This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 79 genes and 12 clinical features across 977 patients, 18 significant findings detected with Q value < 0.25.
-
PIK3CA mutation correlated to 'HISTOLOGICAL_TYPE'.
-
TP53 mutation correlated to 'YEARS_TO_BIRTH', 'HISTOLOGICAL_TYPE', and 'RACE'.
-
GATA3 mutation correlated to 'RADIATION_THERAPY'.
-
CDH1 mutation correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', and 'HISTOLOGICAL_TYPE'.
-
MLL3 mutation correlated to 'YEARS_TO_BIRTH'.
-
FOXA1 mutation correlated to 'Time to Death' and 'YEARS_TO_BIRTH'.
-
SPEN mutation correlated to 'YEARS_TO_BIRTH'.
-
RAB42 mutation correlated to 'Time to Death'.
-
NBPF9 mutation correlated to 'PATHOLOGY_M_STAGE'.
-
SP3 mutation correlated to 'Time to Death'.
-
TGS1 mutation correlated to 'YEARS_TO_BIRTH'.
-
LRIG2 mutation correlated to 'Time to Death'.
-
RHOA mutation correlated to 'PATHOLOGY_T_STAGE'.
Table 1. Get Full Table Overview of the association between mutation status of 79 genes and 12 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, 18 significant findings detected.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
NUMBER OF LYMPH NODES |
RACE | ETHNICITY | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
TP53 | 296 (30%) | 681 |
0.207 (1.00) |
0.00283 (0.168) |
0.21 (1.00) |
0.039 (0.838) |
0.131 (1.00) |
0.111 (1.00) |
0.0642 (0.949) |
0.5 (1.00) |
1e-05 (0.00158) |
0.25 (1.00) |
1e-05 (0.00158) |
0.191 (1.00) |
CDH1 | 107 (11%) | 870 |
0.148 (1.00) |
0.0583 (0.937) |
0.0189 (0.527) |
1e-05 (0.00158) |
0.00372 (0.196) |
0.388 (1.00) |
0.608 (1.00) |
0.28 (1.00) |
1e-05 (0.00158) |
0.731 (1.00) |
0.348 (1.00) |
1 (1.00) |
FOXA1 | 23 (2%) | 954 |
1.53e-05 (0.00207) |
8.08e-05 (0.00851) |
0.336 (1.00) |
0.191 (1.00) |
0.633 (1.00) |
1 (1.00) |
1 (1.00) |
0.203 (1.00) |
0.0117 (0.415) |
0.303 (1.00) |
0.359 (1.00) |
0.523 (1.00) |
PIK3CA | 316 (32%) | 661 |
0.918 (1.00) |
0.0322 (0.777) |
0.48 (1.00) |
0.833 (1.00) |
0.929 (1.00) |
1 (1.00) |
1 (1.00) |
0.66 (1.00) |
0.00023 (0.0182) |
0.491 (1.00) |
0.0708 (0.96) |
0.575 (1.00) |
GATA3 | 97 (10%) | 880 |
0.805 (1.00) |
0.0157 (0.482) |
0.0857 (0.96) |
0.199 (1.00) |
0.406 (1.00) |
0.206 (1.00) |
1 (1.00) |
2.06e-06 (0.000977) |
0.00789 (0.34) |
0.122 (1.00) |
0.308 (1.00) |
0.77 (1.00) |
MLL3 | 70 (7%) | 907 |
0.0138 (0.452) |
2.84e-05 (0.00337) |
0.464 (1.00) |
0.537 (1.00) |
0.116 (1.00) |
0.317 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.905 (1.00) |
0.803 (1.00) |
0.163 (1.00) |
0.505 (1.00) |
SPEN | 32 (3%) | 945 |
0.315 (1.00) |
0.00103 (0.0652) |
0.525 (1.00) |
0.15 (1.00) |
0.989 (1.00) |
1 (1.00) |
1 (1.00) |
0.689 (1.00) |
0.784 (1.00) |
0.929 (1.00) |
0.309 (1.00) |
1 (1.00) |
RAB42 | 4 (0%) | 973 |
1.44e-08 (1.36e-05) |
0.862 (1.00) |
0.616 (1.00) |
0.656 (1.00) |
0.841 (1.00) |
1 (1.00) |
1 (1.00) |
0.197 (1.00) |
0.281 (1.00) |
0.861 (1.00) |
0.109 (1.00) |
1 (1.00) |
NBPF9 | 5 (1%) | 972 |
0.509 (1.00) |
0.458 (1.00) |
0.00573 (0.286) |
0.275 (1.00) |
0.513 (1.00) |
0.00317 (0.177) |
1 (1.00) |
0.66 (1.00) |
0.752 (1.00) |
1 (1.00) |
||
SP3 | 7 (1%) | 970 |
0.000154 (0.0144) |
0.317 (1.00) |
0.0537 (0.878) |
0.577 (1.00) |
0.843 (1.00) |
0.0901 (0.96) |
1 (1.00) |
0.415 (1.00) |
0.574 (1.00) |
0.378 (1.00) |
0.752 (1.00) |
1 (1.00) |
TGS1 | 13 (1%) | 964 |
0.947 (1.00) |
0.00071 (0.0517) |
0.782 (1.00) |
0.859 (1.00) |
0.179 (1.00) |
1 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.352 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.323 (1.00) |
LRIG2 | 7 (1%) | 970 |
0.000167 (0.0144) |
0.392 (1.00) |
0.908 (1.00) |
0.9 (1.00) |
0.739 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.573 (1.00) |
0.441 (1.00) |
1 (1.00) |
1 (1.00) |
RHOA | 6 (1%) | 971 |
0.765 (1.00) |
0.383 (1.00) |
0.34 (1.00) |
0.00101 (0.0652) |
0.0992 (0.97) |
1 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.389 (1.00) |
0.882 (1.00) |
1 (1.00) |
1 (1.00) |
MAP3K1 | 71 (7%) | 906 |
0.989 (1.00) |
0.00681 (0.307) |
0.7 (1.00) |
0.266 (1.00) |
0.96 (1.00) |
0.627 (1.00) |
1 (1.00) |
0.236 (1.00) |
0.787 (1.00) |
0.426 (1.00) |
0.885 (1.00) |
0.293 (1.00) |
CBFB | 22 (2%) | 955 |
0.716 (1.00) |
0.756 (1.00) |
0.341 (1.00) |
0.261 (1.00) |
0.0807 (0.96) |
0.304 (1.00) |
0.186 (1.00) |
1 (1.00) |
0.631 (1.00) |
0.454 (1.00) |
0.481 (1.00) |
0.544 (1.00) |
PTEN | 35 (4%) | 942 |
0.76 (1.00) |
0.102 (0.986) |
0.442 (1.00) |
0.142 (1.00) |
0.532 (1.00) |
0.0932 (0.96) |
1 (1.00) |
0.271 (1.00) |
0.123 (1.00) |
0.251 (1.00) |
1 (1.00) |
1 (1.00) |
RUNX1 | 29 (3%) | 948 |
0.479 (1.00) |
0.808 (1.00) |
0.256 (1.00) |
0.476 (1.00) |
0.338 (1.00) |
1 (1.00) |
1 (1.00) |
0.518 (1.00) |
0.0138 (0.452) |
0.171 (1.00) |
0.334 (1.00) |
0.582 (1.00) |
CDKN1B | 10 (1%) | 967 |
0.744 (1.00) |
0.594 (1.00) |
0.113 (1.00) |
0.0491 (0.853) |
0.0233 (0.598) |
0.14 (1.00) |
1 (1.00) |
0.311 (1.00) |
0.787 (1.00) |
0.0777 (0.96) |
0.755 (1.00) |
1 (1.00) |
MAP2K4 | 32 (3%) | 945 |
0.894 (1.00) |
0.398 (1.00) |
0.65 (1.00) |
0.358 (1.00) |
0.494 (1.00) |
0.426 (1.00) |
1 (1.00) |
0.451 (1.00) |
0.204 (1.00) |
0.31 (1.00) |
0.674 (1.00) |
1 (1.00) |
ARID1A | 27 (3%) | 950 |
0.511 (1.00) |
0.979 (1.00) |
0.518 (1.00) |
0.366 (1.00) |
0.287 (1.00) |
1 (1.00) |
1 (1.00) |
0.23 (1.00) |
0.585 (1.00) |
0.464 (1.00) |
0.2 (1.00) |
0.523 (1.00) |
GPS2 | 10 (1%) | 967 |
0.871 (1.00) |
0.151 (1.00) |
0.91 (1.00) |
0.26 (1.00) |
0.651 (1.00) |
1 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.472 (1.00) |
0.656 (1.00) |
0.447 (1.00) |
0.352 (1.00) |
TBX3 | 27 (3%) | 950 |
0.217 (1.00) |
0.0731 (0.96) |
0.738 (1.00) |
0.764 (1.00) |
0.414 (1.00) |
1 (1.00) |
1 (1.00) |
0.307 (1.00) |
0.0451 (0.853) |
0.429 (1.00) |
0.404 (1.00) |
1 (1.00) |
RB1 | 19 (2%) | 958 |
0.933 (1.00) |
0.272 (1.00) |
0.463 (1.00) |
0.301 (1.00) |
0.781 (1.00) |
1 (1.00) |
0.163 (1.00) |
0.602 (1.00) |
0.729 (1.00) |
0.552 (1.00) |
1 (1.00) |
0.523 (1.00) |
CTCF | 16 (2%) | 961 |
0.0913 (0.96) |
0.873 (1.00) |
0.257 (1.00) |
0.0798 (0.96) |
0.312 (1.00) |
1 (1.00) |
1 (1.00) |
0.175 (1.00) |
0.584 (1.00) |
0.172 (1.00) |
0.448 (1.00) |
0.456 (1.00) |
RBMX | 13 (1%) | 964 |
0.992 (1.00) |
0.368 (1.00) |
0.898 (1.00) |
0.42 (1.00) |
0.0847 (0.96) |
1 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.861 (1.00) |
0.963 (1.00) |
1 (1.00) |
1 (1.00) |
HRNR | 31 (3%) | 946 |
0.0877 (0.96) |
0.245 (1.00) |
0.179 (1.00) |
0.124 (1.00) |
0.125 (1.00) |
1 (1.00) |
1 (1.00) |
0.456 (1.00) |
0.929 (1.00) |
0.599 (1.00) |
0.656 (1.00) |
0.301 (1.00) |
ZMYM3 | 15 (2%) | 962 |
0.436 (1.00) |
0.626 (1.00) |
0.782 (1.00) |
0.959 (1.00) |
1 (1.00) |
0.248 (1.00) |
1 (1.00) |
0.419 (1.00) |
1 (1.00) |
0.834 (1.00) |
0.423 (1.00) |
1 (1.00) |
NCOR1 | 40 (4%) | 937 |
0.852 (1.00) |
0.57 (1.00) |
0.945 (1.00) |
0.718 (1.00) |
0.887 (1.00) |
1 (1.00) |
1 (1.00) |
0.583 (1.00) |
0.651 (1.00) |
0.871 (1.00) |
0.319 (1.00) |
0.636 (1.00) |
GPRIN2 | 11 (1%) | 966 |
0.858 (1.00) |
0.223 (1.00) |
0.66 (1.00) |
0.936 (1.00) |
0.333 (1.00) |
1 (1.00) |
1 (1.00) |
0.758 (1.00) |
0.162 (1.00) |
0.108 (1.00) |
0.258 (1.00) |
1 (1.00) |
NF1 | 28 (3%) | 949 |
0.213 (1.00) |
0.116 (1.00) |
0.2 (1.00) |
0.138 (1.00) |
0.399 (1.00) |
0.355 (1.00) |
1 (1.00) |
0.107 (1.00) |
0.414 (1.00) |
0.129 (1.00) |
0.684 (1.00) |
1 (1.00) |
TCP11 | 6 (1%) | 971 |
0.0807 (0.96) |
0.832 (1.00) |
0.752 (1.00) |
0.455 (1.00) |
0.565 (1.00) |
1 (1.00) |
1 (1.00) |
0.177 (1.00) |
0.271 (1.00) |
0.184 (1.00) |
0.678 (1.00) |
1 (1.00) |
SF3B1 | 16 (2%) | 961 |
0.316 (1.00) |
0.411 (1.00) |
0.486 (1.00) |
0.466 (1.00) |
0.835 (1.00) |
1 (1.00) |
1 (1.00) |
0.782 (1.00) |
0.906 (1.00) |
0.945 (1.00) |
0.784 (1.00) |
1 (1.00) |
ERBB2 | 20 (2%) | 957 |
0.0476 (0.853) |
0.153 (1.00) |
0.489 (1.00) |
0.255 (1.00) |
0.0932 (0.96) |
1 (1.00) |
0.17 (1.00) |
1 (1.00) |
0.737 (1.00) |
0.299 (1.00) |
0.146 (1.00) |
0.456 (1.00) |
CDC42EP1 | 5 (1%) | 972 |
0.41 (1.00) |
0.32 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.466 (1.00) |
1 (1.00) |
1 (1.00) |
0.328 (1.00) |
1 (1.00) |
0.378 (1.00) |
1 (1.00) |
1 (1.00) |
KDM6A | 15 (2%) | 962 |
0.834 (1.00) |
0.0689 (0.96) |
0.84 (1.00) |
0.457 (1.00) |
0.0103 (0.406) |
1 (1.00) |
1 (1.00) |
0.595 (1.00) |
0.741 (1.00) |
0.638 (1.00) |
0.864 (1.00) |
1 (1.00) |
AQP12A | 6 (1%) | 971 |
0.41 (1.00) |
0.326 (1.00) |
0.836 (1.00) |
0.675 (1.00) |
0.225 (1.00) |
1 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.501 (1.00) |
0.36 (1.00) |
0.677 (1.00) |
1 (1.00) |
KRAS | 6 (1%) | 971 |
0.733 (1.00) |
0.125 (1.00) |
0.821 (1.00) |
0.883 (1.00) |
0.821 (1.00) |
1 (1.00) |
1 (1.00) |
0.415 (1.00) |
1 (1.00) |
0.921 (1.00) |
0.069 (0.96) |
1 (1.00) |
MYB | 12 (1%) | 965 |
0.15 (1.00) |
0.177 (1.00) |
0.475 (1.00) |
0.454 (1.00) |
0.963 (1.00) |
1 (1.00) |
1 (1.00) |
0.311 (1.00) |
0.211 (1.00) |
0.281 (1.00) |
1 (1.00) |
1 (1.00) |
ZNF362 | 5 (1%) | 972 |
0.609 (1.00) |
0.257 (1.00) |
0.321 (1.00) |
0.376 (1.00) |
0.194 (1.00) |
1 (1.00) |
1 (1.00) |
0.328 (1.00) |
0.751 (1.00) |
0.0604 (0.938) |
1 (1.00) |
1 (1.00) |
TBL1XR1 | 9 (1%) | 968 |
0.494 (1.00) |
0.264 (1.00) |
0.0633 (0.949) |
0.0463 (0.853) |
0.0334 (0.777) |
0.157 (1.00) |
1 (1.00) |
0.0696 (0.96) |
0.518 (1.00) |
0.605 (1.00) |
0.751 (1.00) |
1 (1.00) |
FGFR2 | 11 (1%) | 966 |
0.649 (1.00) |
0.562 (1.00) |
0.542 (1.00) |
0.0116 (0.415) |
0.708 (1.00) |
1 (1.00) |
0.0973 (0.961) |
0.525 (1.00) |
0.58 (1.00) |
0.15 (1.00) |
0.527 (1.00) |
1 (1.00) |
ZBTB7C | 5 (1%) | 972 |
0.473 (1.00) |
0.536 (1.00) |
0.718 (1.00) |
1 (1.00) |
0.169 (1.00) |
1 (1.00) |
1 (1.00) |
0.177 (1.00) |
0.273 (1.00) |
0.175 (1.00) |
1 (1.00) |
1 (1.00) |
NCDN | 4 (0%) | 973 |
0.601 (1.00) |
0.784 (1.00) |
0.547 (1.00) |
0.529 (1.00) |
0.374 (1.00) |
1 (1.00) |
1 (1.00) |
0.0872 (0.96) |
0.162 (1.00) |
0.0604 (0.938) |
0.595 (1.00) |
1 (1.00) |
MUC6 | 14 (1%) | 963 |
0.165 (1.00) |
0.386 (1.00) |
0.723 (1.00) |
0.773 (1.00) |
0.093 (0.96) |
0.233 (1.00) |
1 (1.00) |
1 (1.00) |
0.242 (1.00) |
0.406 (1.00) |
0.164 (1.00) |
1 (1.00) |
TFE3 | 7 (1%) | 970 |
0.211 (1.00) |
0.426 (1.00) |
0.853 (1.00) |
0.9 (1.00) |
0.591 (1.00) |
1 (1.00) |
1 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.76 (1.00) |
1 (1.00) |
1 (1.00) |
IRS4 | 11 (1%) | 966 |
0.881 (1.00) |
0.289 (1.00) |
0.0766 (0.96) |
0.784 (1.00) |
0.0455 (0.853) |
0.173 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.517 (1.00) |
0.499 (1.00) |
0.359 (1.00) |
1 (1.00) |
NLGN3 | 11 (1%) | 966 |
0.596 (1.00) |
0.123 (1.00) |
0.384 (1.00) |
0.179 (1.00) |
0.708 (1.00) |
1 (1.00) |
1 (1.00) |
0.521 (1.00) |
0.749 (1.00) |
0.991 (1.00) |
0.132 (1.00) |
0.323 (1.00) |
IL1RAP | 9 (1%) | 968 |
0.418 (1.00) |
0.0803 (0.96) |
0.948 (1.00) |
0.513 (1.00) |
0.46 (1.00) |
1 (1.00) |
1 (1.00) |
0.086 (0.96) |
0.874 (1.00) |
0.129 (1.00) |
0.527 (1.00) |
1 (1.00) |
USP36 | 8 (1%) | 969 |
0.463 (1.00) |
0.143 (1.00) |
0.0336 (0.777) |
0.128 (1.00) |
0.576 (1.00) |
1 (1.00) |
1 (1.00) |
0.415 (1.00) |
1 (1.00) |
0.578 (1.00) |
0.478 (1.00) |
1 (1.00) |
CASZ1 | 14 (1%) | 963 |
0.276 (1.00) |
0.863 (1.00) |
0.83 (1.00) |
0.524 (1.00) |
0.936 (1.00) |
1 (1.00) |
1 (1.00) |
0.387 (1.00) |
0.831 (1.00) |
0.82 (1.00) |
0.613 (1.00) |
1 (1.00) |
EYS | 21 (2%) | 956 |
0.439 (1.00) |
0.0175 (0.503) |
0.751 (1.00) |
0.489 (1.00) |
0.0951 (0.961) |
1 (1.00) |
1 (1.00) |
0.492 (1.00) |
0.0957 (0.961) |
0.142 (1.00) |
0.0118 (0.415) |
1 (1.00) |
KCNN3 | 9 (1%) | 968 |
0.531 (1.00) |
0.718 (1.00) |
0.63 (1.00) |
0.417 (1.00) |
0.514 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.521 (1.00) |
0.252 (1.00) |
0.822 (1.00) |
0.477 (1.00) |
0.293 (1.00) |
ZFP36L1 | 8 (1%) | 969 |
0.549 (1.00) |
0.403 (1.00) |
0.833 (1.00) |
0.908 (1.00) |
0.827 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.512 (1.00) |
0.24 (1.00) |
1 (1.00) |
ICOSLG | 5 (1%) | 972 |
0.746 (1.00) |
0.872 (1.00) |
0.261 (1.00) |
0.719 (1.00) |
0.605 (1.00) |
1 (1.00) |
1 (1.00) |
0.389 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.598 (1.00) |
1 (1.00) |
ACTL6B | 10 (1%) | 967 |
0.609 (1.00) |
0.115 (1.00) |
0.4 (1.00) |
0.157 (1.00) |
0.23 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.738 (1.00) |
0.662 (1.00) |
0.858 (1.00) |
0.525 (1.00) |
1 (1.00) |
MYH9 | 18 (2%) | 959 |
0.479 (1.00) |
0.302 (1.00) |
0.65 (1.00) |
0.915 (1.00) |
0.405 (1.00) |
1 (1.00) |
1 (1.00) |
0.602 (1.00) |
0.215 (1.00) |
0.282 (1.00) |
0.264 (1.00) |
1 (1.00) |
FBXW7 | 15 (2%) | 962 |
0.576 (1.00) |
0.416 (1.00) |
0.569 (1.00) |
0.19 (1.00) |
0.696 (1.00) |
1 (1.00) |
1 (1.00) |
0.595 (1.00) |
0.85 (1.00) |
0.282 (1.00) |
0.0504 (0.853) |
0.406 (1.00) |
FRMPD2 | 13 (1%) | 964 |
0.184 (1.00) |
0.647 (1.00) |
0.387 (1.00) |
0.00921 (0.38) |
0.968 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.202 (1.00) |
0.363 (1.00) |
0.481 (1.00) |
0.352 (1.00) |
ZFP36L2 | 7 (1%) | 970 |
0.342 (1.00) |
0.875 (1.00) |
0.748 (1.00) |
0.899 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.425 (1.00) |
0.0968 (0.961) |
0.229 (1.00) |
TPP2 | 8 (1%) | 969 |
0.673 (1.00) |
0.373 (1.00) |
0.478 (1.00) |
1 (1.00) |
0.281 (1.00) |
1 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.429 (1.00) |
0.0402 (0.838) |
0.243 (1.00) |
1 (1.00) |
C17ORF95 | 5 (1%) | 972 |
0.0888 (0.96) |
0.0898 (0.96) |
0.975 (1.00) |
0.507 (1.00) |
1 (1.00) |
1 (1.00) |
0.0453 (0.853) |
0.328 (1.00) |
1 (1.00) |
0.362 (1.00) |
1 (1.00) |
1 (1.00) |
RUFY1 | 6 (1%) | 971 |
0.0165 (0.489) |
0.0148 (0.467) |
0.565 (1.00) |
0.236 (1.00) |
0.822 (1.00) |
1 (1.00) |
1 (1.00) |
0.197 (1.00) |
0.501 (1.00) |
0.294 (1.00) |
0.402 (1.00) |
1 (1.00) |
MED23 | 14 (1%) | 963 |
0.32 (1.00) |
0.0356 (0.803) |
0.256 (1.00) |
0.298 (1.00) |
0.775 (1.00) |
1 (1.00) |
1 (1.00) |
0.161 (1.00) |
0.654 (1.00) |
0.349 (1.00) |
0.326 (1.00) |
1 (1.00) |
PAX2 | 4 (0%) | 973 |
0.132 (1.00) |
0.146 (1.00) |
0.857 (1.00) |
1 (1.00) |
0.842 (1.00) |
1 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.719 (1.00) |
0.208 (1.00) |
1 (1.00) |
1 (1.00) |
MED12 | 21 (2%) | 956 |
0.883 (1.00) |
0.431 (1.00) |
0.738 (1.00) |
0.546 (1.00) |
0.444 (1.00) |
1 (1.00) |
1 (1.00) |
0.133 (1.00) |
0.687 (1.00) |
0.273 (1.00) |
0.0798 (0.96) |
1 (1.00) |
CHD4 | 19 (2%) | 958 |
0.871 (1.00) |
0.706 (1.00) |
0.22 (1.00) |
0.0229 (0.598) |
0.00677 (0.307) |
1 (1.00) |
1 (1.00) |
0.0905 (0.96) |
0.202 (1.00) |
0.98 (1.00) |
0.115 (1.00) |
1 (1.00) |
PFKP | 6 (1%) | 971 |
0.519 (1.00) |
0.227 (1.00) |
0.513 (1.00) |
0.574 (1.00) |
0.565 (1.00) |
1 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.784 (1.00) |
0.0213 (0.576) |
0.738 (1.00) |
1 (1.00) |
RHBG | 4 (0%) | 973 |
0.0304 (0.76) |
0.0495 (0.853) |
0.823 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
PSIP1 | 8 (1%) | 969 |
0.136 (1.00) |
0.268 (1.00) |
0.227 (1.00) |
0.248 (1.00) |
0.927 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.252 (1.00) |
0.514 (1.00) |
0.662 (1.00) |
0.302 (1.00) |
1 (1.00) |
RIBC1 | 4 (0%) | 973 |
0.775 (1.00) |
0.885 (1.00) |
0.494 (1.00) |
0.524 (1.00) |
0.225 (1.00) |
1 (1.00) |
1 (1.00) |
0.328 (1.00) |
0.719 (1.00) |
0.232 (1.00) |
1 (1.00) |
|
PLK2 | 9 (1%) | 968 |
0.648 (1.00) |
0.154 (1.00) |
0.536 (1.00) |
0.582 (1.00) |
0.538 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.394 (1.00) |
0.677 (1.00) |
0.613 (1.00) |
1 (1.00) |
ANKRD20A4 | 7 (1%) | 970 |
0.481 (1.00) |
0.473 (1.00) |
0.365 (1.00) |
0.234 (1.00) |
0.238 (1.00) |
1 (1.00) |
1 (1.00) |
0.389 (1.00) |
1 (1.00) |
0.065 (0.949) |
1 (1.00) |
1 (1.00) |
PHACTR1 | 7 (1%) | 970 |
0.0454 (0.853) |
0.33 (1.00) |
0.338 (1.00) |
0.254 (1.00) |
0.549 (1.00) |
0.124 (1.00) |
1 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.915 (1.00) |
0.477 (1.00) |
1 (1.00) |
DLG1 | 13 (1%) | 964 |
0.536 (1.00) |
0.521 (1.00) |
0.774 (1.00) |
0.699 (1.00) |
0.626 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0529 (0.878) |
0.21 (1.00) |
0.582 (1.00) |
1 (1.00) |
GPRASP2 | 10 (1%) | 967 |
0.858 (1.00) |
0.184 (1.00) |
0.651 (1.00) |
0.384 (1.00) |
0.654 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.739 (1.00) |
0.786 (1.00) |
0.928 (1.00) |
0.48 (1.00) |
1 (1.00) |
CCDC82 | 6 (1%) | 971 |
0.0931 (0.96) |
0.275 (1.00) |
0.909 (1.00) |
0.884 (1.00) |
0.563 (1.00) |
1 (1.00) |
1 (1.00) |
0.0872 (0.96) |
1 (1.00) |
0.104 (0.997) |
0.0621 (0.949) |
1 (1.00) |
CCDC27 | 7 (1%) | 970 |
0.632 (1.00) |
0.243 (1.00) |
0.888 (1.00) |
0.9 (1.00) |
0.506 (1.00) |
1 (1.00) |
1 (1.00) |
0.698 (1.00) |
0.0383 (0.838) |
0.93 (1.00) |
0.0407 (0.838) |
1 (1.00) |
MAMLD1 | 10 (1%) | 967 |
0.488 (1.00) |
0.114 (1.00) |
0.444 (1.00) |
0.763 (1.00) |
0.24 (1.00) |
1 (1.00) |
1 (1.00) |
0.0488 (0.853) |
0.889 (1.00) |
0.4 (1.00) |
1 (1.00) |
1 (1.00) |
OR8D1 | 5 (1%) | 972 |
0.308 (1.00) |
0.49 (1.00) |
0.841 (1.00) |
0.439 (1.00) |
0.873 (1.00) |
1 (1.00) |
1 (1.00) |
0.66 (1.00) |
0.75 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.159 (1.00) |
P value = 0.00023 (Fisher's exact test), Q value = 0.018
Table S1. Gene #1: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 712 | 171 | 5 | 6 | 26 | 14 | 41 |
PIK3CA MUTATED | 0 | 216 | 74 | 0 | 0 | 12 | 0 | 14 |
PIK3CA WILD-TYPE | 1 | 496 | 97 | 5 | 6 | 14 | 14 | 27 |
Figure S1. Get High-res Image Gene #1: 'PIK3CA MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D1V9.png)
P value = 0.00283 (Wilcoxon-test), Q value = 0.17
Table S2. Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 964 | 58.7 (13.1) |
TP53 MUTATED | 291 | 56.9 (12.3) |
TP53 WILD-TYPE | 673 | 59.5 (13.4) |
Figure S2. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D2V2.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
Table S3. Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 712 | 171 | 5 | 6 | 26 | 14 | 41 |
TP53 MUTATED | 1 | 261 | 9 | 3 | 4 | 6 | 1 | 10 |
TP53 WILD-TYPE | 0 | 451 | 162 | 2 | 2 | 20 | 13 | 31 |
Figure S3. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D2V9.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
Table S4. Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'
nPatients | AMERICAN INDIAN OR ALASKA NATIVE | ASIAN | BLACK OR AFRICAN AMERICAN | WHITE |
---|---|---|---|---|
ALL | 1 | 57 | 121 | 705 |
TP53 MUTATED | 1 | 29 | 56 | 189 |
TP53 WILD-TYPE | 0 | 28 | 65 | 516 |
Figure S4. Get High-res Image Gene #2: 'TP53 MUTATION STATUS' versus Clinical Feature #11: 'RACE'
![](D2V11.png)
P value = 2.06e-06 (Fisher's exact test), Q value = 0.00098
Table S5. Gene #3: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'RADIATION_THERAPY'
nPatients | NO | YES |
---|---|---|
ALL | 377 | 472 |
GATA3 MUTATED | 59 | 27 |
GATA3 WILD-TYPE | 318 | 445 |
Figure S5. Get High-res Image Gene #3: 'GATA3 MUTATION STATUS' versus Clinical Feature #8: 'RADIATION_THERAPY'
![](D3V8.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
Table S6. Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 563 | 119 | 35 |
CDH1 MUTATED | 16 | 56 | 33 | 2 |
CDH1 WILD-TYPE | 242 | 507 | 86 | 33 |
Figure S6. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D5V4.png)
P value = 0.00372 (Fisher's exact test), Q value = 0.2
Table S7. Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 462 | 325 | 107 | 68 |
CDH1 MUTATED | 56 | 27 | 8 | 16 |
CDH1 WILD-TYPE | 406 | 298 | 99 | 52 |
Figure S7. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #5: 'PATHOLOGY_N_STAGE'
![](D5V5.png)
P value = 1e-05 (Fisher's exact test), Q value = 0.0016
Table S8. Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 712 | 171 | 5 | 6 | 26 | 14 | 41 |
CDH1 MUTATED | 0 | 13 | 89 | 1 | 0 | 3 | 0 | 1 |
CDH1 WILD-TYPE | 1 | 699 | 82 | 4 | 6 | 23 | 14 | 40 |
Figure S8. Get High-res Image Gene #5: 'CDH1 MUTATION STATUS' versus Clinical Feature #9: 'HISTOLOGICAL_TYPE'
![](D5V9.png)
P value = 2.84e-05 (Wilcoxon-test), Q value = 0.0034
Table S9. Gene #9: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 964 | 58.7 (13.1) |
MLL3 MUTATED | 70 | 65.2 (13.0) |
MLL3 WILD-TYPE | 894 | 58.2 (13.0) |
Figure S9. Get High-res Image Gene #9: 'MLL3 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D9V2.png)
P value = 1.53e-05 (logrank test), Q value = 0.0021
Table S10. Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 962 | 137 | 0.0 - 282.9 (30.2) |
FOXA1 MUTATED | 21 | 7 | 1.0 - 118.6 (20.4) |
FOXA1 WILD-TYPE | 941 | 130 | 0.0 - 282.9 (31.0) |
Figure S10. Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D13V1.png)
P value = 8.08e-05 (Wilcoxon-test), Q value = 0.0085
Table S11. Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 964 | 58.7 (13.1) |
FOXA1 MUTATED | 23 | 70.6 (13.3) |
FOXA1 WILD-TYPE | 941 | 58.5 (13.0) |
Figure S11. Get High-res Image Gene #13: 'FOXA1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D13V2.png)
P value = 0.00103 (Wilcoxon-test), Q value = 0.065
Table S12. Gene #23: 'SPEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 964 | 58.7 (13.1) |
SPEN MUTATED | 32 | 66.4 (13.6) |
SPEN WILD-TYPE | 932 | 58.5 (13.1) |
Figure S12. Get High-res Image Gene #23: 'SPEN MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D23V2.png)
P value = 1.44e-08 (logrank test), Q value = 1.4e-05
Table S13. Gene #28: 'RAB42 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 962 | 137 | 0.0 - 282.9 (30.2) |
RAB42 MUTATED | 4 | 2 | 9.6 - 24.8 (16.7) |
RAB42 WILD-TYPE | 958 | 135 | 0.0 - 282.9 (30.4) |
Figure S13. Get High-res Image Gene #28: 'RAB42 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D28V1.png)
P value = 0.00317 (Fisher's exact test), Q value = 0.18
Table S14. Gene #33: 'NBPF9 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
nPatients | 0 | 1 |
---|---|---|
ALL | 841 | 16 |
NBPF9 MUTATED | 3 | 2 |
NBPF9 WILD-TYPE | 838 | 14 |
Figure S14. Get High-res Image Gene #33: 'NBPF9 MUTATION STATUS' versus Clinical Feature #6: 'PATHOLOGY_M_STAGE'
![](D33V6.png)
P value = 0.000154 (logrank test), Q value = 0.014
Table S15. Gene #37: 'SP3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 962 | 137 | 0.0 - 282.9 (30.2) |
SP3 MUTATED | 6 | 3 | 5.7 - 84.6 (19.4) |
SP3 WILD-TYPE | 956 | 134 | 0.0 - 282.9 (30.4) |
Figure S15. Get High-res Image Gene #37: 'SP3 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D37V1.png)
P value = 0.00071 (Wilcoxon-test), Q value = 0.052
Table S16. Gene #42: 'TGS1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 964 | 58.7 (13.1) |
TGS1 MUTATED | 13 | 71.5 (10.8) |
TGS1 WILD-TYPE | 951 | 58.6 (13.1) |
Figure S16. Get High-res Image Gene #42: 'TGS1 MUTATION STATUS' versus Clinical Feature #2: 'YEARS_TO_BIRTH'
![](D42V2.png)
P value = 0.000167 (logrank test), Q value = 0.014
Table S17. Gene #68: 'LRIG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 962 | 137 | 0.0 - 282.9 (30.2) |
LRIG2 MUTATED | 7 | 3 | 5.2 - 63.1 (16.6) |
LRIG2 WILD-TYPE | 955 | 134 | 0.0 - 282.9 (30.4) |
Figure S17. Get High-res Image Gene #68: 'LRIG2 MUTATION STATUS' versus Clinical Feature #1: 'Time to Death'
![](D68V1.png)
P value = 0.00101 (Fisher's exact test), Q value = 0.065
Table S18. Gene #77: 'RHOA MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 258 | 563 | 119 | 35 |
RHOA MUTATED | 0 | 1 | 4 | 1 |
RHOA WILD-TYPE | 258 | 562 | 115 | 34 |
Figure S18. Get High-res Image Gene #77: 'RHOA MUTATION STATUS' versus Clinical Feature #4: 'PATHOLOGY_T_STAGE'
![](D77V4.png)
-
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/BRCA-TP/20231617/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/19775058/BRCA-TP.merged_data.txt
-
Number of patients = 977
-
Number of significantly mutated genes = 79
-
Number of selected clinical features = 12
-
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.