This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 81 genes and 10 clinical features across 771 patients, 19 significant findings detected with Q value < 0.25.
-
ZNF384 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
DCP1B mutation correlated to 'NEOPLASM.DISEASESTAGE'.
-
PIK3R1 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
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'.
-
CCDC144NL mutation correlated to 'Time to Death'.
-
AQP7 mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
CDKN1B mutation correlated to 'LYMPH.NODE.METASTASIS'.
-
CASP8 mutation correlated to 'NUMBER.OF.LYMPH.NODES'.
-
CTU2 mutation correlated to 'HISTOLOGICAL.TYPE' and 'NEOPLASM.DISEASESTAGE'.
-
HLA-A mutation correlated to 'HISTOLOGICAL.TYPE' and 'LYMPH.NODE.METASTASIS'.
-
ODF1 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
KRT38 mutation correlated to 'LYMPH.NODE.METASTASIS'.
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ASXL2 mutation correlated to 'LYMPH.NODE.METASTASIS' and 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE | GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
NEOPLASM DISEASESTAGE |
||
nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | Chi-square test | t-test | t-test | Chi-square test | |
CTU2 | 5 (1%) | 766 |
0.556 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.000114 (0.0809) |
0.335 (1.00) |
1 (1.00) |
0.946 (1.00) |
0.058 (1.00) |
1.58e-09 (1.14e-06) |
|
HLA-A | 4 (1%) | 767 |
0.211 (1.00) |
0.437 (1.00) |
1 (1.00) |
9.35e-06 (0.0067) |
0.275 (1.00) |
1 (1.00) |
2.91e-33 (2.11e-30) |
0.585 (1.00) |
0.807 (1.00) |
|
ASXL2 | 8 (1%) | 763 |
0.906 (1.00) |
0.947 (1.00) |
1 (1.00) |
0.969 (1.00) |
0.432 (1.00) |
1 (1.00) |
7.73e-07 (0.000556) |
7.01e-05 (0.0498) |
0.978 (1.00) |
|
ZNF384 | 14 (2%) | 757 |
0.408 (1.00) |
0.0127 (1.00) |
1 (1.00) |
0.916 (1.00) |
1 (1.00) |
0.453 (1.00) |
0.964 (1.00) |
1.16e-05 (0.00832) |
0.444 (1.00) |
|
DCP1B | 5 (1%) | 766 |
0.55 (1.00) |
0.025 (1.00) |
1 (1.00) |
0.936 (1.00) |
0.335 (1.00) |
0.375 (1.00) |
0.512 (1.00) |
0.44 (1.00) |
1.08e-07 (7.79e-05) |
|
PIK3R1 | 21 (3%) | 750 |
0.174 (1.00) |
0.686 (1.00) |
1 (1.00) |
0.842 (1.00) |
0.801 (1.00) |
0.484 (1.00) |
5.69e-05 (0.0404) |
0.0805 (1.00) |
0.286 (1.00) |
|
GATA3 | 81 (11%) | 690 |
0.739 (1.00) |
0.000217 (0.154) |
0.59 (1.00) |
0.147 (1.00) |
0.139 (1.00) |
0.0979 (1.00) |
0.781 (1.00) |
0.598 (1.00) |
0.22 (1.00) |
|
TP53 | 257 (33%) | 514 |
0.456 (1.00) |
0.0384 (1.00) |
0.0574 (1.00) |
1.03e-06 (0.000737) |
0.433 (1.00) |
0.0552 (1.00) |
0.379 (1.00) |
0.414 (1.00) |
0.732 (1.00) |
|
CDH1 | 55 (7%) | 716 |
0.418 (1.00) |
0.0861 (1.00) |
1 (1.00) |
3.17e-69 (2.3e-66) |
1 (1.00) |
0.799 (1.00) |
0.0257 (1.00) |
0.129 (1.00) |
0.134 (1.00) |
|
MAP3K1 | 57 (7%) | 714 |
0.782 (1.00) |
0.00183 (1.00) |
1 (1.00) |
0.612 (1.00) |
0.753 (1.00) |
0.565 (1.00) |
0.103 (1.00) |
7.24e-07 (0.000522) |
0.679 (1.00) |
|
CCDC144NL | 8 (1%) | 763 |
5.2e-05 (0.037) |
0.0508 (1.00) |
1 (1.00) |
0.969 (1.00) |
0.121 (1.00) |
1 (1.00) |
0.41 (1.00) |
0.296 (1.00) |
0.448 (1.00) |
|
AQP7 | 8 (1%) | 763 |
0.0123 (1.00) |
0.661 (1.00) |
1 (1.00) |
0.969 (1.00) |
0.215 (1.00) |
1 (1.00) |
1.7e-06 (0.00122) |
0.196 (1.00) |
0.786 (1.00) |
|
CDKN1B | 7 (1%) | 764 |
0.848 (1.00) |
0.945 (1.00) |
1 (1.00) |
0.967 (1.00) |
1 (1.00) |
0.0221 (1.00) |
4.09e-05 (0.0293) |
0.0478 (1.00) |
0.0512 (1.00) |
|
CASP8 | 10 (1%) | 761 |
0.93 (1.00) |
0.581 (1.00) |
1 (1.00) |
0.714 (1.00) |
0.467 (1.00) |
0.611 (1.00) |
0.896 (1.00) |
5.57e-05 (0.0396) |
0.753 (1.00) |
|
ODF1 | 5 (1%) | 766 |
0.722 (1.00) |
0.569 (1.00) |
1 (1.00) |
4.38e-05 (0.0313) |
0.608 (1.00) |
0.0751 (1.00) |
0.698 (1.00) |
0.966 (1.00) |
0.592 (1.00) |
|
KRT38 | 4 (1%) | 767 |
0.5 (1.00) |
0.242 (1.00) |
1 (1.00) |
0.975 (1.00) |
0.275 (1.00) |
1 (1.00) |
7.55e-15 (5.47e-12) |
0.0539 (1.00) |
0.991 (1.00) |
|
PTEN | 29 (4%) | 742 |
0.889 (1.00) |
0.458 (1.00) |
1 (1.00) |
0.554 (1.00) |
0.83 (1.00) |
0.0618 (1.00) |
0.387 (1.00) |
0.221 (1.00) |
0.0208 (1.00) |
|
MLL3 | 56 (7%) | 715 |
0.525 (1.00) |
0.0118 (1.00) |
1 (1.00) |
0.917 (1.00) |
0.752 (1.00) |
0.418 (1.00) |
0.317 (1.00) |
0.918 (1.00) |
0.862 (1.00) |
|
PIK3CA | 261 (34%) | 510 |
0.92 (1.00) |
0.0233 (1.00) |
1 (1.00) |
0.0217 (1.00) |
0.862 (1.00) |
0.357 (1.00) |
0.437 (1.00) |
0.339 (1.00) |
0.479 (1.00) |
|
NCOA3 | 29 (4%) | 742 |
0.464 (1.00) |
0.875 (1.00) |
1 (1.00) |
0.514 (1.00) |
0.667 (1.00) |
0.142 (1.00) |
0.221 (1.00) |
0.177 (1.00) |
0.478 (1.00) |
|
AOAH | 19 (2%) | 752 |
0.283 (1.00) |
0.425 (1.00) |
1 (1.00) |
0.791 (1.00) |
0.0353 (1.00) |
0.276 (1.00) |
0.916 (1.00) |
0.282 (1.00) |
0.187 (1.00) |
|
RBMX | 13 (2%) | 758 |
0.65 (1.00) |
0.874 (1.00) |
1 (1.00) |
0.792 (1.00) |
0.337 (1.00) |
1 (1.00) |
0.95 (1.00) |
0.241 (1.00) |
0.972 (1.00) |
|
RUNX1 | 25 (3%) | 746 |
0.45 (1.00) |
0.603 (1.00) |
1 (1.00) |
0.053 (1.00) |
0.353 (1.00) |
1 (1.00) |
0.884 (1.00) |
0.532 (1.00) |
0.103 (1.00) |
|
MEF2A | 14 (2%) | 757 |
0.788 (1.00) |
0.522 (1.00) |
1 (1.00) |
0.0174 (1.00) |
0.537 (1.00) |
0.719 (1.00) |
0.758 (1.00) |
0.0142 (1.00) |
0.436 (1.00) |
|
NCOR2 | 29 (4%) | 742 |
0.815 (1.00) |
0.709 (1.00) |
1 (1.00) |
0.864 (1.00) |
1 (1.00) |
0.375 (1.00) |
0.93 (1.00) |
0.218 (1.00) |
0.957 (1.00) |
|
AKT1 | 19 (2%) | 752 |
0.196 (1.00) |
0.133 (1.00) |
1 (1.00) |
0.984 (1.00) |
0.183 (1.00) |
0.597 (1.00) |
0.0405 (1.00) |
0.902 (1.00) |
0.541 (1.00) |
|
NR1H2 | 18 (2%) | 753 |
0.557 (1.00) |
0.714 (1.00) |
1 (1.00) |
0.819 (1.00) |
1 (1.00) |
0.00281 (1.00) |
0.641 (1.00) |
0.954 (1.00) |
0.0163 (1.00) |
|
MAP3K4 | 18 (2%) | 753 |
0.989 (1.00) |
0.542 (1.00) |
1 (1.00) |
0.755 (1.00) |
0.585 (1.00) |
0.00145 (1.00) |
0.854 (1.00) |
0.912 (1.00) |
0.808 (1.00) |
|
TPRX1 | 7 (1%) | 764 |
0.695 (1.00) |
0.123 (1.00) |
1 (1.00) |
0.00174 (1.00) |
1 (1.00) |
0.483 (1.00) |
0.977 (1.00) |
0.205 (1.00) |
0.805 (1.00) |
|
ATN1 | 17 (2%) | 754 |
0.293 (1.00) |
0.959 (1.00) |
1 (1.00) |
0.727 (1.00) |
0.264 (1.00) |
0.104 (1.00) |
0.988 (1.00) |
0.609 (1.00) |
0.834 (1.00) |
|
MAP2K4 | 32 (4%) | 739 |
0.181 (1.00) |
0.386 (1.00) |
1 (1.00) |
0.526 (1.00) |
0.685 (1.00) |
0.647 (1.00) |
0.334 (1.00) |
0.911 (1.00) |
0.987 (1.00) |
|
CBFB | 16 (2%) | 755 |
0.968 (1.00) |
0.725 (1.00) |
1 (1.00) |
0.606 (1.00) |
1 (1.00) |
0.203 (1.00) |
0.473 (1.00) |
0.821 (1.00) |
0.916 (1.00) |
|
CTCF | 18 (2%) | 753 |
0.117 (1.00) |
0.931 (1.00) |
1 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.571 (1.00) |
0.991 (1.00) |
0.0498 (1.00) |
0.361 (1.00) |
|
AKD1 | 19 (2%) | 752 |
0.808 (1.00) |
0.469 (1.00) |
1 (1.00) |
0.0661 (1.00) |
0.794 (1.00) |
0.276 (1.00) |
0.372 (1.00) |
0.437 (1.00) |
0.708 (1.00) |
|
RB1 | 14 (2%) | 757 |
0.881 (1.00) |
0.12 (1.00) |
0.137 (1.00) |
0.911 (1.00) |
0.131 (1.00) |
0.719 (1.00) |
0.0714 (1.00) |
0.459 (1.00) |
0.00169 (1.00) |
|
PHLDA1 | 9 (1%) | 762 |
0.788 (1.00) |
0.752 (1.00) |
1 (1.00) |
0.676 (1.00) |
0.46 (1.00) |
0.198 (1.00) |
0.908 (1.00) |
0.000817 (0.575) |
0.249 (1.00) |
|
FOXA1 | 15 (2%) | 756 |
0.0781 (1.00) |
0.00249 (1.00) |
1 (1.00) |
0.00917 (1.00) |
0.377 (1.00) |
0.484 (1.00) |
0.99 (1.00) |
0.833 (1.00) |
0.0955 (1.00) |
|
VEZF1 | 8 (1%) | 763 |
0.581 (1.00) |
0.0879 (1.00) |
1 (1.00) |
0.891 (1.00) |
0.432 (1.00) |
0.529 (1.00) |
0.995 (1.00) |
0.0425 (1.00) |
0.943 (1.00) |
|
ZFP36L1 | 10 (1%) | 761 |
0.981 (1.00) |
0.0124 (1.00) |
1 (1.00) |
0.962 (1.00) |
0.0718 (1.00) |
0.222 (1.00) |
0.943 (1.00) |
0.41 (1.00) |
0.668 (1.00) |
|
NCOR1 | 31 (4%) | 740 |
0.879 (1.00) |
0.934 (1.00) |
1 (1.00) |
0.265 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.82 (1.00) |
0.462 (1.00) |
0.878 (1.00) |
|
TBX3 | 18 (2%) | 753 |
0.185 (1.00) |
0.0154 (1.00) |
1 (1.00) |
0.669 (1.00) |
1 (1.00) |
0.571 (1.00) |
0.989 (1.00) |
0.472 (1.00) |
0.673 (1.00) |
|
DSPP | 26 (3%) | 745 |
0.868 (1.00) |
0.166 (1.00) |
1 (1.00) |
0.957 (1.00) |
1 (1.00) |
1 (1.00) |
0.479 (1.00) |
0.375 (1.00) |
0.839 (1.00) |
|
BCL6B | 8 (1%) | 763 |
0.607 (1.00) |
0.749 (1.00) |
1 (1.00) |
0.812 (1.00) |
0.121 (1.00) |
0.0408 (1.00) |
0.824 (1.00) |
0.805 (1.00) |
0.938 (1.00) |
|
RPGR | 14 (2%) | 757 |
0.869 (1.00) |
0.459 (1.00) |
1 (1.00) |
0.859 (1.00) |
1 (1.00) |
0.318 (1.00) |
0.88 (1.00) |
0.856 (1.00) |
0.892 (1.00) |
|
TBL1XR1 | 9 (1%) | 762 |
0.565 (1.00) |
0.0223 (1.00) |
1 (1.00) |
0.691 (1.00) |
0.702 (1.00) |
0.198 (1.00) |
0.413 (1.00) |
0.454 (1.00) |
0.447 (1.00) |
|
MYB | 11 (1%) | 760 |
0.176 (1.00) |
0.18 (1.00) |
1 (1.00) |
0.25 (1.00) |
0.487 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.0364 (1.00) |
0.758 (1.00) |
|
PABPC3 | 8 (1%) | 763 |
0.302 (1.00) |
0.941 (1.00) |
0.0804 (1.00) |
0.655 (1.00) |
1 (1.00) |
1 (1.00) |
0.973 (1.00) |
0.164 (1.00) |
0.885 (1.00) |
|
GPS2 | 6 (1%) | 765 |
0.219 (1.00) |
0.966 (1.00) |
1 (1.00) |
0.695 (1.00) |
0.651 (1.00) |
1 (1.00) |
0.36 (1.00) |
0.638 (1.00) |
0.109 (1.00) |
|
E2F4 | 4 (1%) | 767 |
0.366 (1.00) |
1 (1.00) |
0.492 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.987 (1.00) |
0.982 (1.00) |
|||
DNAH12 | 12 (2%) | 759 |
0.81 (1.00) |
0.98 (1.00) |
1 (1.00) |
0.944 (1.00) |
0.518 (1.00) |
0.678 (1.00) |
0.886 (1.00) |
0.86 (1.00) |
0.881 (1.00) |
|
HNF1A | 9 (1%) | 762 |
0.538 (1.00) |
0.205 (1.00) |
1 (1.00) |
0.00855 (1.00) |
0.247 (1.00) |
0.0654 (1.00) |
0.99 (1.00) |
0.636 (1.00) |
0.98 (1.00) |
|
CRIPAK | 6 (1%) | 765 |
0.496 (1.00) |
0.473 (1.00) |
1 (1.00) |
0.939 (1.00) |
1 (1.00) |
1 (1.00) |
0.86 (1.00) |
0.00491 (1.00) |
0.82 (1.00) |
|
STXBP2 | 9 (1%) | 762 |
0.251 (1.00) |
0.0464 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.702 (1.00) |
1 (1.00) |
0.995 (1.00) |
0.935 (1.00) |
0.7 (1.00) |
|
CCDC66 | 9 (1%) | 762 |
0.695 (1.00) |
0.752 (1.00) |
1 (1.00) |
0.705 (1.00) |
0.702 (1.00) |
0.572 (1.00) |
0.809 (1.00) |
0.772 (1.00) |
0.749 (1.00) |
|
HIST1H3B | 7 (1%) | 764 |
0.395 (1.00) |
0.285 (1.00) |
1 (1.00) |
0.916 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.875 (1.00) |
0.452 (1.00) |
0.805 (1.00) |
|
TTN | 122 (16%) | 649 |
0.0569 (1.00) |
0.00748 (1.00) |
0.369 (1.00) |
0.372 (1.00) |
0.91 (1.00) |
0.607 (1.00) |
0.949 (1.00) |
0.399 (1.00) |
0.0262 (1.00) |
|
SLC25A5 | 3 (0%) | 768 |
0.521 (1.00) |
1 (1.00) |
0.112 (1.00) |
0.573 (1.00) |
0.245 (1.00) |
0.948 (1.00) |
0.932 (1.00) |
0.999 (1.00) |
||
SELPLG | 7 (1%) | 764 |
0.662 (1.00) |
0.266 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.383 (1.00) |
0.134 (1.00) |
0.71 (1.00) |
0.000817 (0.575) |
0.795 (1.00) |
|
KRTAP9-9 | 6 (1%) | 765 |
0.595 (1.00) |
0.408 (1.00) |
1 (1.00) |
0.381 (1.00) |
0.182 (1.00) |
0.431 (1.00) |
0.98 (1.00) |
0.293 (1.00) |
0.93 (1.00) |
|
KRTAP4-5 | 4 (1%) | 767 |
0.596 (1.00) |
0.194 (1.00) |
1 (1.00) |
0.264 (1.00) |
0.275 (1.00) |
0.313 (1.00) |
0.972 (1.00) |
0.466 (1.00) |
0.905 (1.00) |
|
SF3B1 | 14 (2%) | 757 |
0.291 (1.00) |
0.74 (1.00) |
1 (1.00) |
0.862 (1.00) |
0.369 (1.00) |
0.719 (1.00) |
0.982 (1.00) |
0.778 (1.00) |
0.298 (1.00) |
|
FGFR2 | 7 (1%) | 764 |
0.000464 (0.327) |
0.751 (1.00) |
1 (1.00) |
0.627 (1.00) |
0.684 (1.00) |
0.134 (1.00) |
0.789 (1.00) |
0.0471 (1.00) |
0.755 (1.00) |
|
SHROOM4 | 11 (1%) | 760 |
0.302 (1.00) |
0.619 (1.00) |
0.109 (1.00) |
0.804 (1.00) |
0.163 (1.00) |
0.353 (1.00) |
0.894 (1.00) |
0.72 (1.00) |
0.933 (1.00) |
|
MED12 | 20 (3%) | 751 |
0.607 (1.00) |
0.777 (1.00) |
1 (1.00) |
0.989 (1.00) |
0.313 (1.00) |
0.366 (1.00) |
0.959 (1.00) |
0.489 (1.00) |
0.669 (1.00) |
|
DENND4B | 8 (1%) | 763 |
0.546 (1.00) |
0.734 (1.00) |
1 (1.00) |
0.00359 (1.00) |
1 (1.00) |
0.529 (1.00) |
0.998 (1.00) |
0.806 (1.00) |
0.925 (1.00) |
|
AXL | 6 (1%) | 765 |
0.438 (1.00) |
0.734 (1.00) |
1 (1.00) |
0.00305 (1.00) |
0.347 (1.00) |
0.431 (1.00) |
0.635 (1.00) |
0.447 (1.00) |
0.614 (1.00) |
|
RPL18 | 4 (1%) | 767 |
0.794 (1.00) |
0.857 (1.00) |
1 (1.00) |
0.492 (1.00) |
0.275 (1.00) |
1 (1.00) |
0.767 (1.00) |
0.027 (1.00) |
0.751 (1.00) |
|
RAI1 | 7 (1%) | 764 |
0.679 (1.00) |
0.917 (1.00) |
1 (1.00) |
0.967 (1.00) |
0.383 (1.00) |
1 (1.00) |
0.963 (1.00) |
0.0482 (1.00) |
0.38 (1.00) |
|
ERBB2 | 12 (2%) | 759 |
0.139 (1.00) |
0.542 (1.00) |
0.118 (1.00) |
0.383 (1.00) |
0.74 (1.00) |
1 (1.00) |
0.976 (1.00) |
0.522 (1.00) |
0.932 (1.00) |
|
TICAM1 | 5 (1%) | 766 |
0.563 (1.00) |
0.54 (1.00) |
1 (1.00) |
0.959 (1.00) |
0.608 (1.00) |
0.0751 (1.00) |
0.0376 (1.00) |
0.724 (1.00) |
0.0683 (1.00) |
|
ASPHD1 | 3 (0%) | 768 |
0.0443 (1.00) |
0.782 (1.00) |
1 (1.00) |
0.288 (1.00) |
0.573 (1.00) |
1 (1.00) |
0.879 (1.00) |
0.727 (1.00) |
0.966 (1.00) |
|
FAM171B | 8 (1%) | 763 |
0.745 (1.00) |
0.00375 (1.00) |
0.0804 (1.00) |
0.891 (1.00) |
0.432 (1.00) |
0.529 (1.00) |
0.999 (1.00) |
0.383 (1.00) |
0.885 (1.00) |
|
MUC20 | 10 (1%) | 761 |
0.421 (1.00) |
0.169 (1.00) |
1 (1.00) |
0.0697 (1.00) |
0.724 (1.00) |
0.611 (1.00) |
0.813 (1.00) |
0.533 (1.00) |
0.97 (1.00) |
|
PPEF1 | 8 (1%) | 763 |
0.748 (1.00) |
0.704 (1.00) |
1 (1.00) |
0.891 (1.00) |
1 (1.00) |
1 (1.00) |
0.885 (1.00) |
0.164 (1.00) |
0.982 (1.00) |
|
PRRX1 | 6 (1%) | 765 |
0.487 (1.00) |
0.9 (1.00) |
1 (1.00) |
0.939 (1.00) |
0.182 (1.00) |
1 (1.00) |
0.778 (1.00) |
0.722 (1.00) |
0.988 (1.00) |
|
ATP13A4 | 9 (1%) | 762 |
0.301 (1.00) |
0.545 (1.00) |
1 (1.00) |
0.863 (1.00) |
0.702 (1.00) |
1 (1.00) |
0.988 (1.00) |
0.0558 (1.00) |
0.000397 (0.28) |
|
MUC2 | 18 (2%) | 753 |
0.466 (1.00) |
0.783 (1.00) |
1 (1.00) |
0.9 (1.00) |
0.0972 (1.00) |
0.19 (1.00) |
0.547 (1.00) |
0.445 (1.00) |
0.529 (1.00) |
|
UBC | 8 (1%) | 763 |
0.216 (1.00) |
0.671 (1.00) |
1 (1.00) |
0.891 (1.00) |
1 (1.00) |
1 (1.00) |
0.906 (1.00) |
0.844 (1.00) |
0.934 (1.00) |
|
KCNN3 | 6 (1%) | 765 |
0.619 (1.00) |
0.744 (1.00) |
1 (1.00) |
0.237 (1.00) |
0.347 (1.00) |
0.431 (1.00) |
0.981 (1.00) |
0.019 (1.00) |
0.669 (1.00) |
|
RBM23 | 6 (1%) | 765 |
0.663 (1.00) |
0.746 (1.00) |
1 (1.00) |
0.000403 (0.285) |
0.182 (1.00) |
0.103 (1.00) |
0.89 (1.00) |
0.794 (1.00) |
0.792 (1.00) |
|
GNRH2 | 3 (0%) | 768 |
0.91 (1.00) |
0.178 (1.00) |
1 (1.00) |
0.756 (1.00) |
0.573 (1.00) |
0.245 (1.00) |
0.205 (1.00) |
0.434 (1.00) |
0.999 (1.00) |
P value = 1.16e-05 (t-test), Q value = 0.0083
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 = 1.08e-07 (Chi-square test), Q value = 7.8e-05
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 | 61 | 61 | 6 | 3 | 267 | 167 | 117 | 23 | 33 | 15 | 1 | 16 |
DCP1B MUTATED | 1 | 0 | 0 | 1 | 0 | 2 | 1 | 0 | 0 | 0 | 0 | 0 |
DCP1B WILD-TYPE | 60 | 61 | 6 | 2 | 267 | 165 | 116 | 23 | 33 | 15 | 1 | 16 |
P value = 5.69e-05 (Chi-square test), Q value = 0.04
nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 224 | 19 | 113 | 1 | 93 | 116 | 30 | 2 | 18 | 50 | 49 | 15 | 25 | 2 | 1 | 13 |
PIK3R1 MUTATED | 5 | 0 | 3 | 1 | 5 | 1 | 0 | 0 | 1 | 3 | 2 | 0 | 0 | 0 | 0 | 0 |
PIK3R1 WILD-TYPE | 219 | 19 | 110 | 0 | 88 | 115 | 30 | 2 | 17 | 47 | 47 | 15 | 25 | 2 | 1 | 13 |
P value = 0.000217 (t-test), Q value = 0.15
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 = 1.03e-06 (Chi-square test), Q value = 0.00074
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 638 | 64 | 4 | 25 | 6 | 34 |
TP53 MUTATED | 236 | 3 | 3 | 5 | 0 | 10 |
TP53 WILD-TYPE | 402 | 61 | 1 | 20 | 6 | 24 |
P value = 3.17e-69 (Chi-square test), Q value = 2.3e-66
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 638 | 64 | 4 | 25 | 6 | 34 |
CDH1 MUTATED | 11 | 40 | 1 | 3 | 0 | 0 |
CDH1 WILD-TYPE | 627 | 24 | 3 | 22 | 6 | 34 |
P value = 7.24e-07 (t-test), Q value = 0.00052
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 = 5.2e-05 (logrank test), Q value = 0.037
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 714 | 91 | 0.0 - 223.4 (18.3) |
CCDC144NL MUTATED | 6 | 1 | 1.6 - 15.0 (7.5) |
CCDC144NL WILD-TYPE | 708 | 90 | 0.0 - 223.4 (18.9) |
P value = 1.7e-06 (Chi-square test), Q value = 0.0012
nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 224 | 19 | 113 | 1 | 93 | 116 | 30 | 2 | 18 | 50 | 49 | 15 | 25 | 2 | 1 | 13 |
AQP7 MUTATED | 1 | 1 | 0 | 0 | 2 | 1 | 0 | 0 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 0 |
AQP7 WILD-TYPE | 223 | 18 | 113 | 1 | 91 | 115 | 30 | 2 | 18 | 49 | 48 | 15 | 25 | 1 | 1 | 13 |
P value = 4.09e-05 (Chi-square test), Q value = 0.029
nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 224 | 19 | 113 | 1 | 93 | 116 | 30 | 2 | 18 | 50 | 49 | 15 | 25 | 2 | 1 | 13 |
CDKN1B MUTATED | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 2 | 0 | 3 | 0 | 0 | 0 |
CDKN1B WILD-TYPE | 224 | 19 | 112 | 1 | 93 | 116 | 29 | 2 | 18 | 50 | 47 | 15 | 22 | 2 | 1 | 13 |
P value = 5.57e-05 (t-test), Q value = 0.04
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 = 0.000114 (Chi-square test), Q value = 0.081
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 638 | 64 | 4 | 25 | 6 | 34 |
CTU2 MUTATED | 3 | 1 | 0 | 0 | 1 | 0 |
CTU2 WILD-TYPE | 635 | 63 | 4 | 25 | 5 | 34 |
P value = 1.58e-09 (Chi-square test), Q value = 1.1e-06
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 | 61 | 61 | 6 | 3 | 267 | 167 | 117 | 23 | 33 | 15 | 1 | 16 |
CTU2 MUTATED | 0 | 2 | 0 | 1 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 0 |
CTU2 WILD-TYPE | 61 | 59 | 6 | 2 | 266 | 167 | 117 | 22 | 33 | 15 | 1 | 16 |
P value = 9.35e-06 (Chi-square test), Q value = 0.0067
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 638 | 64 | 4 | 25 | 6 | 34 |
HLA-A MUTATED | 3 | 0 | 0 | 0 | 1 | 0 |
HLA-A WILD-TYPE | 635 | 64 | 4 | 25 | 5 | 34 |
P value = 2.91e-33 (Chi-square test), Q value = 2.1e-30
nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 224 | 19 | 113 | 1 | 93 | 116 | 30 | 2 | 18 | 50 | 49 | 15 | 25 | 2 | 1 | 13 |
HLA-A MUTATED | 1 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 0 |
HLA-A WILD-TYPE | 223 | 19 | 112 | 1 | 92 | 116 | 30 | 2 | 18 | 50 | 49 | 15 | 25 | 2 | 0 | 13 |
P value = 4.38e-05 (Chi-square test), Q value = 0.031
nPatients | INFILTRATING DUCTAL CARCINOMA | INFILTRATING LOBULAR CARCINOMA | MEDULLARY CARCINOMA | MIXED HISTOLOGY (PLEASE SPECIFY) | MUCINOUS CARCINOMA | OTHER SPECIFY |
---|---|---|---|---|---|---|
ALL | 638 | 64 | 4 | 25 | 6 | 34 |
ODF1 MUTATED | 3 | 0 | 0 | 0 | 1 | 1 |
ODF1 WILD-TYPE | 635 | 64 | 4 | 25 | 5 | 33 |
P value = 7.55e-15 (Chi-square test), Q value = 5.5e-12
nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 224 | 19 | 113 | 1 | 93 | 116 | 30 | 2 | 18 | 50 | 49 | 15 | 25 | 2 | 1 | 13 |
KRT38 MUTATED | 0 | 0 | 1 | 0 | 0 | 2 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
KRT38 WILD-TYPE | 224 | 19 | 112 | 1 | 93 | 114 | 30 | 1 | 18 | 50 | 49 | 15 | 25 | 2 | 1 | 13 |
P value = 7.73e-07 (Chi-square test), Q value = 0.00056
nPatients | N0 | N0 (I+) | N0 (I-) | N0 (MOL+) | N1 | N1A | N1B | N1C | N1MI | N2 | N2A | N3 | N3A | N3B | N3C | NX |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 224 | 19 | 113 | 1 | 93 | 116 | 30 | 2 | 18 | 50 | 49 | 15 | 25 | 2 | 1 | 13 |
ASXL2 MUTATED | 1 | 0 | 2 | 0 | 0 | 2 | 0 | 1 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
ASXL2 WILD-TYPE | 223 | 19 | 111 | 1 | 93 | 114 | 30 | 1 | 17 | 50 | 49 | 15 | 24 | 2 | 1 | 13 |
P value = 7.01e-05 (t-test), Q value = 0.05
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) |
-
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 = 81
-
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 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 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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.