This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 89 genes and 10 clinical features across 771 patients, 13 significant findings detected with Q value < 0.25.
-
ZNF384 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
GATA3 mutation correlated to 'AGE'.
-
TP53 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
CDH1 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
MAP3K1 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
RB1 mutation correlated to 'NEOPLASM.DISEASESTAGE'.
-
CASP8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
CTU2 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
HLA-A mutation correlated to 'HISTOLOGICAL.TYPE'.
-
ODF1 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
ASXL2 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
ATP13A4 mutation correlated to 'NEOPLASM.DISEASESTAGE'.
-
MED15 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
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 | |
ZNF384 | 14 (2%) | 757 |
0.337 (1.00) |
0.0127 (1.00) |
0.439 (1.00) |
0.26 (1.00) |
0.428 (1.00) |
0.453 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.767 (1.00) |
1.16e-05 (0.0102) |
GATA3 | 81 (11%) | 690 |
0.612 (1.00) |
0.000217 (0.19) |
0.229 (1.00) |
0.00817 (1.00) |
0.664 (1.00) |
0.0979 (1.00) |
0.59 (1.00) |
0.145 (1.00) |
0.151 (1.00) |
0.598 (1.00) |
TP53 | 257 (33%) | 514 |
0.529 (1.00) |
0.0384 (1.00) |
0.655 (1.00) |
0.0647 (1.00) |
0.0687 (1.00) |
0.0552 (1.00) |
0.0574 (1.00) |
9.97e-07 (0.000882) |
0.498 (1.00) |
0.414 (1.00) |
CDH1 | 55 (7%) | 716 |
0.554 (1.00) |
0.0861 (1.00) |
0.148 (1.00) |
0.000345 (0.302) |
0.00513 (1.00) |
0.799 (1.00) |
1 (1.00) |
4.43e-69 (3.93e-66) |
1 (1.00) |
0.129 (1.00) |
MAP3K1 | 57 (7%) | 714 |
0.707 (1.00) |
0.00183 (1.00) |
0.652 (1.00) |
0.112 (1.00) |
0.976 (1.00) |
0.565 (1.00) |
1 (1.00) |
0.634 (1.00) |
1 (1.00) |
7.24e-07 (0.000641) |
RB1 | 14 (2%) | 757 |
0.885 (1.00) |
0.12 (1.00) |
5.48e-05 (0.0483) |
0.521 (1.00) |
0.197 (1.00) |
0.719 (1.00) |
0.137 (1.00) |
0.921 (1.00) |
0.371 (1.00) |
0.459 (1.00) |
CASP8 | 10 (1%) | 761 |
0.793 (1.00) |
0.581 (1.00) |
0.724 (1.00) |
0.93 (1.00) |
0.313 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.732 (1.00) |
0.297 (1.00) |
5.57e-05 (0.0489) |
CTU2 | 5 (1%) | 766 |
0.542 (1.00) |
0.569 (1.00) |
0.187 (1.00) |
0.257 (1.00) |
0.594 (1.00) |
1 (1.00) |
1 (1.00) |
0.000116 (0.102) |
0.329 (1.00) |
0.058 (1.00) |
HLA-A | 4 (1%) | 767 |
0.215 (1.00) |
0.437 (1.00) |
0.789 (1.00) |
1 (1.00) |
0.366 (1.00) |
1 (1.00) |
1 (1.00) |
9.52e-06 (0.00841) |
0.318 (1.00) |
0.585 (1.00) |
ODF1 | 5 (1%) | 766 |
0.0936 (1.00) |
0.569 (1.00) |
0.592 (1.00) |
0.106 (1.00) |
0.376 (1.00) |
0.0751 (1.00) |
1 (1.00) |
4.19e-05 (0.0369) |
0.625 (1.00) |
0.966 (1.00) |
ASXL2 | 8 (1%) | 763 |
0.968 (1.00) |
0.947 (1.00) |
0.976 (1.00) |
0.75 (1.00) |
0.417 (1.00) |
1 (1.00) |
1 (1.00) |
0.969 (1.00) |
0.694 (1.00) |
7.01e-05 (0.0616) |
ATP13A4 | 9 (1%) | 762 |
0.248 (1.00) |
0.545 (1.00) |
1.54e-06 (0.00136) |
0.851 (1.00) |
0.501 (1.00) |
1 (1.00) |
1 (1.00) |
0.863 (1.00) |
0.718 (1.00) |
0.0558 (1.00) |
MED15 | 7 (1%) | 764 |
0.38 (1.00) |
0.721 (1.00) |
0.26 (1.00) |
0.5 (1.00) |
0.844 (1.00) |
0.483 (1.00) |
0.0707 (1.00) |
0.916 (1.00) |
1 (1.00) |
7.01e-05 (0.0616) |
PTEN | 29 (4%) | 742 |
0.578 (1.00) |
0.458 (1.00) |
0.00561 (1.00) |
0.421 (1.00) |
0.278 (1.00) |
0.0618 (1.00) |
1 (1.00) |
0.523 (1.00) |
0.834 (1.00) |
0.221 (1.00) |
MLL3 | 61 (8%) | 710 |
0.455 (1.00) |
0.00965 (1.00) |
0.923 (1.00) |
0.684 (1.00) |
0.222 (1.00) |
0.518 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.238 (1.00) |
0.62 (1.00) |
NUDT11 | 8 (1%) | 763 |
0.615 (1.00) |
0.575 (1.00) |
0.998 (1.00) |
0.416 (1.00) |
0.868 (1.00) |
0.0408 (1.00) |
1 (1.00) |
0.75 (1.00) |
1 (1.00) |
0.513 (1.00) |
GIGYF2 | 13 (2%) | 758 |
0.313 (1.00) |
0.649 (1.00) |
0.328 (1.00) |
0.00367 (1.00) |
0.0598 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.915 (1.00) |
0.0577 (1.00) |
0.968 (1.00) |
DCP1B | 5 (1%) | 766 |
0.538 (1.00) |
0.025 (1.00) |
0.991 (1.00) |
0.69 (1.00) |
0.776 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.937 (1.00) |
0.329 (1.00) |
0.44 (1.00) |
PIK3CA | 261 (34%) | 510 |
0.865 (1.00) |
0.0233 (1.00) |
0.523 (1.00) |
0.796 (1.00) |
0.951 (1.00) |
0.357 (1.00) |
1 (1.00) |
0.0299 (1.00) |
1 (1.00) |
0.339 (1.00) |
NCOA3 | 29 (4%) | 742 |
0.68 (1.00) |
0.875 (1.00) |
0.562 (1.00) |
0.335 (1.00) |
0.35 (1.00) |
0.142 (1.00) |
1 (1.00) |
0.473 (1.00) |
0.681 (1.00) |
0.177 (1.00) |
AOAH | 19 (2%) | 752 |
0.352 (1.00) |
0.425 (1.00) |
0.197 (1.00) |
0.0516 (1.00) |
0.907 (1.00) |
0.276 (1.00) |
1 (1.00) |
0.779 (1.00) |
0.119 (1.00) |
0.282 (1.00) |
RBMX | 13 (2%) | 758 |
0.709 (1.00) |
0.874 (1.00) |
0.971 (1.00) |
0.1 (1.00) |
0.401 (1.00) |
1 (1.00) |
1 (1.00) |
0.799 (1.00) |
0.534 (1.00) |
0.241 (1.00) |
RUNX1 | 25 (3%) | 746 |
0.445 (1.00) |
0.603 (1.00) |
0.0208 (1.00) |
0.122 (1.00) |
0.654 (1.00) |
1 (1.00) |
1 (1.00) |
0.0572 (1.00) |
0.498 (1.00) |
0.532 (1.00) |
PIK3R1 | 21 (3%) | 750 |
0.283 (1.00) |
0.686 (1.00) |
0.3 (1.00) |
0.0681 (1.00) |
0.411 (1.00) |
0.484 (1.00) |
1 (1.00) |
0.832 (1.00) |
1 (1.00) |
0.0805 (1.00) |
MEF2A | 14 (2%) | 757 |
0.246 (1.00) |
0.522 (1.00) |
0.42 (1.00) |
0.541 (1.00) |
0.37 (1.00) |
0.719 (1.00) |
1 (1.00) |
0.0202 (1.00) |
1 (1.00) |
0.0142 (1.00) |
NCOR2 | 29 (4%) | 742 |
0.793 (1.00) |
0.709 (1.00) |
0.957 (1.00) |
0.431 (1.00) |
0.605 (1.00) |
0.375 (1.00) |
1 (1.00) |
0.884 (1.00) |
1 (1.00) |
0.218 (1.00) |
AKT1 | 19 (2%) | 752 |
0.182 (1.00) |
0.133 (1.00) |
0.541 (1.00) |
0.321 (1.00) |
0.646 (1.00) |
0.597 (1.00) |
1 (1.00) |
0.523 (1.00) |
0.119 (1.00) |
0.902 (1.00) |
NR1H2 | 18 (2%) | 753 |
0.147 (1.00) |
0.714 (1.00) |
0.00131 (1.00) |
0.274 (1.00) |
0.589 (1.00) |
0.00281 (1.00) |
1 (1.00) |
0.823 (1.00) |
0.792 (1.00) |
0.954 (1.00) |
MAP3K4 | 18 (2%) | 753 |
0.553 (1.00) |
0.542 (1.00) |
0.786 (1.00) |
0.0598 (1.00) |
0.787 (1.00) |
0.00145 (1.00) |
1 (1.00) |
0.742 (1.00) |
0.792 (1.00) |
0.912 (1.00) |
TPRX1 | 7 (1%) | 764 |
0.615 (1.00) |
0.123 (1.00) |
0.795 (1.00) |
0.0165 (1.00) |
1 (1.00) |
0.483 (1.00) |
1 (1.00) |
0.00236 (1.00) |
0.41 (1.00) |
0.205 (1.00) |
ATN1 | 17 (2%) | 754 |
0.342 (1.00) |
0.959 (1.00) |
0.839 (1.00) |
0.466 (1.00) |
0.772 (1.00) |
0.104 (1.00) |
1 (1.00) |
0.733 (1.00) |
0.422 (1.00) |
0.609 (1.00) |
MAP2K4 | 32 (4%) | 739 |
0.174 (1.00) |
0.386 (1.00) |
0.974 (1.00) |
0.421 (1.00) |
0.461 (1.00) |
0.647 (1.00) |
1 (1.00) |
0.548 (1.00) |
0.548 (1.00) |
0.911 (1.00) |
CBFB | 16 (2%) | 755 |
0.929 (1.00) |
0.725 (1.00) |
0.907 (1.00) |
0.204 (1.00) |
0.118 (1.00) |
0.203 (1.00) |
1 (1.00) |
0.607 (1.00) |
1 (1.00) |
0.821 (1.00) |
CTCF | 18 (2%) | 753 |
0.101 (1.00) |
0.931 (1.00) |
0.379 (1.00) |
0.128 (1.00) |
0.655 (1.00) |
0.571 (1.00) |
1 (1.00) |
0.681 (1.00) |
0.792 (1.00) |
0.0498 (1.00) |
CCDC144NL | 8 (1%) | 763 |
0.0518 (1.00) |
0.0508 (1.00) |
0.45 (1.00) |
0.484 (1.00) |
0.135 (1.00) |
1 (1.00) |
1 (1.00) |
0.969 (1.00) |
0.452 (1.00) |
0.296 (1.00) |
AKD1 | 19 (2%) | 752 |
0.325 (1.00) |
0.469 (1.00) |
0.706 (1.00) |
0.182 (1.00) |
0.722 (1.00) |
0.276 (1.00) |
1 (1.00) |
0.0816 (1.00) |
0.441 (1.00) |
0.437 (1.00) |
FOXA1 | 15 (2%) | 756 |
0.0139 (1.00) |
0.00249 (1.00) |
0.0997 (1.00) |
0.00214 (1.00) |
0.877 (1.00) |
0.484 (1.00) |
1 (1.00) |
0.00959 (1.00) |
0.255 (1.00) |
0.833 (1.00) |
PHLDA1 | 9 (1%) | 762 |
0.0283 (1.00) |
0.752 (1.00) |
0.227 (1.00) |
0.356 (1.00) |
0.798 (1.00) |
0.198 (1.00) |
1 (1.00) |
0.686 (1.00) |
0.458 (1.00) |
0.000817 (0.713) |
VEZF1 | 8 (1%) | 763 |
0.492 (1.00) |
0.0879 (1.00) |
0.923 (1.00) |
0.912 (1.00) |
0.928 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.89 (1.00) |
0.232 (1.00) |
0.0425 (1.00) |
ZFP36L1 | 10 (1%) | 761 |
0.958 (1.00) |
0.0124 (1.00) |
0.662 (1.00) |
0.591 (1.00) |
0.531 (1.00) |
0.222 (1.00) |
1 (1.00) |
0.962 (1.00) |
0.0701 (1.00) |
0.41 (1.00) |
NCOR1 | 31 (4%) | 740 |
0.996 (1.00) |
0.934 (1.00) |
0.889 (1.00) |
0.817 (1.00) |
0.619 (1.00) |
0.349 (1.00) |
1 (1.00) |
0.269 (1.00) |
0.684 (1.00) |
0.462 (1.00) |
AQP7 | 9 (1%) | 762 |
0.00822 (1.00) |
0.481 (1.00) |
0.803 (1.00) |
0.543 (1.00) |
0.215 (1.00) |
1 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.127 (1.00) |
0.155 (1.00) |
TBX3 | 18 (2%) | 753 |
0.522 (1.00) |
0.0154 (1.00) |
0.691 (1.00) |
0.597 (1.00) |
0.884 (1.00) |
0.571 (1.00) |
1 (1.00) |
0.669 (1.00) |
0.792 (1.00) |
0.472 (1.00) |
DSPP | 26 (3%) | 745 |
0.597 (1.00) |
0.166 (1.00) |
0.839 (1.00) |
0.314 (1.00) |
0.654 (1.00) |
1 (1.00) |
1 (1.00) |
0.952 (1.00) |
1 (1.00) |
0.375 (1.00) |
RPGR | 16 (2%) | 755 |
0.991 (1.00) |
0.763 (1.00) |
0.907 (1.00) |
1 (1.00) |
0.695 (1.00) |
0.279 (1.00) |
1 (1.00) |
0.943 (1.00) |
0.408 (1.00) |
0.851 (1.00) |
BCL6B | 8 (1%) | 763 |
0.547 (1.00) |
0.749 (1.00) |
0.943 (1.00) |
0.385 (1.00) |
0.868 (1.00) |
0.0408 (1.00) |
1 (1.00) |
0.8 (1.00) |
0.114 (1.00) |
0.805 (1.00) |
TBL1XR1 | 9 (1%) | 762 |
0.54 (1.00) |
0.0223 (1.00) |
0.422 (1.00) |
0.0827 (1.00) |
0.138 (1.00) |
0.198 (1.00) |
1 (1.00) |
0.712 (1.00) |
0.718 (1.00) |
0.454 (1.00) |
CRIPAK | 13 (2%) | 758 |
0.959 (1.00) |
0.746 (1.00) |
0.953 (1.00) |
0.364 (1.00) |
0.092 (1.00) |
0.707 (1.00) |
0.128 (1.00) |
0.737 (1.00) |
1 (1.00) |
0.218 (1.00) |
MYB | 11 (1%) | 760 |
0.169 (1.00) |
0.18 (1.00) |
0.783 (1.00) |
0.24 (1.00) |
0.878 (1.00) |
1 (1.00) |
1 (1.00) |
0.24 (1.00) |
0.516 (1.00) |
0.0364 (1.00) |
GPS2 | 6 (1%) | 765 |
0.209 (1.00) |
0.966 (1.00) |
0.105 (1.00) |
0.284 (1.00) |
0.0566 (1.00) |
1 (1.00) |
1 (1.00) |
0.678 (1.00) |
0.678 (1.00) |
0.638 (1.00) |
PABPC3 | 8 (1%) | 763 |
0.339 (1.00) |
0.941 (1.00) |
0.909 (1.00) |
0.75 (1.00) |
0.868 (1.00) |
1 (1.00) |
0.0804 (1.00) |
0.679 (1.00) |
1 (1.00) |
0.164 (1.00) |
E2F4 | 4 (1%) | 767 |
0.366 (1.00) |
0.982 (1.00) |
0.136 (1.00) |
0.314 (1.00) |
1 (1.00) |
1 (1.00) |
0.47 (1.00) |
0.582 (1.00) |
||
DNAH12 | 12 (2%) | 759 |
0.983 (1.00) |
0.98 (1.00) |
0.882 (1.00) |
0.283 (1.00) |
0.775 (1.00) |
0.678 (1.00) |
1 (1.00) |
0.944 (1.00) |
0.335 (1.00) |
0.86 (1.00) |
CDKN1B | 7 (1%) | 764 |
0.855 (1.00) |
0.945 (1.00) |
0.0513 (1.00) |
0.0222 (1.00) |
0.00173 (1.00) |
0.0221 (1.00) |
1 (1.00) |
0.967 (1.00) |
1 (1.00) |
0.0478 (1.00) |
HNF1A | 9 (1%) | 762 |
0.397 (1.00) |
0.205 (1.00) |
0.982 (1.00) |
0.851 (1.00) |
0.407 (1.00) |
0.0654 (1.00) |
1 (1.00) |
0.00912 (1.00) |
0.28 (1.00) |
0.636 (1.00) |
CCDC66 | 14 (2%) | 757 |
0.0639 (1.00) |
0.667 (1.00) |
0.958 (1.00) |
0.176 (1.00) |
0.66 (1.00) |
1 (1.00) |
1 (1.00) |
0.513 (1.00) |
1 (1.00) |
0.606 (1.00) |
STXBP2 | 10 (1%) | 761 |
0.23 (1.00) |
0.0636 (1.00) |
0.875 (1.00) |
0.93 (1.00) |
0.822 (1.00) |
1 (1.00) |
1 (1.00) |
0.962 (1.00) |
1 (1.00) |
0.935 (1.00) |
HIST1H3B | 7 (1%) | 764 |
0.603 (1.00) |
0.285 (1.00) |
0.795 (1.00) |
0.39 (1.00) |
0.434 (1.00) |
1 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.104 (1.00) |
0.452 (1.00) |
TTN | 122 (16%) | 649 |
0.161 (1.00) |
0.00748 (1.00) |
0.0254 (1.00) |
0.0412 (1.00) |
0.745 (1.00) |
0.607 (1.00) |
0.369 (1.00) |
0.373 (1.00) |
0.913 (1.00) |
0.399 (1.00) |
SHROOM4 | 12 (2%) | 759 |
0.198 (1.00) |
0.481 (1.00) |
0.952 (1.00) |
0.269 (1.00) |
0.314 (1.00) |
0.387 (1.00) |
0.118 (1.00) |
0.833 (1.00) |
0.109 (1.00) |
0.786 (1.00) |
SLC25A5 | 3 (0%) | 768 |
0.521 (1.00) |
0.999 (1.00) |
0.388 (1.00) |
0.607 (1.00) |
0.245 (1.00) |
1 (1.00) |
0.13 (1.00) |
1 (1.00) |
0.932 (1.00) |
|
SELPLG | 7 (1%) | 764 |
0.582 (1.00) |
0.266 (1.00) |
0.804 (1.00) |
0.716 (1.00) |
0.844 (1.00) |
0.134 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.41 (1.00) |
0.000817 (0.713) |
KRTAP9-9 | 6 (1%) | 765 |
0.541 (1.00) |
0.408 (1.00) |
0.923 (1.00) |
0.565 (1.00) |
0.388 (1.00) |
0.431 (1.00) |
1 (1.00) |
0.382 (1.00) |
0.359 (1.00) |
0.293 (1.00) |
KRTAP4-5 | 4 (1%) | 767 |
0.572 (1.00) |
0.194 (1.00) |
0.906 (1.00) |
0.395 (1.00) |
0.143 (1.00) |
0.313 (1.00) |
1 (1.00) |
0.291 (1.00) |
0.318 (1.00) |
0.466 (1.00) |
SF3B1 | 14 (2%) | 757 |
0.232 (1.00) |
0.74 (1.00) |
0.238 (1.00) |
0.326 (1.00) |
0.866 (1.00) |
0.719 (1.00) |
1 (1.00) |
0.862 (1.00) |
0.554 (1.00) |
0.778 (1.00) |
FGFR2 | 7 (1%) | 764 |
0.00758 (1.00) |
0.751 (1.00) |
0.756 (1.00) |
0.122 (1.00) |
0.467 (1.00) |
0.134 (1.00) |
1 (1.00) |
0.654 (1.00) |
0.68 (1.00) |
0.0471 (1.00) |
MUC2 | 22 (3%) | 749 |
0.667 (1.00) |
0.52 (1.00) |
0.401 (1.00) |
0.563 (1.00) |
0.203 (1.00) |
0.332 (1.00) |
0.208 (1.00) |
0.976 (1.00) |
0.0905 (1.00) |
0.153 (1.00) |
MED12 | 20 (3%) | 751 |
0.583 (1.00) |
0.777 (1.00) |
0.681 (1.00) |
0.52 (1.00) |
0.485 (1.00) |
0.366 (1.00) |
1 (1.00) |
0.991 (1.00) |
0.217 (1.00) |
0.489 (1.00) |
USP36 | 13 (2%) | 758 |
0.601 (1.00) |
0.0796 (1.00) |
0.665 (1.00) |
0.485 (1.00) |
0.145 (1.00) |
0.136 (1.00) |
1 (1.00) |
0.933 (1.00) |
0.37 (1.00) |
0.634 (1.00) |
DENND4B | 8 (1%) | 763 |
0.494 (1.00) |
0.734 (1.00) |
0.926 (1.00) |
0.484 (1.00) |
0.868 (1.00) |
0.529 (1.00) |
1 (1.00) |
0.00386 (1.00) |
1 (1.00) |
0.806 (1.00) |
RAI1 | 7 (1%) | 764 |
0.566 (1.00) |
0.917 (1.00) |
0.388 (1.00) |
0.425 (1.00) |
0.844 (1.00) |
1 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.41 (1.00) |
0.0482 (1.00) |
AXL | 6 (1%) | 765 |
0.0255 (1.00) |
0.734 (1.00) |
0.615 (1.00) |
0.485 (1.00) |
0.102 (1.00) |
0.431 (1.00) |
1 (1.00) |
0.00431 (1.00) |
0.192 (1.00) |
0.447 (1.00) |
RPL18 | 4 (1%) | 767 |
0.714 (1.00) |
0.857 (1.00) |
0.755 (1.00) |
0.78 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.47 (1.00) |
0.318 (1.00) |
0.027 (1.00) |
KRT38 | 4 (1%) | 767 |
0.476 (1.00) |
0.242 (1.00) |
0.991 (1.00) |
0.395 (1.00) |
0.496 (1.00) |
1 (1.00) |
1 (1.00) |
0.974 (1.00) |
0.318 (1.00) |
0.0539 (1.00) |
TICAM1 | 5 (1%) | 766 |
0.542 (1.00) |
0.54 (1.00) |
0.0716 (1.00) |
0.69 (1.00) |
0.0175 (1.00) |
0.0751 (1.00) |
1 (1.00) |
0.958 (1.00) |
0.625 (1.00) |
0.724 (1.00) |
RBM5 | 12 (2%) | 759 |
0.252 (1.00) |
0.866 (1.00) |
0.98 (1.00) |
0.341 (1.00) |
0.231 (1.00) |
1 (1.00) |
1 (1.00) |
0.303 (1.00) |
1 (1.00) |
0.245 (1.00) |
ASPHD1 | 3 (0%) | 768 |
0.0394 (1.00) |
0.782 (1.00) |
0.966 (1.00) |
0.719 (1.00) |
0.772 (1.00) |
1 (1.00) |
1 (1.00) |
0.268 (1.00) |
0.563 (1.00) |
0.727 (1.00) |
PPEF1 | 8 (1%) | 763 |
0.783 (1.00) |
0.704 (1.00) |
0.979 (1.00) |
1 (1.00) |
0.372 (1.00) |
1 (1.00) |
1 (1.00) |
0.89 (1.00) |
1 (1.00) |
0.164 (1.00) |
MUC20 | 10 (1%) | 761 |
0.349 (1.00) |
0.169 (1.00) |
0.967 (1.00) |
0.494 (1.00) |
0.248 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.0839 (1.00) |
0.481 (1.00) |
0.533 (1.00) |
TMEM184A | 4 (1%) | 767 |
0.907 (1.00) |
0.981 (1.00) |
0.996 (1.00) |
0.78 (1.00) |
0.112 (1.00) |
1 (1.00) |
1 (1.00) |
0.974 (1.00) |
0.582 (1.00) |
0.632 (1.00) |
FAM171B | 8 (1%) | 763 |
0.865 (1.00) |
0.00375 (1.00) |
0.855 (1.00) |
0.75 (1.00) |
0.928 (1.00) |
0.529 (1.00) |
0.0804 (1.00) |
0.89 (1.00) |
0.694 (1.00) |
0.383 (1.00) |
PRRX1 | 6 (1%) | 765 |
0.439 (1.00) |
0.9 (1.00) |
0.99 (1.00) |
0.755 (1.00) |
0.425 (1.00) |
1 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.0569 (1.00) |
0.722 (1.00) |
MUC21 | 6 (1%) | 765 |
0.372 (1.00) |
0.462 (1.00) |
0.802 (1.00) |
0.36 (1.00) |
0.904 (1.00) |
1 (1.00) |
1 (1.00) |
0.939 (1.00) |
1 (1.00) |
0.00268 (1.00) |
HLA-B | 4 (1%) | 767 |
0.648 (1.00) |
0.744 (1.00) |
0.982 (1.00) |
0.26 (1.00) |
0.702 (1.00) |
1 (1.00) |
1 (1.00) |
0.291 (1.00) |
1 (1.00) |
0.799 (1.00) |
RBM23 | 6 (1%) | 765 |
0.915 (1.00) |
0.746 (1.00) |
0.778 (1.00) |
0.052 (1.00) |
0.464 (1.00) |
0.103 (1.00) |
1 (1.00) |
0.000389 (0.34) |
0.359 (1.00) |
0.794 (1.00) |
UBC | 8 (1%) | 763 |
0.201 (1.00) |
0.671 (1.00) |
0.94 (1.00) |
0.912 (1.00) |
0.816 (1.00) |
1 (1.00) |
1 (1.00) |
0.89 (1.00) |
1 (1.00) |
0.844 (1.00) |
SPRED3 | 4 (1%) | 767 |
0.768 (1.00) |
0.707 (1.00) |
0.972 (1.00) |
1 (1.00) |
0.421 (1.00) |
1 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.318 (1.00) |
0.694 (1.00) |
KCNN3 | 6 (1%) | 765 |
0.634 (1.00) |
0.744 (1.00) |
0.67 (1.00) |
0.485 (1.00) |
0.818 (1.00) |
0.431 (1.00) |
1 (1.00) |
0.244 (1.00) |
0.192 (1.00) |
0.019 (1.00) |
GNRH2 | 3 (0%) | 768 |
0.881 (1.00) |
0.178 (1.00) |
0.999 (1.00) |
1 (1.00) |
0.112 (1.00) |
0.245 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.563 (1.00) |
0.434 (1.00) |
P value = 1.16e-05 (t-test), Q value = 0.01
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 635 | 2.1 (4.0) |
ZNF384 MUTATED | 14 | 0.6 (0.9) |
ZNF384 WILD-TYPE | 621 | 2.2 (4.1) |
P value = 0.000217 (t-test), Q value = 0.19
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 771 | 58.0 (13.1) |
GATA3 MUTATED | 81 | 52.8 (13.0) |
GATA3 WILD-TYPE | 690 | 58.6 (13.0) |
P value = 9.97e-07 (Chi-square test), Q value = 0.00088
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 637 | 64 | 4 | 26 | 6 | 33 |
TP53 MUTATED | 235 | 3 | 3 | 5 | 0 | 10 |
TP53 WILD-TYPE | 402 | 61 | 1 | 21 | 6 | 23 |
P value = 4.43e-69 (Chi-square test), Q value = 3.9e-66
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 637 | 64 | 4 | 26 | 6 | 33 |
CDH1 MUTATED | 11 | 40 | 1 | 3 | 0 | 0 |
CDH1 WILD-TYPE | 626 | 24 | 3 | 23 | 6 | 33 |
P value = 7.24e-07 (t-test), Q value = 0.00064
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 635 | 2.1 (4.0) |
MAP3K1 MUTATED | 45 | 0.9 (1.3) |
MAP3K1 WILD-TYPE | 590 | 2.2 (4.1) |
P value = 5.48e-05 (Chi-square test), Q value = 0.048
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 65 | 57 | 6 | 2 | 268 | 167 | 117 | 23 | 33 | 15 | 1 | 16 |
RB1 MUTATED | 2 | 0 | 1 | 1 | 5 | 3 | 0 | 1 | 1 | 0 | 0 | 0 |
RB1 WILD-TYPE | 63 | 57 | 5 | 1 | 263 | 164 | 117 | 22 | 32 | 15 | 1 | 16 |
P value = 5.57e-05 (t-test), Q value = 0.049
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 635 | 2.1 (4.0) |
CASP8 MUTATED | 8 | 0.4 (0.7) |
CASP8 WILD-TYPE | 627 | 2.2 (4.0) |
P value = 0.000116 (Chi-square test), Q value = 0.1
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 637 | 64 | 4 | 26 | 6 | 33 |
CTU2 MUTATED | 3 | 1 | 0 | 0 | 1 | 0 |
CTU2 WILD-TYPE | 634 | 63 | 4 | 26 | 5 | 33 |
P value = 9.52e-06 (Chi-square test), Q value = 0.0084
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 637 | 64 | 4 | 26 | 6 | 33 |
HLA-A MUTATED | 3 | 0 | 0 | 0 | 1 | 0 |
HLA-A WILD-TYPE | 634 | 64 | 4 | 26 | 5 | 33 |
P value = 4.19e-05 (Chi-square test), Q value = 0.037
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 637 | 64 | 4 | 26 | 6 | 33 |
ODF1 MUTATED | 3 | 0 | 0 | 0 | 1 | 1 |
ODF1 WILD-TYPE | 634 | 64 | 4 | 26 | 5 | 32 |
P value = 7.01e-05 (t-test), Q value = 0.062
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 635 | 2.1 (4.0) |
ASXL2 MUTATED | 6 | 0.5 (0.5) |
ASXL2 WILD-TYPE | 629 | 2.2 (4.0) |
P value = 1.54e-06 (Chi-square test), Q value = 0.0014
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE TIS | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 65 | 57 | 6 | 2 | 268 | 167 | 117 | 23 | 33 | 15 | 1 | 16 |
ATP13A4 MUTATED | 2 | 0 | 0 | 1 | 4 | 1 | 0 | 0 | 1 | 0 | 0 | 0 |
ATP13A4 WILD-TYPE | 63 | 57 | 6 | 1 | 264 | 166 | 117 | 23 | 32 | 15 | 1 | 16 |
P value = 7.01e-05 (t-test), Q value = 0.062
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 635 | 2.1 (4.0) |
MED15 MUTATED | 6 | 0.5 (0.5) |
MED15 WILD-TYPE | 629 | 2.2 (4.0) |
-
Mutation data file = BRCA-TP.mutsig.cluster.txt
-
Clinical data file = BRCA-TP.clin.merged.picked.txt
-
Number of patients = 771
-
Number of significantly mutated genes = 89
-
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.
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.