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 949 patients, 19 significant findings detected with Q value < 0.25.
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TP53 mutation correlated to 'HISTOLOGICAL.TYPE'.
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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'.
-
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'.
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HRNR mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
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DMXL2 mutation correlated to 'HISTOLOGICAL.TYPE' and 'NUMBER.OF.LYMPH.NODES'.
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MUC5B mutation correlated to 'HISTOLOGICAL.TYPE'.
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XBP1 mutation correlated to 'Time to Death'.
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%) | 853 |
0.145 (1.00) |
0.0116 (1.00) |
0.028 (1.00) |
1.3e-06 (0.000938) |
0.00747 (1.00) |
0.0048 (1.00) |
0.61 (1.00) |
1.51e-69 (1.1e-66) |
0.00907 (1.00) |
0.194 (1.00) |
DMXL2 | 18 (2%) | 931 |
0.727 (1.00) |
0.22 (1.00) |
0.361 (1.00) |
0.0781 (1.00) |
0.0616 (1.00) |
0.792 (1.00) |
0.159 (1.00) |
1.15e-28 (8.32e-26) |
0.304 (1.00) |
2.81e-29 (2.04e-26) |
TP53 | 284 (30%) | 665 |
0.116 (1.00) |
0.00502 (1.00) |
0.246 (1.00) |
0.0225 (1.00) |
0.161 (1.00) |
0.0565 (1.00) |
0.0645 (1.00) |
2.4e-12 (1.74e-09) |
0.0509 (1.00) |
0.868 (1.00) |
MLL3 | 67 (7%) | 882 |
0.203 (1.00) |
4.63e-05 (0.033) |
0.735 (1.00) |
0.638 (1.00) |
0.0746 (1.00) |
0.556 (1.00) |
1 (1.00) |
0.912 (1.00) |
0.577 (1.00) |
0.992 (1.00) |
FAM86B1 | 8 (1%) | 941 |
0.112 (1.00) |
0.0853 (1.00) |
0.89 (1.00) |
0.908 (1.00) |
0.824 (1.00) |
0.341 (1.00) |
1 (1.00) |
0.914 (1.00) |
0.45 (1.00) |
2.3e-07 (0.000166) |
CASP8 | 10 (1%) | 939 |
0.825 (1.00) |
0.574 (1.00) |
0.787 (1.00) |
0.929 (1.00) |
0.355 (1.00) |
1 (1.00) |
1 (1.00) |
0.629 (1.00) |
1 (1.00) |
1.53e-06 (0.0011) |
ASXL2 | 16 (2%) | 933 |
0.00686 (1.00) |
0.264 (1.00) |
0.821 (1.00) |
0.964 (1.00) |
0.138 (1.00) |
1 (1.00) |
1 (1.00) |
0.887 (1.00) |
1 (1.00) |
0.000203 (0.145) |
TRPM5 | 11 (1%) | 938 |
0.629 (1.00) |
0.747 (1.00) |
0.423 (1.00) |
0.742 (1.00) |
0.709 (1.00) |
0.695 (1.00) |
0.00421 (1.00) |
0.0113 (1.00) |
0.192 (1.00) |
4.85e-06 (0.00348) |
PRICKLE3 | 11 (1%) | 938 |
0.904 (1.00) |
0.303 (1.00) |
0.0621 (1.00) |
0.0207 (1.00) |
0.953 (1.00) |
0.206 (1.00) |
1 (1.00) |
0.857 (1.00) |
0.192 (1.00) |
0.000189 (0.134) |
WDR52 | 16 (2%) | 933 |
0.345 (1.00) |
0.393 (1.00) |
0.679 (1.00) |
0.616 (1.00) |
0.191 (1.00) |
0.433 (1.00) |
0.142 (1.00) |
0.756 (1.00) |
1 (1.00) |
9.27e-08 (6.71e-05) |
ERBB3 | 18 (2%) | 931 |
2.24e-05 (0.016) |
0.089 (1.00) |
0.429 (1.00) |
0.0636 (1.00) |
0.469 (1.00) |
1 (1.00) |
1 (1.00) |
0.858 (1.00) |
0.00289 (1.00) |
0.729 (1.00) |
PTHLH | 7 (1%) | 942 |
0.517 (1.00) |
0.254 (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) |
1.11e-41 (8.08e-39) |
HLA-DRB5 | 6 (1%) | 943 |
0.544 (1.00) |
0.227 (1.00) |
0.979 (1.00) |
0.669 (1.00) |
0.468 (1.00) |
1 (1.00) |
1 (1.00) |
0.944 (1.00) |
1 (1.00) |
4.02e-06 (0.00289) |
GYG2 | 8 (1%) | 941 |
0.597 (1.00) |
0.449 (1.00) |
0.425 (1.00) |
0.833 (1.00) |
0.789 (1.00) |
0.66 (1.00) |
1 (1.00) |
0.952 (1.00) |
0.239 (1.00) |
4.31e-06 (0.0031) |
HRNR | 31 (3%) | 918 |
0.146 (1.00) |
0.268 (1.00) |
0.345 (1.00) |
0.126 (1.00) |
0.126 (1.00) |
0.755 (1.00) |
1 (1.00) |
0.926 (1.00) |
0.231 (1.00) |
1.15e-05 (0.00822) |
MUC5B | 32 (3%) | 917 |
0.849 (1.00) |
0.821 (1.00) |
0.066 (1.00) |
0.549 (1.00) |
0.798 (1.00) |
0.407 (1.00) |
1 (1.00) |
3.53e-06 (0.00254) |
1 (1.00) |
0.935 (1.00) |
XBP1 | 4 (0%) | 945 |
5.47e-06 (0.00392) |
0.0268 (1.00) |
0.986 (1.00) |
0.792 (1.00) |
0.381 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.33 (1.00) |
|
PIK3CA | 304 (32%) | 645 |
0.316 (1.00) |
0.028 (1.00) |
0.778 (1.00) |
0.827 (1.00) |
0.858 (1.00) |
0.65 (1.00) |
1 (1.00) |
0.0022 (1.00) |
0.878 (1.00) |
0.503 (1.00) |
CBFB | 23 (2%) | 926 |
0.878 (1.00) |
0.947 (1.00) |
0.787 (1.00) |
0.183 (1.00) |
0.0811 (1.00) |
0.393 (1.00) |
0.199 (1.00) |
0.945 (1.00) |
1 (1.00) |
0.442 (1.00) |
RUNX1 | 29 (3%) | 920 |
0.833 (1.00) |
0.746 (1.00) |
0.567 (1.00) |
0.421 (1.00) |
0.368 (1.00) |
0.863 (1.00) |
1 (1.00) |
0.00161 (1.00) |
0.68 (1.00) |
0.175 (1.00) |
GATA3 | 95 (10%) | 854 |
0.339 (1.00) |
0.0104 (1.00) |
0.34 (1.00) |
0.154 (1.00) |
0.45 (1.00) |
0.142 (1.00) |
1 (1.00) |
0.0423 (1.00) |
0.0748 (1.00) |
0.00116 (0.814) |
FOXA1 | 22 (2%) | 927 |
0.000574 (0.407) |
0.00058 (0.411) |
0.92 (1.00) |
0.311 (1.00) |
0.919 (1.00) |
0.541 (1.00) |
1 (1.00) |
0.00883 (1.00) |
0.152 (1.00) |
0.442 (1.00) |
SF3B1 | 16 (2%) | 933 |
0.305 (1.00) |
0.381 (1.00) |
0.419 (1.00) |
0.636 (1.00) |
0.832 (1.00) |
0.433 (1.00) |
1 (1.00) |
0.942 (1.00) |
1 (1.00) |
0.654 (1.00) |
MAP3K1 | 68 (7%) | 881 |
0.926 (1.00) |
0.00552 (1.00) |
0.717 (1.00) |
0.455 (1.00) |
0.912 (1.00) |
0.358 (1.00) |
1 (1.00) |
0.776 (1.00) |
0.782 (1.00) |
0.0178 (1.00) |
MAP2K4 | 32 (3%) | 917 |
0.715 (1.00) |
0.393 (1.00) |
0.946 (1.00) |
0.297 (1.00) |
0.475 (1.00) |
0.586 (1.00) |
1 (1.00) |
0.228 (1.00) |
0.696 (1.00) |
0.556 (1.00) |
PTEN | 35 (4%) | 914 |
0.971 (1.00) |
0.107 (1.00) |
0.0608 (1.00) |
0.252 (1.00) |
0.527 (1.00) |
0.0569 (1.00) |
1 (1.00) |
0.153 (1.00) |
0.261 (1.00) |
0.439 (1.00) |
TBX3 | 26 (3%) | 923 |
0.332 (1.00) |
0.0302 (1.00) |
0.6 (1.00) |
0.859 (1.00) |
0.601 (1.00) |
0.85 (1.00) |
1 (1.00) |
0.276 (1.00) |
1 (1.00) |
0.497 (1.00) |
RB1 | 19 (2%) | 930 |
0.6 (1.00) |
0.155 (1.00) |
0.459 (1.00) |
0.342 (1.00) |
0.769 (1.00) |
0.401 (1.00) |
0.167 (1.00) |
0.891 (1.00) |
0.306 (1.00) |
0.473 (1.00) |
NCOR1 | 41 (4%) | 908 |
0.656 (1.00) |
0.363 (1.00) |
0.939 (1.00) |
0.557 (1.00) |
0.948 (1.00) |
0.31 (1.00) |
1 (1.00) |
0.659 (1.00) |
0.599 (1.00) |
0.46 (1.00) |
CTCF | 17 (2%) | 932 |
0.118 (1.00) |
0.623 (1.00) |
0.532 (1.00) |
0.184 (1.00) |
0.622 (1.00) |
1 (1.00) |
1 (1.00) |
0.494 (1.00) |
0.421 (1.00) |
0.0335 (1.00) |
GPS2 | 11 (1%) | 938 |
0.457 (1.00) |
0.136 (1.00) |
0.993 (1.00) |
0.108 (1.00) |
0.592 (1.00) |
1 (1.00) |
1 (1.00) |
0.62 (1.00) |
0.739 (1.00) |
0.56 (1.00) |
THEM5 | 11 (1%) | 938 |
0.534 (1.00) |
0.202 (1.00) |
0.643 (1.00) |
0.0375 (1.00) |
0.386 (1.00) |
1 (1.00) |
1 (1.00) |
0.00766 (1.00) |
0.739 (1.00) |
0.367 (1.00) |
RPGR | 17 (2%) | 932 |
0.484 (1.00) |
0.28 (1.00) |
0.903 (1.00) |
0.817 (1.00) |
0.203 (1.00) |
0.587 (1.00) |
1 (1.00) |
0.986 (1.00) |
0.79 (1.00) |
0.00065 (0.459) |
DNAH12 | 17 (2%) | 932 |
0.671 (1.00) |
0.531 (1.00) |
0.916 (1.00) |
0.716 (1.00) |
0.18 (1.00) |
1 (1.00) |
1 (1.00) |
0.639 (1.00) |
0.592 (1.00) |
0.287 (1.00) |
CDKN1B | 9 (1%) | 940 |
0.987 (1.00) |
0.932 (1.00) |
0.183 (1.00) |
0.0339 (1.00) |
0.0138 (1.00) |
0.0681 (1.00) |
1 (1.00) |
0.982 (1.00) |
1 (1.00) |
0.114 (1.00) |
ZFP36L1 | 9 (1%) | 940 |
0.386 (1.00) |
0.381 (1.00) |
0.953 (1.00) |
0.787 (1.00) |
0.895 (1.00) |
1 (1.00) |
1 (1.00) |
0.972 (1.00) |
0.46 (1.00) |
0.0542 (1.00) |
ASB10 | 8 (1%) | 941 |
0.0813 (1.00) |
0.506 (1.00) |
0.929 (1.00) |
0.763 (1.00) |
0.174 (1.00) |
1 (1.00) |
1 (1.00) |
0.164 (1.00) |
1 (1.00) |
0.38 (1.00) |
HIST1H3B | 10 (1%) | 939 |
0.846 (1.00) |
0.0535 (1.00) |
0.531 (1.00) |
0.559 (1.00) |
0.622 (1.00) |
1 (1.00) |
1 (1.00) |
0.956 (1.00) |
0.487 (1.00) |
0.465 (1.00) |
PIK3R1 | 15 (2%) | 934 |
0.0101 (1.00) |
0.302 (1.00) |
0.428 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.305 (1.00) |
1 (1.00) |
0.909 (1.00) |
1 (1.00) |
0.00748 (1.00) |
MYH9 | 19 (2%) | 930 |
0.601 (1.00) |
0.422 (1.00) |
0.73 (1.00) |
0.841 (1.00) |
0.307 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.104 (1.00) |
0.0786 (1.00) |
0.00061 (0.431) |
COL6A5 | 23 (2%) | 926 |
0.353 (1.00) |
0.4 (1.00) |
0.997 (1.00) |
0.899 (1.00) |
0.973 (1.00) |
1 (1.00) |
1 (1.00) |
0.232 (1.00) |
0.642 (1.00) |
0.685 (1.00) |
TBL1XR1 | 10 (1%) | 939 |
0.883 (1.00) |
0.218 (1.00) |
0.379 (1.00) |
0.0879 (1.00) |
0.0291 (1.00) |
0.131 (1.00) |
1 (1.00) |
0.87 (1.00) |
1 (1.00) |
0.309 (1.00) |
ARID1A | 27 (3%) | 922 |
0.514 (1.00) |
0.896 (1.00) |
0.589 (1.00) |
0.355 (1.00) |
0.269 (1.00) |
1 (1.00) |
1 (1.00) |
0.706 (1.00) |
0.667 (1.00) |
0.938 (1.00) |
AQP12A | 6 (1%) | 943 |
0.511 (1.00) |
0.401 (1.00) |
0.999 (1.00) |
0.669 (1.00) |
0.241 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.889 (1.00) |
0.364 (1.00) |
0.925 (1.00) |
EPDR1 | 5 (1%) | 944 |
0.509 (1.00) |
0.463 (1.00) |
0.8 (1.00) |
0.374 (1.00) |
0.245 (1.00) |
1 (1.00) |
1 (1.00) |
0.883 (1.00) |
0.631 (1.00) |
0.76 (1.00) |
ERBB2 | 21 (2%) | 928 |
0.204 (1.00) |
0.117 (1.00) |
0.784 (1.00) |
0.186 (1.00) |
0.0841 (1.00) |
1 (1.00) |
0.183 (1.00) |
0.664 (1.00) |
0.465 (1.00) |
0.53 (1.00) |
MYB | 12 (1%) | 937 |
0.173 (1.00) |
0.135 (1.00) |
0.776 (1.00) |
0.41 (1.00) |
0.965 (1.00) |
0.501 (1.00) |
1 (1.00) |
0.429 (1.00) |
0.344 (1.00) |
0.0115 (1.00) |
TMEM151B | 6 (1%) | 943 |
0.557 (1.00) |
0.659 (1.00) |
0.61 (1.00) |
0.328 (1.00) |
0.564 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.944 (1.00) |
0.19 (1.00) |
0.000693 (0.489) |
GALNTL6 | 5 (1%) | 944 |
0.465 (1.00) |
0.189 (1.00) |
0.999 (1.00) |
1 (1.00) |
0.606 (1.00) |
1 (1.00) |
1 (1.00) |
0.941 (1.00) |
0.149 (1.00) |
0.251 (1.00) |
AKD1 | 18 (2%) | 931 |
0.709 (1.00) |
0.16 (1.00) |
0.736 (1.00) |
0.792 (1.00) |
0.593 (1.00) |
0.609 (1.00) |
1 (1.00) |
0.748 (1.00) |
0.304 (1.00) |
0.154 (1.00) |
AARS | 9 (1%) | 940 |
0.592 (1.00) |
0.299 (1.00) |
0.983 (1.00) |
0.129 (1.00) |
0.731 (1.00) |
0.668 (1.00) |
1 (1.00) |
0.972 (1.00) |
0.724 (1.00) |
0.298 (1.00) |
HLA-C | 9 (1%) | 940 |
0.607 (1.00) |
0.166 (1.00) |
0.957 (1.00) |
0.224 (1.00) |
0.895 (1.00) |
0.392 (1.00) |
1 (1.00) |
0.982 (1.00) |
0.724 (1.00) |
0.256 (1.00) |
GPRIN2 | 11 (1%) | 938 |
0.936 (1.00) |
0.304 (1.00) |
0.933 (1.00) |
0.935 (1.00) |
0.333 (1.00) |
0.695 (1.00) |
1 (1.00) |
0.337 (1.00) |
0.739 (1.00) |
0.194 (1.00) |
ANKRD12 | 17 (2%) | 932 |
0.285 (1.00) |
0.178 (1.00) |
0.963 (1.00) |
0.586 (1.00) |
0.647 (1.00) |
0.36 (1.00) |
1 (1.00) |
0.809 (1.00) |
0.421 (1.00) |
0.000375 (0.266) |
FBXW7 | 15 (2%) | 934 |
0.717 (1.00) |
0.407 (1.00) |
0.707 (1.00) |
0.193 (1.00) |
0.639 (1.00) |
0.766 (1.00) |
1 (1.00) |
0.87 (1.00) |
1 (1.00) |
0.00166 (1.00) |
CDC42EP1 | 4 (0%) | 945 |
0.394 (1.00) |
0.576 (1.00) |
0.00437 (1.00) |
1 (1.00) |
0.44 (1.00) |
1 (1.00) |
1 (1.00) |
0.966 (1.00) |
1 (1.00) |
0.31 (1.00) |
FHOD3 | 13 (1%) | 936 |
0.143 (1.00) |
0.0782 (1.00) |
0.997 (1.00) |
0.493 (1.00) |
0.78 (1.00) |
0.729 (1.00) |
0.117 (1.00) |
0.806 (1.00) |
0.538 (1.00) |
0.0533 (1.00) |
SHISA4 | 5 (1%) | 944 |
0.471 (1.00) |
0.872 (1.00) |
0.994 (1.00) |
0.505 (1.00) |
0.521 (1.00) |
0.51 (1.00) |
1 (1.00) |
0.997 (1.00) |
0.631 (1.00) |
0.151 (1.00) |
KCNN3 | 9 (1%) | 940 |
0.164 (1.00) |
0.549 (1.00) |
0.81 (1.00) |
0.417 (1.00) |
0.513 (1.00) |
0.163 (1.00) |
1 (1.00) |
0.596 (1.00) |
1 (1.00) |
0.0688 (1.00) |
FGFR2 | 10 (1%) | 939 |
0.163 (1.00) |
0.386 (1.00) |
0.561 (1.00) |
0.0149 (1.00) |
0.697 (1.00) |
0.441 (1.00) |
0.0913 (1.00) |
0.85 (1.00) |
1 (1.00) |
0.00186 (1.00) |
ICOSLG | 6 (1%) | 943 |
0.473 (1.00) |
0.126 (1.00) |
0.625 (1.00) |
0.88 (1.00) |
0.738 (1.00) |
0.576 (1.00) |
1 (1.00) |
0.944 (1.00) |
1 (1.00) |
0.735 (1.00) |
PPEF1 | 11 (1%) | 938 |
0.0382 (1.00) |
0.489 (1.00) |
0.997 (1.00) |
1 (1.00) |
0.371 (1.00) |
1 (1.00) |
1 (1.00) |
0.934 (1.00) |
0.525 (1.00) |
0.0776 (1.00) |
MAP4K1 | 10 (1%) | 939 |
0.449 (1.00) |
0.943 (1.00) |
0.93 (1.00) |
0.529 (1.00) |
0.341 (1.00) |
1 (1.00) |
1 (1.00) |
0.956 (1.00) |
0.732 (1.00) |
0.526 (1.00) |
ZNF41 | 11 (1%) | 938 |
0.483 (1.00) |
0.839 (1.00) |
0.933 (1.00) |
0.667 (1.00) |
0.571 (1.00) |
0.488 (1.00) |
1 (1.00) |
0.978 (1.00) |
0.739 (1.00) |
0.393 (1.00) |
FBXO17 | 5 (1%) | 944 |
0.00264 (1.00) |
0.636 (1.00) |
0.981 (1.00) |
0.505 (1.00) |
0.163 (1.00) |
0.184 (1.00) |
1 (1.00) |
0.997 (1.00) |
1 (1.00) |
0.611 (1.00) |
STAG2 | 13 (1%) | 936 |
0.0165 (1.00) |
0.042 (1.00) |
0.831 (1.00) |
0.951 (1.00) |
0.922 (1.00) |
0.254 (1.00) |
1 (1.00) |
0.597 (1.00) |
0.538 (1.00) |
0.735 (1.00) |
CEP57 | 4 (0%) | 945 |
0.23 (1.00) |
0.207 (1.00) |
0.951 (1.00) |
0.523 (1.00) |
0.139 (1.00) |
0.435 (1.00) |
1 (1.00) |
0.966 (1.00) |
0.584 (1.00) |
0.88 (1.00) |
SPRR2B | 3 (0%) | 946 |
0.715 (1.00) |
0.369 (1.00) |
0.998 (1.00) |
0.731 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.984 (1.00) |
1 (1.00) |
0.0115 (1.00) |
ZFP36L2 | 7 (1%) | 942 |
0.428 (1.00) |
0.929 (1.00) |
0.984 (1.00) |
0.901 (1.00) |
0.928 (1.00) |
1 (1.00) |
1 (1.00) |
0.992 (1.00) |
0.112 (1.00) |
0.00669 (1.00) |
ZBTB7C | 5 (1%) | 944 |
0.541 (1.00) |
0.687 (1.00) |
0.958 (1.00) |
1 (1.00) |
0.168 (1.00) |
1 (1.00) |
1 (1.00) |
0.486 (1.00) |
0.329 (1.00) |
0.946 (1.00) |
FXYD5 | 4 (0%) | 945 |
0.767 (1.00) |
0.931 (1.00) |
0.872 (1.00) |
0.149 (1.00) |
0.842 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
1 (1.00) |
0.0115 (1.00) |
ATXN2 | 15 (2%) | 934 |
0.614 (1.00) |
0.121 (1.00) |
0.965 (1.00) |
0.573 (1.00) |
0.692 (1.00) |
1 (1.00) |
1 (1.00) |
0.983 (1.00) |
0.573 (1.00) |
0.553 (1.00) |
CCL13 | 4 (0%) | 945 |
0.351 (1.00) |
0.161 (1.00) |
0.979 (1.00) |
0.65 (1.00) |
0.842 (1.00) |
1 (1.00) |
1 (1.00) |
0.741 (1.00) |
0.584 (1.00) |
0.0115 (1.00) |
P value = 2.4e-12 (Chi-square test), Q value = 1.7e-09
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 703 | 154 | 5 | 28 | 14 | 43 |
TP53 MUTATED | 1 | 251 | 8 | 3 | 5 | 1 | 14 |
TP53 WILD-TYPE | 0 | 452 | 146 | 2 | 23 | 13 | 29 |
P value = 1.3e-06 (Fisher's exact test), Q value = 0.00094
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 252 | 549 | 111 | 35 |
CDH1 MUTATED | 15 | 50 | 29 | 2 |
CDH1 WILD-TYPE | 237 | 499 | 82 | 33 |
P value = 1.51e-69 (Chi-square test), Q value = 1.1e-66
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 703 | 154 | 5 | 28 | 14 | 43 |
CDH1 MUTATED | 0 | 14 | 78 | 1 | 3 | 0 | 0 |
CDH1 WILD-TYPE | 1 | 689 | 76 | 4 | 25 | 14 | 43 |
P value = 4.63e-05 (t-test), Q value = 0.033
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 936 | 58.7 (13.1) |
MLL3 MUTATED | 67 | 65.3 (13.0) |
MLL3 WILD-TYPE | 869 | 58.2 (13.0) |
P value = 2.3e-07 (t-test), Q value = 0.00017
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
FAM86B1 MUTATED | 8 | 0.5 (0.5) |
FAM86B1 WILD-TYPE | 788 | 2.4 (4.6) |
P value = 1.53e-06 (t-test), Q value = 0.0011
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
CASP8 MUTATED | 9 | 0.3 (0.7) |
CASP8 WILD-TYPE | 787 | 2.4 (4.6) |
P value = 0.000203 (t-test), Q value = 0.14
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
ASXL2 MUTATED | 11 | 0.7 (1.0) |
ASXL2 WILD-TYPE | 785 | 2.4 (4.6) |
P value = 4.85e-06 (t-test), Q value = 0.0035
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
TRPM5 MUTATED | 9 | 0.4 (0.7) |
TRPM5 WILD-TYPE | 787 | 2.4 (4.6) |
P value = 0.000189 (t-test), Q value = 0.13
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
PRICKLE3 MUTATED | 7 | 0.4 (0.8) |
PRICKLE3 WILD-TYPE | 789 | 2.4 (4.6) |
P value = 9.27e-08 (t-test), Q value = 6.7e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
WDR52 MUTATED | 12 | 0.3 (0.8) |
WDR52 WILD-TYPE | 784 | 2.4 (4.6) |
P value = 2.24e-05 (logrank test), Q value = 0.016
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 928 | 110 | 0.0 - 234.3 (21.6) |
ERBB3 MUTATED | 15 | 7 | 0.3 - 97.5 (18.8) |
ERBB3 WILD-TYPE | 913 | 103 | 0.0 - 234.3 (21.6) |
P value = 1.11e-41 (t-test), Q value = 8.1e-39
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
PTHLH MUTATED | 4 | 0.0 (0.0) |
PTHLH WILD-TYPE | 792 | 2.4 (4.6) |
P value = 4.02e-06 (t-test), Q value = 0.0029
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
HLA-DRB5 MUTATED | 5 | 0.2 (0.4) |
HLA-DRB5 WILD-TYPE | 791 | 2.4 (4.6) |
P value = 4.31e-06 (t-test), Q value = 0.0031
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
GYG2 MUTATED | 6 | 0.3 (0.5) |
GYG2 WILD-TYPE | 790 | 2.4 (4.6) |
P value = 1.15e-05 (t-test), Q value = 0.0082
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
HRNR MUTATED | 29 | 1.0 (1.2) |
HRNR WILD-TYPE | 767 | 2.4 (4.7) |
P value = 1.15e-28 (Chi-square test), Q value = 8.3e-26
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 703 | 154 | 5 | 28 | 14 | 43 |
DMXL2 MUTATED | 1 | 9 | 3 | 3 | 1 | 0 | 1 |
DMXL2 WILD-TYPE | 0 | 694 | 151 | 2 | 27 | 14 | 42 |
P value = 2.81e-29 (t-test), Q value = 2e-26
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 796 | 2.3 (4.6) |
DMXL2 MUTATED | 13 | 0.1 (0.3) |
DMXL2 WILD-TYPE | 783 | 2.4 (4.6) |
P value = 3.53e-06 (Chi-square test), Q value = 0.0025
nPatients | INFILTRATING CARCINOMA NOS | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|---|
ALL | 1 | 703 | 154 | 5 | 28 | 14 | 43 |
MUC5B MUTATED | 1 | 23 | 5 | 0 | 1 | 2 | 0 |
MUC5B WILD-TYPE | 0 | 680 | 149 | 5 | 27 | 12 | 43 |
P value = 5.47e-06 (logrank test), Q value = 0.0039
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 928 | 110 | 0.0 - 234.3 (21.6) |
XBP1 MUTATED | 4 | 2 | 0.1 - 51.2 (1.7) |
XBP1 WILD-TYPE | 924 | 108 | 0.0 - 234.3 (21.6) |
-
Mutation data file = transformed.cor.cli.txt
-
Clinical data file = BRCA-TP.merged_data.txt
-
Number of patients = 949
-
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.
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.