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, 19 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 'PATHOLOGIC_STAGE' and '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'.
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 |
0.197 (1.00) |
0.00283 (0.168) |
0.303 (1.00) |
0.0544 (0.886) |
0.132 (1.00) |
0.111 (0.984) |
0.0642 (0.936) |
0.605 (1.00) |
1e-05 (0.0019) |
0.253 (1.00) |
1e-05 (0.0019) |
0.191 (1.00) |
CDH1 | 107 (11%) | 870 |
0.238 (1.00) |
0.0583 (0.921) |
0.0194 (0.541) |
1e-05 (0.0019) |
0.00387 (0.204) |
0.388 (1.00) |
0.608 (1.00) |
0.241 (1.00) |
1e-05 (0.0019) |
0.727 (1.00) |
0.351 (1.00) |
1 (1.00) |
FOXA1 | 23 (2%) | 954 |
2.02e-05 (0.00319) |
8.08e-05 (0.00851) |
0.315 (1.00) |
0.192 (1.00) |
0.634 (1.00) |
1 (1.00) |
1 (1.00) |
0.0869 (0.936) |
0.0125 (0.425) |
0.302 (1.00) |
0.355 (1.00) |
0.523 (1.00) |
NBPF9 | 5 (1%) | 972 |
0.499 (1.00) |
0.458 (1.00) |
0.00419 (0.209) |
0.275 (1.00) |
0.513 (1.00) |
0.00316 (0.176) |
1 (1.00) |
0.658 (1.00) |
0.751 (1.00) |
1 (1.00) |
||
PIK3CA | 316 (32%) | 661 |
0.94 (1.00) |
0.0322 (0.746) |
0.491 (1.00) |
0.812 (1.00) |
0.931 (1.00) |
1 (1.00) |
1 (1.00) |
0.774 (1.00) |
0.00031 (0.0245) |
0.498 (1.00) |
0.0716 (0.936) |
0.575 (1.00) |
GATA3 | 97 (10%) | 880 |
0.925 (1.00) |
0.0157 (0.472) |
0.0661 (0.936) |
0.212 (1.00) |
0.403 (1.00) |
0.205 (1.00) |
1 (1.00) |
3.31e-05 (0.00393) |
0.00743 (0.306) |
0.123 (1.00) |
0.308 (1.00) |
0.77 (1.00) |
MLL3 | 70 (7%) | 907 |
0.0207 (0.56) |
2.84e-05 (0.00385) |
0.472 (1.00) |
0.535 (1.00) |
0.115 (0.984) |
0.317 (1.00) |
1 (1.00) |
0.297 (1.00) |
0.91 (1.00) |
0.806 (1.00) |
0.162 (1.00) |
0.505 (1.00) |
SPEN | 32 (3%) | 945 |
0.27 (1.00) |
0.00103 (0.0652) |
0.484 (1.00) |
0.156 (1.00) |
0.99 (1.00) |
1 (1.00) |
1 (1.00) |
0.443 (1.00) |
0.782 (1.00) |
0.933 (1.00) |
0.306 (1.00) |
1 (1.00) |
RAB42 | 4 (0%) | 973 |
1.01e-08 (9.53e-06) |
0.862 (1.00) |
0.61 (1.00) |
0.657 (1.00) |
0.844 (1.00) |
1 (1.00) |
1 (1.00) |
0.583 (1.00) |
0.286 (1.00) |
0.861 (1.00) |
0.107 (0.979) |
1 (1.00) |
SP3 | 7 (1%) | 970 |
0.000133 (0.0126) |
0.317 (1.00) |
0.0475 (0.849) |
0.576 (1.00) |
0.841 (1.00) |
0.09 (0.936) |
1 (1.00) |
0.477 (1.00) |
0.573 (1.00) |
0.379 (1.00) |
0.754 (1.00) |
1 (1.00) |
TGS1 | 13 (1%) | 964 |
0.982 (1.00) |
0.00071 (0.0517) |
0.77 (1.00) |
0.861 (1.00) |
0.176 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.253 (1.00) |
1 (1.00) |
0.323 (1.00) |
LRIG2 | 7 (1%) | 970 |
0.000192 (0.0166) |
0.392 (1.00) |
0.892 (1.00) |
0.9 (1.00) |
0.738 (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 |
0.769 (1.00) |
0.383 (1.00) |
0.341 (1.00) |
0.00087 (0.0589) |
0.0978 (0.936) |
1 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.391 (1.00) |
0.882 (1.00) |
1 (1.00) |
1 (1.00) |
MAP3K1 | 71 (7%) | 906 |
0.986 (1.00) |
0.00681 (0.296) |
0.66 (1.00) |
0.257 (1.00) |
0.959 (1.00) |
0.627 (1.00) |
1 (1.00) |
0.292 (1.00) |
0.79 (1.00) |
0.428 (1.00) |
0.886 (1.00) |
0.293 (1.00) |
CBFB | 22 (2%) | 955 |
0.685 (1.00) |
0.756 (1.00) |
0.271 (1.00) |
0.25 (1.00) |
0.0818 (0.936) |
0.303 (1.00) |
0.186 (1.00) |
1 (1.00) |
0.615 (1.00) |
0.452 (1.00) |
0.481 (1.00) |
0.544 (1.00) |
PTEN | 35 (4%) | 942 |
0.711 (1.00) |
0.102 (0.956) |
0.407 (1.00) |
0.145 (1.00) |
0.534 (1.00) |
0.093 (0.936) |
1 (1.00) |
0.292 (1.00) |
0.117 (0.984) |
0.25 (1.00) |
1 (1.00) |
1 (1.00) |
RUNX1 | 29 (3%) | 948 |
0.659 (1.00) |
0.808 (1.00) |
0.264 (1.00) |
0.493 (1.00) |
0.339 (1.00) |
1 (1.00) |
1 (1.00) |
0.307 (1.00) |
0.0156 (0.472) |
0.171 (1.00) |
0.334 (1.00) |
0.582 (1.00) |
CDKN1B | 10 (1%) | 967 |
0.742 (1.00) |
0.594 (1.00) |
0.107 (0.979) |
0.0487 (0.854) |
0.023 (0.573) |
0.14 (1.00) |
1 (1.00) |
0.477 (1.00) |
0.787 (1.00) |
0.0777 (0.936) |
0.755 (1.00) |
1 (1.00) |
MAP2K4 | 32 (3%) | 945 |
0.868 (1.00) |
0.398 (1.00) |
0.653 (1.00) |
0.365 (1.00) |
0.494 (1.00) |
0.426 (1.00) |
1 (1.00) |
0.363 (1.00) |
0.209 (1.00) |
0.349 (1.00) |
0.674 (1.00) |
1 (1.00) |
ARID1A | 27 (3%) | 950 |
0.531 (1.00) |
0.979 (1.00) |
0.345 (1.00) |
0.382 (1.00) |
0.287 (1.00) |
1 (1.00) |
1 (1.00) |
0.112 (0.984) |
0.495 (1.00) |
0.465 (1.00) |
0.203 (1.00) |
0.523 (1.00) |
GPS2 | 10 (1%) | 967 |
0.874 (1.00) |
0.151 (1.00) |
0.901 (1.00) |
0.274 (1.00) |
0.652 (1.00) |
1 (1.00) |
1 (1.00) |
0.754 (1.00) |
0.472 (1.00) |
0.658 (1.00) |
0.447 (1.00) |
0.352 (1.00) |
TBX3 | 27 (3%) | 950 |
0.212 (1.00) |
0.0731 (0.936) |
0.729 (1.00) |
0.774 (1.00) |
0.412 (1.00) |
1 (1.00) |
1 (1.00) |
0.238 (1.00) |
0.0456 (0.849) |
0.428 (1.00) |
0.405 (1.00) |
1 (1.00) |
RB1 | 19 (2%) | 958 |
0.895 (1.00) |
0.272 (1.00) |
0.439 (1.00) |
0.287 (1.00) |
0.779 (1.00) |
1 (1.00) |
0.163 (1.00) |
0.446 (1.00) |
0.73 (1.00) |
0.553 (1.00) |
1 (1.00) |
0.523 (1.00) |
CTCF | 16 (2%) | 961 |
0.0958 (0.936) |
0.873 (1.00) |
0.233 (1.00) |
0.0745 (0.936) |
0.31 (1.00) |
1 (1.00) |
1 (1.00) |
0.293 (1.00) |
0.588 (1.00) |
0.173 (1.00) |
0.448 (1.00) |
0.456 (1.00) |
RBMX | 13 (1%) | 964 |
0.994 (1.00) |
0.368 (1.00) |
0.897 (1.00) |
0.421 (1.00) |
0.0861 (0.936) |
1 (1.00) |
1 (1.00) |
0.26 (1.00) |
0.861 (1.00) |
0.965 (1.00) |
1 (1.00) |
1 (1.00) |
HRNR | 31 (3%) | 946 |
0.0852 (0.936) |
0.245 (1.00) |
0.131 (1.00) |
0.13 (1.00) |
0.123 (1.00) |
1 (1.00) |
1 (1.00) |
0.462 (1.00) |
0.921 (1.00) |
0.603 (1.00) |
0.657 (1.00) |
0.301 (1.00) |
ZMYM3 | 15 (2%) | 962 |
0.453 (1.00) |
0.626 (1.00) |
0.779 (1.00) |
0.961 (1.00) |
1 (1.00) |
0.248 (1.00) |
1 (1.00) |
0.416 (1.00) |
1 (1.00) |
0.835 (1.00) |
0.42 (1.00) |
1 (1.00) |
NCOR1 | 40 (4%) | 937 |
0.862 (1.00) |
0.57 (1.00) |
0.949 (1.00) |
0.733 (1.00) |
0.888 (1.00) |
1 (1.00) |
1 (1.00) |
0.73 (1.00) |
0.655 (1.00) |
0.874 (1.00) |
0.314 (1.00) |
0.636 (1.00) |
GPRIN2 | 11 (1%) | 966 |
0.828 (1.00) |
0.223 (1.00) |
0.851 (1.00) |
0.935 (1.00) |
0.335 (1.00) |
1 (1.00) |
1 (1.00) |
0.754 (1.00) |
0.163 (1.00) |
0.108 (0.98) |
0.259 (1.00) |
1 (1.00) |
NF1 | 28 (3%) | 949 |
0.213 (1.00) |
0.116 (0.984) |
0.156 (1.00) |
0.141 (1.00) |
0.401 (1.00) |
0.355 (1.00) |
1 (1.00) |
0.0803 (0.936) |
0.424 (1.00) |
0.129 (1.00) |
0.683 (1.00) |
1 (1.00) |
TCP11 | 6 (1%) | 971 |
0.0873 (0.936) |
0.832 (1.00) |
0.739 (1.00) |
0.456 (1.00) |
0.562 (1.00) |
1 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.272 (1.00) |
0.184 (1.00) |
0.68 (1.00) |
1 (1.00) |
SF3B1 | 16 (2%) | 961 |
0.323 (1.00) |
0.411 (1.00) |
0.474 (1.00) |
0.469 (1.00) |
0.838 (1.00) |
1 (1.00) |
1 (1.00) |
0.447 (1.00) |
0.907 (1.00) |
0.946 (1.00) |
0.785 (1.00) |
1 (1.00) |
ERBB2 | 20 (2%) | 957 |
0.00555 (0.263) |
0.153 (1.00) |
0.679 (1.00) |
0.249 (1.00) |
0.0921 (0.936) |
1 (1.00) |
0.17 (1.00) |
0.8 (1.00) |
0.738 (1.00) |
0.299 (1.00) |
0.147 (1.00) |
0.456 (1.00) |
CDC42EP1 | 5 (1%) | 972 |
0.411 (1.00) |
0.32 (1.00) |
0.591 (1.00) |
1 (1.00) |
0.468 (1.00) |
1 (1.00) |
1 (1.00) |
0.323 (1.00) |
1 (1.00) |
0.379 (1.00) |
1 (1.00) |
1 (1.00) |
KDM6A | 15 (2%) | 962 |
0.805 (1.00) |
0.0689 (0.936) |
0.832 (1.00) |
0.458 (1.00) |
0.0108 (0.408) |
1 (1.00) |
1 (1.00) |
0.6 (1.00) |
0.691 (1.00) |
0.639 (1.00) |
0.864 (1.00) |
1 (1.00) |
AQP12A | 6 (1%) | 971 |
0.391 (1.00) |
0.326 (1.00) |
0.835 (1.00) |
0.673 (1.00) |
0.225 (1.00) |
1 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.502 (1.00) |
0.36 (1.00) |
0.678 (1.00) |
1 (1.00) |
KRAS | 6 (1%) | 971 |
0.723 (1.00) |
0.125 (1.00) |
0.816 (1.00) |
0.883 (1.00) |
0.823 (1.00) |
1 (1.00) |
1 (1.00) |
0.412 (1.00) |
1 (1.00) |
0.923 (1.00) |
0.0673 (0.936) |
1 (1.00) |
MYB | 12 (1%) | 965 |
0.156 (1.00) |
0.177 (1.00) |
0.479 (1.00) |
0.478 (1.00) |
0.964 (1.00) |
1 (1.00) |
1 (1.00) |
0.313 (1.00) |
0.212 (1.00) |
0.281 (1.00) |
1 (1.00) |
1 (1.00) |
ZNF362 | 5 (1%) | 972 |
0.604 (1.00) |
0.257 (1.00) |
0.317 (1.00) |
0.373 (1.00) |
0.193 (1.00) |
1 (1.00) |
1 (1.00) |
0.658 (1.00) |
0.751 (1.00) |
0.0604 (0.923) |
1 (1.00) |
1 (1.00) |
TBL1XR1 | 9 (1%) | 968 |
0.459 (1.00) |
0.264 (1.00) |
0.101 (0.956) |
0.046 (0.849) |
0.0338 (0.762) |
0.157 (1.00) |
1 (1.00) |
0.0723 (0.936) |
0.522 (1.00) |
0.605 (1.00) |
0.751 (1.00) |
1 (1.00) |
FGFR2 | 11 (1%) | 966 |
0.643 (1.00) |
0.562 (1.00) |
0.515 (1.00) |
0.0122 (0.425) |
0.708 (1.00) |
1 (1.00) |
0.0973 (0.936) |
0.527 (1.00) |
0.618 (1.00) |
0.15 (1.00) |
0.528 (1.00) |
1 (1.00) |
ZBTB7C | 5 (1%) | 972 |
0.471 (1.00) |
0.536 (1.00) |
0.734 (1.00) |
1 (1.00) |
0.169 (1.00) |
1 (1.00) |
1 (1.00) |
0.173 (1.00) |
0.275 (1.00) |
0.174 (1.00) |
1 (1.00) |
1 (1.00) |
NCDN | 4 (0%) | 973 |
0.598 (1.00) |
0.784 (1.00) |
0.541 (1.00) |
0.528 (1.00) |
0.377 (1.00) |
1 (1.00) |
1 (1.00) |
0.0821 (0.936) |
0.164 (1.00) |
0.0604 (0.923) |
0.597 (1.00) |
1 (1.00) |
MUC6 | 14 (1%) | 963 |
0.188 (1.00) |
0.386 (1.00) |
0.725 (1.00) |
0.773 (1.00) |
0.0945 (0.936) |
0.233 (1.00) |
1 (1.00) |
1 (1.00) |
0.24 (1.00) |
0.407 (1.00) |
0.166 (1.00) |
1 (1.00) |
TFE3 | 7 (1%) | 970 |
0.213 (1.00) |
0.426 (1.00) |
0.861 (1.00) |
0.9 (1.00) |
0.589 (1.00) |
1 (1.00) |
1 (1.00) |
0.702 (1.00) |
1 (1.00) |
0.761 (1.00) |
1 (1.00) |
1 (1.00) |
IRS4 | 11 (1%) | 966 |
0.884 (1.00) |
0.289 (1.00) |
0.0731 (0.936) |
0.784 (1.00) |
0.047 (0.849) |
0.172 (1.00) |
1 (1.00) |
0.188 (1.00) |
0.551 (1.00) |
0.497 (1.00) |
0.359 (1.00) |
1 (1.00) |
NLGN3 | 11 (1%) | 966 |
0.721 (1.00) |
0.123 (1.00) |
0.354 (1.00) |
0.189 (1.00) |
0.707 (1.00) |
1 (1.00) |
1 (1.00) |
0.754 (1.00) |
0.747 (1.00) |
0.99 (1.00) |
0.132 (1.00) |
0.323 (1.00) |
IL1RAP | 9 (1%) | 968 |
0.424 (1.00) |
0.0803 (0.936) |
0.938 (1.00) |
0.514 (1.00) |
0.462 (1.00) |
1 (1.00) |
1 (1.00) |
0.046 (0.849) |
0.875 (1.00) |
0.129 (1.00) |
0.531 (1.00) |
1 (1.00) |
USP36 | 8 (1%) | 969 |
0.463 (1.00) |
0.143 (1.00) |
0.0274 (0.665) |
0.128 (1.00) |
0.573 (1.00) |
1 (1.00) |
1 (1.00) |
0.412 (1.00) |
1 (1.00) |
0.579 (1.00) |
0.477 (1.00) |
1 (1.00) |
CASZ1 | 14 (1%) | 963 |
0.0751 (0.936) |
0.863 (1.00) |
0.827 (1.00) |
0.545 (1.00) |
0.938 (1.00) |
1 (1.00) |
1 (1.00) |
0.575 (1.00) |
0.834 (1.00) |
0.822 (1.00) |
0.616 (1.00) |
1 (1.00) |
EYS | 21 (2%) | 956 |
0.439 (1.00) |
0.0175 (0.503) |
0.731 (1.00) |
0.507 (1.00) |
0.0932 (0.936) |
1 (1.00) |
1 (1.00) |
0.486 (1.00) |
0.0954 (0.936) |
0.142 (1.00) |
0.0112 (0.408) |
1 (1.00) |
KCNN3 | 9 (1%) | 968 |
0.56 (1.00) |
0.718 (1.00) |
0.631 (1.00) |
0.417 (1.00) |
0.513 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.514 (1.00) |
0.251 (1.00) |
0.819 (1.00) |
0.48 (1.00) |
0.293 (1.00) |
ZFP36L1 | 8 (1%) | 969 |
0.541 (1.00) |
0.403 (1.00) |
0.822 (1.00) |
0.907 (1.00) |
0.828 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.513 (1.00) |
0.24 (1.00) |
1 (1.00) |
ICOSLG | 5 (1%) | 972 |
0.742 (1.00) |
0.872 (1.00) |
0.262 (1.00) |
0.72 (1.00) |
0.606 (1.00) |
1 (1.00) |
1 (1.00) |
0.394 (1.00) |
1 (1.00) |
0.635 (1.00) |
0.594 (1.00) |
1 (1.00) |
ACTL6B | 10 (1%) | 967 |
0.667 (1.00) |
0.115 (0.984) |
0.385 (1.00) |
0.155 (1.00) |
0.231 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.527 (1.00) |
0.663 (1.00) |
0.858 (1.00) |
0.524 (1.00) |
1 (1.00) |
MYH9 | 18 (2%) | 959 |
0.504 (1.00) |
0.302 (1.00) |
0.622 (1.00) |
0.865 (1.00) |
0.406 (1.00) |
1 (1.00) |
1 (1.00) |
0.223 (1.00) |
0.222 (1.00) |
0.283 (1.00) |
0.265 (1.00) |
1 (1.00) |
FBXW7 | 15 (2%) | 962 |
0.58 (1.00) |
0.416 (1.00) |
0.564 (1.00) |
0.193 (1.00) |
0.694 (1.00) |
1 (1.00) |
1 (1.00) |
0.6 (1.00) |
0.893 (1.00) |
0.283 (1.00) |
0.0504 (0.854) |
0.406 (1.00) |
FRMPD2 | 13 (1%) | 964 |
0.205 (1.00) |
0.647 (1.00) |
0.354 (1.00) |
0.00977 (0.386) |
0.969 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.203 (1.00) |
0.364 (1.00) |
0.484 (1.00) |
0.352 (1.00) |
ZFP36L2 | 7 (1%) | 970 |
0.345 (1.00) |
0.875 (1.00) |
0.746 (1.00) |
0.9 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.705 (1.00) |
1 (1.00) |
0.426 (1.00) |
0.0963 (0.936) |
0.229 (1.00) |
TPP2 | 8 (1%) | 969 |
0.713 (1.00) |
0.373 (1.00) |
0.476 (1.00) |
1 (1.00) |
0.28 (1.00) |
1 (1.00) |
1 (1.00) |
0.25 (1.00) |
0.429 (1.00) |
0.0403 (0.844) |
0.243 (1.00) |
1 (1.00) |
C17ORF95 | 5 (1%) | 972 |
0.0855 (0.936) |
0.0898 (0.936) |
0.974 (1.00) |
0.507 (1.00) |
1 (1.00) |
1 (1.00) |
0.0453 (0.849) |
0.323 (1.00) |
1 (1.00) |
0.362 (1.00) |
1 (1.00) |
1 (1.00) |
RUFY1 | 6 (1%) | 971 |
0.0159 (0.472) |
0.0148 (0.472) |
0.55 (1.00) |
0.239 (1.00) |
0.823 (1.00) |
1 (1.00) |
1 (1.00) |
0.189 (1.00) |
0.346 (1.00) |
0.293 (1.00) |
0.404 (1.00) |
1 (1.00) |
MED23 | 14 (1%) | 963 |
0.32 (1.00) |
0.0356 (0.784) |
0.238 (1.00) |
0.299 (1.00) |
0.779 (1.00) |
1 (1.00) |
1 (1.00) |
0.165 (1.00) |
0.658 (1.00) |
0.35 (1.00) |
0.326 (1.00) |
1 (1.00) |
PAX2 | 4 (0%) | 973 |
0.143 (1.00) |
0.146 (1.00) |
0.851 (1.00) |
1 (1.00) |
0.843 (1.00) |
1 (1.00) |
1 (1.00) |
0.637 (1.00) |
0.721 (1.00) |
0.208 (1.00) |
1 (1.00) |
1 (1.00) |
MED12 | 21 (2%) | 956 |
0.867 (1.00) |
0.431 (1.00) |
0.724 (1.00) |
0.557 (1.00) |
0.447 (1.00) |
1 (1.00) |
1 (1.00) |
0.475 (1.00) |
0.695 (1.00) |
0.271 (1.00) |
0.0789 (0.936) |
1 (1.00) |
CHD4 | 19 (2%) | 958 |
0.871 (1.00) |
0.706 (1.00) |
0.212 (1.00) |
0.0227 (0.573) |
0.00688 (0.296) |
1 (1.00) |
1 (1.00) |
0.0551 (0.886) |
0.209 (1.00) |
0.98 (1.00) |
0.115 (0.984) |
1 (1.00) |
PFKP | 6 (1%) | 971 |
0.52 (1.00) |
0.227 (1.00) |
0.509 (1.00) |
0.572 (1.00) |
0.563 (1.00) |
1 (1.00) |
1 (1.00) |
0.702 (1.00) |
0.784 (1.00) |
0.0213 (0.56) |
0.733 (1.00) |
1 (1.00) |
RHBG | 4 (0%) | 973 |
0.0288 (0.683) |
0.0495 (0.854) |
0.797 (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 |
0.141 (1.00) |
0.268 (1.00) |
0.223 (1.00) |
0.251 (1.00) |
0.926 (1.00) |
0.14 (1.00) |
1 (1.00) |
0.25 (1.00) |
0.516 (1.00) |
0.665 (1.00) |
0.299 (1.00) |
1 (1.00) |
RIBC1 | 4 (0%) | 973 |
0.774 (1.00) |
0.885 (1.00) |
0.488 (1.00) |
0.526 (1.00) |
0.224 (1.00) |
1 (1.00) |
1 (1.00) |
0.323 (1.00) |
0.72 (1.00) |
0.231 (1.00) |
1 (1.00) |
|
PLK2 | 9 (1%) | 968 |
0.678 (1.00) |
0.154 (1.00) |
0.535 (1.00) |
0.58 (1.00) |
0.539 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.398 (1.00) |
0.678 (1.00) |
0.612 (1.00) |
1 (1.00) |
ANKRD20A4 | 7 (1%) | 970 |
0.479 (1.00) |
0.473 (1.00) |
0.367 (1.00) |
0.234 (1.00) |
0.238 (1.00) |
1 (1.00) |
1 (1.00) |
0.241 (1.00) |
1 (1.00) |
0.065 (0.936) |
1 (1.00) |
1 (1.00) |
PHACTR1 | 7 (1%) | 970 |
0.0418 (0.844) |
0.33 (1.00) |
0.331 (1.00) |
0.255 (1.00) |
0.55 (1.00) |
0.124 (1.00) |
1 (1.00) |
1 (1.00) |
0.682 (1.00) |
0.917 (1.00) |
0.477 (1.00) |
1 (1.00) |
DLG1 | 13 (1%) | 964 |
0.53 (1.00) |
0.521 (1.00) |
0.77 (1.00) |
0.697 (1.00) |
0.626 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0529 (0.879) |
0.211 (1.00) |
0.58 (1.00) |
1 (1.00) |
GPRASP2 | 10 (1%) | 967 |
0.892 (1.00) |
0.184 (1.00) |
0.649 (1.00) |
0.427 (1.00) |
0.651 (1.00) |
0.157 (1.00) |
1 (1.00) |
0.734 (1.00) |
0.786 (1.00) |
0.927 (1.00) |
0.478 (1.00) |
1 (1.00) |
CCDC82 | 6 (1%) | 971 |
0.0898 (0.936) |
0.275 (1.00) |
0.916 (1.00) |
0.884 (1.00) |
0.564 (1.00) |
1 (1.00) |
1 (1.00) |
0.0821 (0.936) |
1 (1.00) |
0.104 (0.968) |
0.0618 (0.93) |
1 (1.00) |
CCDC27 | 7 (1%) | 970 |
0.635 (1.00) |
0.243 (1.00) |
0.885 (1.00) |
0.9 (1.00) |
0.51 (1.00) |
1 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.0414 (0.844) |
0.93 (1.00) |
0.0411 (0.844) |
1 (1.00) |
MAMLD1 | 10 (1%) | 967 |
0.48 (1.00) |
0.114 (0.984) |
0.425 (1.00) |
0.765 (1.00) |
0.239 (1.00) |
1 (1.00) |
1 (1.00) |
0.0846 (0.936) |
0.889 (1.00) |
0.4 (1.00) |
1 (1.00) |
1 (1.00) |
OR8D1 | 5 (1%) | 972 |
0.311 (1.00) |
0.49 (1.00) |
0.841 (1.00) |
0.438 (1.00) |
0.873 (1.00) |
1 (1.00) |
1 (1.00) |
0.658 (1.00) |
0.751 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.159 (1.00) |
P value = 0.00031 (Fisher's exact test), Q value = 0.024
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 711 | 172 | 5 | 6 | 27 | 14 | 40 |
PIK3CA MUTATED | 0 | 216 | 74 | 0 | 0 | 12 | 0 | 14 |
PIK3CA WILD-TYPE | 1 | 495 | 98 | 5 | 6 | 15 | 14 | 26 |
P value = 0.00283 (Wilcoxon-test), Q value = 0.17
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) |
P value = 1e-05 (Fisher's exact test), Q value = 0.0019
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 711 | 172 | 5 | 6 | 27 | 14 | 40 |
TP53 MUTATED | 1 | 261 | 9 | 3 | 4 | 6 | 1 | 10 |
TP53 WILD-TYPE | 0 | 450 | 163 | 2 | 2 | 21 | 13 | 30 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0019
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 |
P value = 3.31e-05 (Fisher's exact test), Q value = 0.0039
nPatients | NO | YES |
---|---|---|
ALL | 387 | 502 |
GATA3 MUTATED | 59 | 33 |
GATA3 WILD-TYPE | 328 | 469 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0019
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 257 | 564 | 120 | 35 |
CDH1 MUTATED | 16 | 56 | 33 | 2 |
CDH1 WILD-TYPE | 241 | 508 | 87 | 33 |
P value = 0.00387 (Fisher's exact test), Q value = 0.2
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 462 | 325 | 107 | 68 |
CDH1 MUTATED | 56 | 27 | 8 | 16 |
CDH1 WILD-TYPE | 406 | 298 | 99 | 52 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0019
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | METAPLASTIC CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER, SPECIFY |
---|---|---|---|---|---|---|---|---|
ALL | 1 | 711 | 172 | 5 | 6 | 27 | 14 | 40 |
CDH1 MUTATED | 0 | 13 | 89 | 1 | 0 | 3 | 0 | 1 |
CDH1 WILD-TYPE | 1 | 698 | 83 | 4 | 6 | 24 | 14 | 39 |
P value = 2.84e-05 (Wilcoxon-test), Q value = 0.0038
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) |
P value = 2.02e-05 (logrank test), Q value = 0.0032
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 964 | 138 | 0.0 - 282.9 (30.8) |
FOXA1 MUTATED | 22 | 7 | 1.0 - 118.6 (20.2) |
FOXA1 WILD-TYPE | 942 | 131 | 0.0 - 282.9 (31.4) |
P value = 8.08e-05 (Wilcoxon-test), Q value = 0.0085
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) |
P value = 0.00103 (Wilcoxon-test), Q value = 0.065
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) |
P value = 1.01e-08 (logrank test), Q value = 9.5e-06
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 964 | 138 | 0.0 - 282.9 (30.8) |
RAB42 MUTATED | 4 | 2 | 9.6 - 24.8 (16.5) |
RAB42 WILD-TYPE | 960 | 136 | 0.0 - 282.9 (31.0) |
P value = 0.00419 (Fisher's exact test), Q value = 0.21
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV | STAGE X |
---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 88 | 71 | 6 | 4 | 326 | 227 | 2 | 137 | 24 | 57 | 15 | 12 |
NBPF9 MUTATED | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 2 | 0 |
NBPF9 WILD-TYPE | 88 | 71 | 6 | 4 | 326 | 226 | 2 | 136 | 23 | 57 | 13 | 12 |
P value = 0.00316 (Fisher's exact test), Q value = 0.18
nPatients | 0 | 1 |
---|---|---|
ALL | 842 | 16 |
NBPF9 MUTATED | 3 | 2 |
NBPF9 WILD-TYPE | 839 | 14 |
P value = 0.000133 (logrank test), Q value = 0.013
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 964 | 138 | 0.0 - 282.9 (30.8) |
SP3 MUTATED | 6 | 3 | 5.7 - 84.6 (19.4) |
SP3 WILD-TYPE | 958 | 135 | 0.0 - 282.9 (31.0) |
P value = 0.00071 (Wilcoxon-test), Q value = 0.052
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) |
P value = 0.000192 (logrank test), Q value = 0.017
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 964 | 138 | 0.0 - 282.9 (30.8) |
LRIG2 MUTATED | 7 | 3 | 5.2 - 63.1 (16.6) |
LRIG2 WILD-TYPE | 957 | 135 | 0.0 - 282.9 (31.0) |
P value = 0.00087 (Fisher's exact test), Q value = 0.059
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 257 | 564 | 120 | 35 |
RHOA MUTATED | 0 | 1 | 4 | 1 |
RHOA WILD-TYPE | 257 | 563 | 116 | 34 |
-
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/22824023/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/BRCA-TP/22506573/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.