (1.00) |
0.488 (1.00) |
0.467 (1.00) |
| PIK3R1 | 15 (2%) | 928 |
0.00941 (1.00) |
0.29 (1.00) |
0.438 (1.00) |
1 (1.00) |
0.376 (1.00) |
0.304 (1.00) |
1 (1.00) |
0.904 (1.00) |
1 (1.00) |
0.0079 (1.00) |
| MYH9 | 19 (2%) | 924 |
0.611 (1.00) |
0.407 (1.00) |
0.725 (1.00) |
0.834 (1.00) |
0.303 (1.00) |
0.629 (1.00) |
1 (1.00) |
0.104 (1.00) |
0.0783 (1.00) |
0.000588 (0.415) |
| COL6A5 | 23 (2%) | 920 |
0.34 (1.00) |
0.384 (1.00) |
0.997 (1.00) |
0.906 (1.00) |
0.973 (1.00) |
1 (1.00) |
1 (1.00) |
0.222 (1.00) |
0.496 (1.00) |
0.688 (1.00) |
| TBL1XR1 | 10 (1%) | 933 |
0.878 (1.00) |
0.211 (1.00) |
0.378 (1.00) |
0.089 (1.00) |
0.029 (1.00) |
0.131 (1.00) |
1 (1.00) |
0.859 (1.00) |
1 (1.00) |
0.31 (1.00) |
| ARID1A | 27 (3%) | 916 |
0.522 (1.00) |
0.777 (1.00) |
0.584 (1.00) |
0.357 (1.00) |
0.261 (1.00) |
1 (1.00) |
1 (1.00) |
0.71 (1.00) |
0.668 (1.00) |
0.941 (1.00) |
| AQP12A | 6 (1%) | 937 |
0.526 (1.00) |
0.396 (1.00) |
0.999 (1.00) |
0.672 (1.00) |
0.223 (1.00) |
0.572 (1.00) |
1 (1.00) |
0.892 (1.00) |
0.365 (1.00) |
0.927 (1.00) |
| EPDR1 | 5 (1%) | 938 |
0.532 (1.00) |
0.281 (1.00) |
0.705 (1.00) |
0.377 (1.00) |
0.245 (1.00) |
1 (1.00) |
1 (1.00) |
0.883 (1.00) |
1 (1.00) |
0.761 (1.00) |
| ERBB2 | 21 (2%) | 922 |
0.195 (1.00) |
0.11 (1.00) |
0.782 (1.00) |
0.191 (1.00) |
0.0805 (1.00) |
1 (1.00) |
0.184 (1.00) |
0.665 (1.00) |
0.466 (1.00) |
0.526 (1.00) |
| MYB | 12 (1%) | 931 |
0.175 (1.00) |
0.129 (1.00) |
0.781 (1.00) |
0.413 (1.00) |
0.965 (1.00) |
0.502 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.345 (1.00) |
0.0113 (1.00) |
| TMEM151B | 5 (1%) | 938 |
0.576 (1.00) |
0.49 (1.00) |
0.61 (1.00) |
0.314 (1.00) |
0.874 (1.00) |
1 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.329 (1.00) |
0.00498 (1.00) |
| GALNTL6 | 5 (1%) | 938 |
0.495 (1.00) |
0.183 (1.00) |
0.999 (1.00) |
1 (1.00) |
0.606 (1.00) |
1 (1.00) |
1 (1.00) |
0.941 (1.00) |
0.15 (1.00) |
0.249 (1.00) |
| AKD1 | 18 (2%) | 925 |
0.701 (1.00) |
0.154 (1.00) |
0.741 (1.00) |
0.796 (1.00) |
0.602 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.742 (1.00) |
0.303 (1.00) |
0.151 (1.00) |
| AARS | 8 (1%) | 935 |
0.573 (1.00) |
0.184 (1.00) |
0.993 (1.00) |
0.162 (1.00) |
0.633 (1.00) |
0.66 (1.00) |
1 (1.00) |
0.984 (1.00) |
0.698 (1.00) |
0.535 (1.00) |
| HLA-C | 9 (1%) | 934 |
0.602 (1.00) |
0.16 (1.00) |
0.958 (1.00) |
0.226 (1.00) |
0.894 (1.00) |
0.389 (1.00) |
1 (1.00) |
0.982 (1.00) |
0.724 (1.00) |
0.254 (1.00) |
| ANKRD12 | 17 (2%) | 926 |
0.291 (1.00) |
0.171 (1.00) |
0.961 (1.00) |
0.589 (1.00) |
0.637 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.81 (1.00) |
0.421 (1.00) |
0.000361 (0.256) |
| FBXW7 | 14 (1%) | 929 |
0.743 (1.00) |
0.613 (1.00) |
0.775 (1.00) |
0.27 (1.00) |
0.633 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.845 (1.00) |
1 (1.00) |
0.00419 (1.00) |
| CDC42EP1 | 4 (0%) | 939 |
0.395 (1.00) |
0.568 (1.00) |
0.00455 (1.00) |
1 (1.00) |
0.438 (1.00) |
1 (1.00) |
1 (1.00) |
0.966 (1.00) |
1 (1.00) |
0.308 (1.00) |
| FHOD3 | 13 (1%) | 930 |
0.15 (1.00) |
0.0747 (1.00) |
0.997 (1.00) |
0.495 (1.00) |
0.78 (1.00) |
0.728 (1.00) |
0.118 (1.00) |
0.807 (1.00) |
0.539 (1.00) |
0.0524 (1.00) |
| SHISA4 | 5 (1%) | 938 |
0.463 (1.00) |
0.886 (1.00) |
0.993 (1.00) |
0.507 (1.00) |
0.521 (1.00) |
0.507 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.631 (1.00) |
0.15 (1.00) |
| KCNN3 | 9 (1%) | 934 |
0.149 (1.00) |
0.564 (1.00) |
0.816 (1.00) |
0.419 (1.00) |
0.513 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.584 (1.00) |
1 (1.00) |
0.0675 (1.00) |
| FGFR2 | 10 (1%) | 933 |
0.154 (1.00) |
0.376 (1.00) |
0.564 (1.00) |
0.0145 (1.00) |
0.697 (1.00) |
0.437 (1.00) |
0.0919 (1.00) |
0.838 (1.00) |
1 (1.00) |
0.00181 (1.00) |
| ICOSLG | 6 (1%) | 937 |
0.468 (1.00) |
0.105 (1.00) |
0.631 (1.00) |
0.881 (1.00) |
0.738 (1.00) |
0.572 (1.00) |
1 (1.00) |
0.944 (1.00) |
1 (1.00) |
0.737 (1.00) |
| PPEF1 | 11 (1%) | 932 |
0.0364 (1.00) |
0.477 (1.00) |
0.997 (1.00) |
1 (1.00) |
0.37 (1.00) |
1 (1.00) |
1 (1.00) |
0.934 (1.00) |
0.525 (1.00) |
0.0761 (1.00) |
| MAP4K1 | 9 (1%) | 934 |
0.467 (1.00) |
0.691 (1.00) |
0.867 (1.00) |
0.515 (1.00) |
0.261 (1.00) |
1 (1.00) |
1 (1.00) |
0.973 (1.00) |
1 (1.00) |
0.462 (1.00) |
| ZNF41 | 11 (1%) | 932 |
0.488 (1.00) |
0.854 (1.00) |
0.931 (1.00) |
0.669 (1.00) |
0.55 (1.00) |
0.484 (1.00) |
1 (1.00) |
0.978 (1.00) |
0.739 (1.00) |
0.389 (1.00) |
| FBXO17 | 5 (1%) | 938 |
0.00226 (1.00) |
0.642 (1.00) |
0.981 (1.00) |
0.507 (1.00) |
0.164 (1.00) |
0.183 (1.00) |
1 (1.00) |
0.997 (1.00) |
1 (1.00) |
0.613 (1.00) |
| STAG2 | 13 (1%) | 930 |
0.0138 (1.00) |
0.0403 (1.00) |
0.83 (1.00) |
0.952 (1.00) |
0.886 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.598 (1.00) |
1 (1.00) |
0.731 (1.00) |
| CEP57 | 4 (0%) | 939 |
0.242 (1.00) |
0.212 (1.00) |
0.949 (1.00) |
0.524 (1.00) |
0.139 (1.00) |
0.432 (1.00) |
1 (1.00) |
0.966 (1.00) |
0.584 (1.00) |
0.878 (1.00) |
| SPRR2B | 3 (0%) | 940 |
0.719 (1.00) |
0.366 (1.00) |
0.998 (1.00) |
0.732 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.984 (1.00) |
1 (1.00) |
0.0112 (1.00) |
| ZFP36L2 | 7 (1%) | 936 |
0.431 (1.00) |
0.943 (1.00) |
0.984 (1.00) |
0.901 (1.00) |
0.927 (1.00) |
1 (1.00) |
1 (1.00) |
0.992 (1.00) |
0.113 (1.00) |
0.00654 (1.00) |
| ZBTB7C | 5 (1%) | 938 |
0.542 (1.00) |
0.696 (1.00) |
0.958 (1.00) |
1 (1.00) |
0.168 (1.00) |
1 (1.00) |
1 (1.00) |
0.462 (1.00) |
0.329 (1.00) |
0.951 (1.00) |
| FXYD5 | 4 (0%) | 939 |
0.772 (1.00) |
0.923 (1.00) |
0.875 (1.00) |
0.151 (1.00) |
0.842 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
1 (1.00) |
0.0112 (1.00) |
| ATXN2 | 15 (2%) | 928 |
0.599 (1.00) |
0.118 (1.00) |
0.964 (1.00) |
0.575 (1.00) |
0.686 (1.00) |
1 (1.00) |
1 (1.00) |
0.983 (1.00) |
0.573 (1.00) |
0.549 (1.00) |
| CCL13 | 4 (0%) | 939 |
0.342 (1.00) |
0.159 (1.00) |
0.979 (1.00) |
0.651 (1.00) |
0.842 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.584 (1.00) |
0.0112 (1.00) |
P value = 3.9e-12 (Chi-square test), Q value = 2.8e-09
Table S1. Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 699 | 153 | 5 | 27 | 14 | 43 |
| TP53 MUTATED | 1 | 249 | 8 | 3 | 5 | 1 | 14 |
| TP53 WILD-TYPE | 0 | 450 | 145 | 2 | 22 | 13 | 29 |
Figure S1. Get High-res Image Gene #6: 'TP53 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.44e-06 (Fisher's exact test), Q value = 0.001
Table S2. Gene #7: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
| nPatients | T1 | T2 | T3 | T4 |
|---|---|---|---|---|
| ALL | 251 | 544 | 111 | 35 |
| CDH1 MUTATED | 15 | 50 | 29 | 2 |
| CDH1 WILD-TYPE | 236 | 494 | 82 | 33 |
Figure S2. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY.T.STAGE'
P value = 1.24e-69 (Chi-square test), Q value = 9e-67
Table S3. Gene #7: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 699 | 153 | 5 | 27 | 14 | 43 |
| CDH1 MUTATED | 0 | 14 | 78 | 1 | 3 | 0 | 0 |
| CDH1 WILD-TYPE | 1 | 685 | 75 | 4 | 24 | 14 | 43 |
Figure S3. Get High-res Image Gene #7: 'CDH1 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.16e-05 (t-test), Q value = 0.022
Table S4. Gene #12: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 940 | 58.7 (13.2) |
| MLL3 MUTATED | 66 | 65.5 (13.0) |
| MLL3 WILD-TYPE | 874 | 58.1 (13.0) |
Figure S4. Get High-res Image Gene #12: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'AGE'
P value = 2.1e-07 (t-test), Q value = 0.00015
Table S5. Gene #25: 'FAM86B1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| FAM86B1 MUTATED | 8 | 0.5 (0.5) |
| FAM86B1 WILD-TYPE | 779 | 2.4 (4.6) |
Figure S5. Get High-res Image Gene #25: 'FAM86B1 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 1.43e-06 (t-test), Q value = 0.001
Table S6. Gene #28: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| CASP8 MUTATED | 9 | 0.3 (0.7) |
| CASP8 WILD-TYPE | 778 | 2.4 (4.6) |
Figure S6. Get High-res Image Gene #28: 'CASP8 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 0.000195 (t-test), Q value = 0.14
Table S7. Gene #31: 'ASXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| ASXL2 MUTATED | 11 | 0.7 (1.0) |
| ASXL2 WILD-TYPE | 776 | 2.4 (4.6) |
Figure S7. Get High-res Image Gene #31: 'ASXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 1.73e-14 (t-test), Q value = 1.3e-11
Table S8. Gene #42: 'GPRIN2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| GPRIN2 MUTATED | 10 | 0.2 (0.4) |
| GPRIN2 WILD-TYPE | 777 | 2.4 (4.6) |
Figure S8. Get High-res Image Gene #42: 'GPRIN2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 4.55e-06 (t-test), Q value = 0.0033
Table S9. Gene #43: 'TRPM5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| TRPM5 MUTATED | 9 | 0.4 (0.7) |
| TRPM5 WILD-TYPE | 778 | 2.4 (4.6) |
Figure S9. Get High-res Image Gene #43: 'TRPM5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 0.000181 (t-test), Q value = 0.13
Table S10. Gene #46: 'PRICKLE3 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| PRICKLE3 MUTATED | 7 | 0.4 (0.8) |
| PRICKLE3 WILD-TYPE | 780 | 2.4 (4.6) |
Figure S10. Get High-res Image Gene #46: 'PRICKLE3 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 8.56e-08 (t-test), Q value = 6.2e-05
Table S11. Gene #47: 'WDR52 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| WDR52 MUTATED | 12 | 0.3 (0.8) |
| WDR52 WILD-TYPE | 775 | 2.4 (4.6) |
Figure S11. Get High-res Image Gene #47: 'WDR52 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 1.72e-05 (logrank test), Q value = 0.012
Table S12. Gene #49: 'ERBB3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 906 | 108 | 0.0 - 234.2 (21.6) |
| ERBB3 MUTATED | 15 | 7 | 0.1 - 97.5 (18.8) |
| ERBB3 WILD-TYPE | 891 | 101 | 0.0 - 234.2 (21.6) |
Figure S12. Get High-res Image Gene #49: 'ERBB3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
P value = 3.34e-41 (t-test), Q value = 2.4e-38
Table S13. Gene #51: 'PTHLH MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| PTHLH MUTATED | 4 | 0.0 (0.0) |
| PTHLH WILD-TYPE | 783 | 2.4 (4.6) |
Figure S13. Get High-res Image Gene #51: 'PTHLH MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 3.68e-06 (t-test), Q value = 0.0026
Table S14. Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| HLA-DRB5 MUTATED | 5 | 0.2 (0.4) |
| HLA-DRB5 WILD-TYPE | 782 | 2.4 (4.6) |
Figure S14. Get High-res Image Gene #55: 'HLA-DRB5 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 3.98e-06 (t-test), Q value = 0.0029
Table S15. Gene #57: 'GYG2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| GYG2 MUTATED | 6 | 0.3 (0.5) |
| GYG2 WILD-TYPE | 781 | 2.4 (4.6) |
Figure S15. Get High-res Image Gene #57: 'GYG2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 1.09e-05 (t-test), Q value = 0.0078
Table S16. Gene #62: 'HRNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| HRNR MUTATED | 29 | 1.0 (1.2) |
| HRNR WILD-TYPE | 758 | 2.4 (4.7) |
Figure S16. Get High-res Image Gene #62: 'HRNR MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 1.76e-28 (Chi-square test), Q value = 1.3e-25
Table S17. Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 699 | 153 | 5 | 27 | 14 | 43 |
| DMXL2 MUTATED | 1 | 9 | 3 | 3 | 1 | 0 | 1 |
| DMXL2 WILD-TYPE | 0 | 690 | 150 | 2 | 26 | 14 | 42 |
Figure S17. Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 3.56e-29 (t-test), Q value = 2.6e-26
Table S18. Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
| nPatients | Mean (Std.Dev) | |
|---|---|---|
| ALL | 787 | 2.3 (4.6) |
| DMXL2 MUTATED | 13 | 0.1 (0.3) |
| DMXL2 WILD-TYPE | 774 | 2.4 (4.6) |
Figure S18. Get High-res Image Gene #67: 'DMXL2 MUTATION STATUS' versus Clinical Feature #10: 'NUMBER.OF.LYMPH.NODES'
P value = 3.9e-06 (Chi-square test), Q value = 0.0028
Table S19. Gene #69: 'MUC5B MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
| nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
|---|---|---|---|---|---|---|---|
| ALL | 1 | 699 | 153 | 5 | 27 | 14 | 43 |
| MUC5B MUTATED | 1 | 23 | 5 | 0 | 1 | 2 | 0 |
| MUC5B WILD-TYPE | 0 | 676 | 148 | 5 | 26 | 12 | 43 |
Figure S19. Get High-res Image Gene #69: 'MUC5B MUTATION STATUS' versus Clinical Feature #8: 'HISTOLOGICAL.TYPE'
P value = 1.92e-05 (logrank test), Q value = 0.014
Table S20. Gene #70: 'XBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
| nPatients | nDeath | Duration Range (Median), Month | |
|---|---|---|---|
| ALL | 906 | 108 | 0.0 - 234.2 (21.6) |
| XBP1 MUTATED | 4 | 2 | 0.7 - 51.2 (7.8) |
| XBP1 WILD-TYPE | 902 | 106 | 0.0 - 234.2 (21.6) |
Figure S20. Get High-res Image Gene #70: 'XBP1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
-
Mutation data file = transformed.cor.cli.txt
-
Clinical data file = BRCA-TP.merged_data.txt
-
Number of patients = 943
-
Number of significantly mutated genes = 73
-
Number of selected clinical features = 10
-
Exclude genes that fewer than K tumors have mutations, K = 3
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the clinical values between tumors with and without gene mutations using 't.test' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.