This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 92 genes and 8 clinical features across 515 patients, 29 significant findings detected with Q value < 0.25.
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IDH1 mutation correlated to 'Time to Death', 'YEARS_TO_BIRTH', 'KARNOFSKY_PERFORMANCE_SCORE', and 'HISTOLOGICAL_TYPE'.
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TP53 mutation correlated to 'YEARS_TO_BIRTH', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
-
ATRX mutation correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
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CIC mutation correlated to 'Time to Death', 'RADIATION_THERAPY', and 'HISTOLOGICAL_TYPE'.
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NOTCH1 mutation correlated to 'HISTOLOGICAL_TYPE'.
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IDH2 mutation correlated to 'HISTOLOGICAL_TYPE'.
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FUBP1 mutation correlated to 'YEARS_TO_BIRTH' and 'HISTOLOGICAL_TYPE'.
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NF1 mutation correlated to 'Time to Death'.
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PTEN mutation correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'HISTOLOGICAL_TYPE'.
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EGFR mutation correlated to 'Time to Death', 'YEARS_TO_BIRTH', and 'KARNOFSKY_PERFORMANCE_SCORE'.
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SMARCA4 mutation correlated to 'Time to Death'.
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ZNF292 mutation correlated to 'YEARS_TO_BIRTH'.
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PLCG1 mutation correlated to 'Time to Death'.
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SETD2 mutation correlated to 'YEARS_TO_BIRTH'.
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TMEM184A mutation correlated to 'Time to Death'.
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WRN mutation correlated to 'ETHNICITY'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
GENDER |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
HISTOLOGICAL TYPE |
RACE | ETHNICITY | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
IDH1 | 400 (78%) | 115 |
0 (0) |
9.81e-09 (1.2e-06) |
1 (1.00) |
0.0123 (0.289) |
0.00286 (0.0914) |
0.00555 (0.151) |
0.025 (0.439) |
1 (1.00) |
TP53 | 250 (49%) | 265 |
0.0444 (0.597) |
3.07e-12 (7.54e-10) |
0.25 (0.9) |
0.000182 (0.0079) |
0.366 (0.921) |
1e-05 (0.000613) |
0.0322 (0.526) |
0.715 (1.00) |
CIC | 108 (21%) | 407 |
8.16e-05 (0.00429) |
0.109 (0.737) |
0.328 (0.921) |
6.82e-06 (0.000613) |
0.236 (0.9) |
1e-05 (0.000613) |
0.748 (1.00) |
0.655 (1.00) |
PTEN | 24 (5%) | 491 |
0.000127 (0.00583) |
0.00176 (0.0646) |
0.297 (0.916) |
0.0684 (0.668) |
0.592 (1.00) |
0.00276 (0.0914) |
0.163 (0.803) |
1 (1.00) |
EGFR | 35 (7%) | 480 |
1.88e-11 (3.45e-09) |
4.92e-11 (7.25e-09) |
1 (1.00) |
0.0227 (0.414) |
0.00535 (0.151) |
0.0503 (0.65) |
0.178 (0.808) |
0.717 (1.00) |
ATRX | 197 (38%) | 318 |
0.0813 (0.682) |
2.71e-12 (7.54e-10) |
0.784 (1.00) |
0.0123 (0.289) |
0.939 (1.00) |
1e-05 (0.000613) |
0.396 (0.936) |
1 (1.00) |
FUBP1 | 47 (9%) | 468 |
0.133 (0.787) |
0.00305 (0.0934) |
0.645 (1.00) |
0.0728 (0.668) |
0.234 (0.9) |
1e-05 (0.000613) |
1 (1.00) |
0.0998 (0.718) |
NOTCH1 | 42 (8%) | 473 |
0.21 (0.863) |
0.043 (0.596) |
0.747 (1.00) |
0.504 (1.00) |
0.879 (1.00) |
5e-05 (0.00283) |
0.334 (0.921) |
1 (1.00) |
IDH2 | 20 (4%) | 495 |
0.0597 (0.668) |
0.0739 (0.668) |
1 (1.00) |
0.474 (0.992) |
0.617 (1.00) |
0.00093 (0.036) |
0.45 (0.982) |
0.125 (0.761) |
NF1 | 33 (6%) | 482 |
9.59e-05 (0.00471) |
0.0126 (0.289) |
0.59 (1.00) |
0.568 (1.00) |
0.555 (1.00) |
0.0158 (0.324) |
0.219 (0.875) |
0.257 (0.9) |
SMARCA4 | 26 (5%) | 489 |
0.00516 (0.151) |
0.525 (1.00) |
0.318 (0.921) |
1 (1.00) |
0.431 (0.956) |
0.816 (1.00) |
0.114 (0.746) |
0.643 (1.00) |
ZNF292 | 14 (3%) | 501 |
0.985 (1.00) |
0.00654 (0.172) |
0.174 (0.808) |
0.576 (1.00) |
0.625 (1.00) |
0.889 (1.00) |
0.14 (0.802) |
0.596 (1.00) |
PLCG1 | 6 (1%) | 509 |
1.08e-07 (1.13e-05) |
0.0147 (0.319) |
0.415 (0.936) |
0.413 (0.936) |
0.311 (0.916) |
0.299 (0.916) |
0.31 (0.916) |
1 (1.00) |
SETD2 | 10 (2%) | 505 |
0.559 (1.00) |
0.00798 (0.202) |
1 (1.00) |
0.748 (1.00) |
0.311 (0.916) |
0.367 (0.921) |
0.464 (0.987) |
1 (1.00) |
TMEM184A | 3 (1%) | 512 |
0.000469 (0.0192) |
0.152 (0.803) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.165 (0.803) |
1 (1.00) |
|
WRN | 5 (1%) | 510 |
0.0836 (0.682) |
0.378 (0.921) |
0.66 (1.00) |
1 (1.00) |
0.0387 (0.566) |
0.549 (1.00) |
0.264 (0.9) |
0.00245 (0.0859) |
PIK3R1 | 22 (4%) | 493 |
0.36 (0.921) |
0.0806 (0.682) |
0.275 (0.916) |
0.37 (0.921) |
0.754 (1.00) |
0.353 (0.921) |
0.0446 (0.597) |
0.623 (1.00) |
TCF12 | 15 (3%) | 500 |
0.61 (1.00) |
0.227 (0.9) |
0.601 (1.00) |
1 (1.00) |
0.909 (1.00) |
0.894 (1.00) |
1 (1.00) |
0.613 (1.00) |
ARID1A | 20 (4%) | 495 |
0.0363 (0.566) |
0.647 (1.00) |
0.493 (1.00) |
0.349 (0.921) |
0.958 (1.00) |
0.196 (0.836) |
1 (1.00) |
1 (1.00) |
GAGE2A | 8 (2%) | 507 |
0.518 (1.00) |
0.734 (1.00) |
0.737 (1.00) |
1 (1.00) |
0.328 (0.921) |
1 (1.00) |
0.054 (0.667) |
0.426 (0.95) |
NUDT11 | 11 (2%) | 504 |
0.475 (0.992) |
0.322 (0.921) |
0.36 (0.921) |
1 (1.00) |
0.639 (1.00) |
0.74 (1.00) |
1 (1.00) |
1 (1.00) |
PIK3CA | 44 (9%) | 471 |
0.648 (1.00) |
0.0733 (0.668) |
0.875 (1.00) |
0.198 (0.836) |
0.106 (0.737) |
0.0176 (0.342) |
0.629 (1.00) |
0.741 (1.00) |
STK19 | 10 (2%) | 505 |
0.301 (0.916) |
0.311 (0.916) |
0.119 (0.75) |
0.681 (1.00) |
0.233 (0.9) |
0.0742 (0.668) |
1 (1.00) |
0.138 (0.802) |
NIPBL | 18 (3%) | 497 |
0.056 (0.668) |
0.175 (0.808) |
0.157 (0.803) |
0.31 (0.916) |
0.601 (1.00) |
0.0691 (0.668) |
0.0744 (0.668) |
0.11 (0.737) |
TRERF1 | 6 (1%) | 509 |
0.258 (0.9) |
0.283 (0.916) |
0.0938 (0.691) |
0.681 (1.00) |
0.801 (1.00) |
0.168 (0.803) |
1 (1.00) |
1 (1.00) |
CREBZF | 7 (1%) | 508 |
0.965 (1.00) |
0.171 (0.803) |
0.251 (0.9) |
1 (1.00) |
0.0726 (0.668) |
0.0311 (0.521) |
0.354 (0.921) |
0.384 (0.921) |
DNMT3A | 11 (2%) | 504 |
0.0333 (0.533) |
0.666 (1.00) |
1 (1.00) |
0.542 (1.00) |
0.946 (1.00) |
0.208 (0.862) |
0.495 (1.00) |
0.535 (1.00) |
EMG1 | 5 (1%) | 510 |
0.535 (1.00) |
0.0839 (0.682) |
0.178 (0.808) |
1 (1.00) |
0.142 (0.803) |
0.851 (1.00) |
1 (1.00) |
1 (1.00) |
IRS4 | 8 (2%) | 507 |
0.139 (0.802) |
0.887 (1.00) |
1 (1.00) |
1 (1.00) |
0.242 (0.9) |
0.092 (0.685) |
1 (1.00) |
0.426 (0.95) |
MYST4 | 11 (2%) | 504 |
0.163 (0.803) |
0.109 (0.737) |
1 (1.00) |
1 (1.00) |
0.925 (1.00) |
0.19 (0.836) |
0.147 (0.803) |
0.501 (1.00) |
MED9 | 3 (1%) | 512 |
0.305 (0.916) |
0.868 (1.00) |
0.257 (0.9) |
0.288 (0.916) |
0.0159 (0.324) |
1 (1.00) |
1 (1.00) |
|
FAM47C | 19 (4%) | 496 |
0.0687 (0.668) |
0.704 (1.00) |
0.25 (0.9) |
0.461 (0.986) |
0.632 (1.00) |
0.763 (1.00) |
1 (1.00) |
1 (1.00) |
NRAS | 4 (1%) | 511 |
0.43 (0.956) |
0.885 (1.00) |
1 (1.00) |
0.642 (1.00) |
0.471 (0.99) |
0.0223 (0.414) |
1 (1.00) |
1 (1.00) |
PLXNA3 | 9 (2%) | 506 |
0.0701 (0.668) |
0.249 (0.9) |
0.197 (0.836) |
0.16 (0.803) |
0.59 (1.00) |
0.834 (1.00) |
0.105 (0.737) |
1 (1.00) |
TNRC18 | 10 (2%) | 505 |
0.361 (0.921) |
0.742 (1.00) |
0.197 (0.836) |
0.33 (0.921) |
0.417 (0.939) |
0.366 (0.921) |
1 (1.00) |
1 (1.00) |
HTRA2 | 5 (1%) | 510 |
0.344 (0.921) |
0.0277 (0.474) |
1 (1.00) |
0.386 (0.921) |
0.452 (0.982) |
1 (1.00) |
0.292 (0.916) |
|
ZMIZ1 | 9 (2%) | 506 |
0.0693 (0.668) |
0.858 (1.00) |
0.522 (1.00) |
1 (1.00) |
0.15 (0.803) |
0.436 (0.964) |
0.0653 (0.668) |
0.0171 (0.34) |
CUL4B | 10 (2%) | 505 |
0.168 (0.803) |
0.822 (1.00) |
0.119 (0.75) |
0.163 (0.803) |
0.639 (1.00) |
0.335 (0.921) |
0.218 (0.875) |
1 (1.00) |
DLX6 | 4 (1%) | 511 |
0.312 (0.916) |
0.976 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.457 (0.982) |
1 (1.00) |
1 (1.00) |
|
RB1 | 6 (1%) | 509 |
0.834 (1.00) |
0.164 (0.803) |
0.415 (0.936) |
1 (1.00) |
0.0965 (0.703) |
0.308 (0.916) |
1 (1.00) |
|
ROBO3 | 5 (1%) | 510 |
0.365 (0.921) |
0.531 (1.00) |
0.66 (1.00) |
0.642 (1.00) |
0.669 (1.00) |
0.38 (0.921) |
1 (1.00) |
0.292 (0.916) |
SRPX | 4 (1%) | 511 |
0.199 (0.836) |
0.0429 (0.596) |
0.0392 (0.566) |
1 (1.00) |
0.554 (1.00) |
0.374 (0.921) |
0.22 (0.876) |
1 (1.00) |
RBPJ | 7 (1%) | 508 |
0.869 (1.00) |
0.0539 (0.667) |
1 (1.00) |
0.681 (1.00) |
0.338 (0.921) |
0.274 (0.916) |
1 (1.00) |
1 (1.00) |
TMEM216 | 3 (1%) | 512 |
0.741 (1.00) |
0.817 (1.00) |
0.0884 (0.682) |
1 (1.00) |
0.368 (0.921) |
1 (1.00) |
1 (1.00) |
|
ARID2 | 11 (2%) | 504 |
0.502 (1.00) |
0.108 (0.737) |
1 (1.00) |
0.217 (0.875) |
0.803 (1.00) |
0.208 (0.862) |
0.245 (0.9) |
1 (1.00) |
SLC6A3 | 9 (2%) | 506 |
0.605 (1.00) |
0.378 (0.921) |
0.522 (1.00) |
1 (1.00) |
0.759 (1.00) |
1 (1.00) |
0.384 (0.921) |
|
PDGFRA | 10 (2%) | 505 |
0.156 (0.803) |
0.707 (1.00) |
0.353 (0.921) |
0.748 (1.00) |
0.146 (0.803) |
0.115 (0.746) |
1 (1.00) |
0.138 (0.802) |
PTPN11 | 7 (1%) | 508 |
0.288 (0.916) |
0.342 (0.921) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.307 (0.916) |
0.351 (0.921) |
1 (1.00) |
MYT1 | 6 (1%) | 509 |
0.263 (0.9) |
0.408 (0.936) |
1 (1.00) |
0.0865 (0.682) |
0.733 (1.00) |
0.166 (0.803) |
1 (1.00) |
1 (1.00) |
PPL | 6 (1%) | 509 |
0.0383 (0.566) |
0.725 (1.00) |
1 (1.00) |
1 (1.00) |
0.801 (1.00) |
0.458 (0.982) |
1 (1.00) |
0.292 (0.916) |
CIB1 | 4 (1%) | 511 |
0.408 (0.936) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
ANKRD36 | 7 (1%) | 508 |
0.0921 (0.685) |
0.59 (1.00) |
0.706 (1.00) |
0.0469 (0.616) |
0.0711 (0.668) |
0.235 (0.9) |
0.0693 (0.668) |
1 (1.00) |
NAP1L2 | 4 (1%) | 511 |
0.263 (0.9) |
0.177 (0.808) |
1 (1.00) |
0.642 (1.00) |
0.191 (0.836) |
1 (1.00) |
1 (1.00) |
|
SMOC1 | 3 (1%) | 512 |
0.338 (0.921) |
0.443 (0.974) |
1 (1.00) |
0.288 (0.916) |
0.471 (0.99) |
0.476 (0.992) |
1 (1.00) |
1 (1.00) |
ABCA7 | 10 (2%) | 505 |
0.925 (1.00) |
0.311 (0.916) |
0.523 (1.00) |
1 (1.00) |
0.639 (1.00) |
0.61 (1.00) |
1 (1.00) |
0.501 (1.00) |
ZNF512B | 5 (1%) | 510 |
0.0782 (0.682) |
0.299 (0.916) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.292 (0.916) |
|
PRX | 10 (2%) | 505 |
0.771 (1.00) |
0.462 (0.986) |
0.353 (0.921) |
0.33 (0.921) |
0.328 (0.921) |
0.78 (1.00) |
1 (1.00) |
0.501 (1.00) |
SMARCB1 | 4 (1%) | 511 |
0.305 (0.916) |
0.809 (1.00) |
0.632 (1.00) |
0.303 (0.916) |
0.753 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
C9ORF79 | 10 (2%) | 505 |
0.111 (0.739) |
0.275 (0.916) |
1 (1.00) |
0.16 (0.803) |
0.169 (0.803) |
0.566 (1.00) |
0.458 (0.982) |
1 (1.00) |
KRT3 | 4 (1%) | 511 |
0.0899 (0.682) |
0.856 (1.00) |
0.632 (1.00) |
1 (1.00) |
0.107 (0.737) |
0.682 (1.00) |
1 (1.00) |
0.241 (0.9) |
ELF4 | 4 (1%) | 511 |
0.0879 (0.682) |
0.816 (1.00) |
0.0392 (0.566) |
0.642 (1.00) |
0.683 (1.00) |
1 (1.00) |
1 (1.00) |
|
NEU2 | 6 (1%) | 509 |
0.526 (1.00) |
0.307 (0.916) |
1 (1.00) |
1 (1.00) |
0.457 (0.982) |
1 (1.00) |
0.34 (0.921) |
|
ZNF709 | 3 (1%) | 512 |
0.503 (1.00) |
0.608 (1.00) |
0.257 (0.9) |
1 (1.00) |
0.367 (0.921) |
0.169 (0.803) |
1 (1.00) |
|
R3HDM1 | 7 (1%) | 508 |
0.0576 (0.668) |
0.871 (1.00) |
1 (1.00) |
1 (1.00) |
0.753 (1.00) |
0.491 (1.00) |
1 (1.00) |
0.384 (0.921) |
C14ORF4 | 3 (1%) | 512 |
0.466 (0.989) |
0.742 (1.00) |
0.589 (1.00) |
1 (1.00) |
0.787 (1.00) |
0.167 (0.803) |
1 (1.00) |
|
ZBTB20 | 21 (4%) | 494 |
0.411 (0.936) |
0.498 (1.00) |
0.372 (0.921) |
0.159 (0.803) |
0.804 (1.00) |
0.183 (0.817) |
0.127 (0.767) |
0.635 (1.00) |
C4BPA | 6 (1%) | 509 |
0.521 (1.00) |
0.642 (1.00) |
0.415 (0.936) |
0.413 (0.936) |
0.171 (0.803) |
0.888 (1.00) |
0.309 (0.916) |
0.34 (0.921) |
ENGASE | 5 (1%) | 510 |
0.506 (1.00) |
0.886 (1.00) |
0.66 (1.00) |
0.162 (0.803) |
0.991 (1.00) |
0.262 (0.9) |
1 (1.00) |
1 (1.00) |
DLC1 | 6 (1%) | 509 |
0.547 (1.00) |
0.549 (1.00) |
0.415 (0.936) |
0.0865 (0.682) |
0.662 (1.00) |
1 (1.00) |
0.34 (0.921) |
|
G6PC | 6 (1%) | 509 |
0.866 (1.00) |
0.4 (0.936) |
0.696 (1.00) |
0.413 (0.936) |
0.514 (1.00) |
0.456 (0.982) |
1 (1.00) |
0.0544 (0.667) |
SLC12A7 | 7 (1%) | 508 |
0.238 (0.9) |
0.538 (1.00) |
0.706 (1.00) |
0.413 (0.936) |
0.519 (1.00) |
1 (1.00) |
0.352 (0.921) |
1 (1.00) |
RET | 7 (1%) | 508 |
0.645 (1.00) |
0.5 (1.00) |
0.251 (0.9) |
0.438 (0.964) |
0.602 (1.00) |
0.0713 (0.668) |
1 (1.00) |
1 (1.00) |
ZC3H11A | 6 (1%) | 509 |
0.613 (1.00) |
0.195 (0.836) |
0.696 (1.00) |
1 (1.00) |
0.338 (0.921) |
0.665 (1.00) |
1 (1.00) |
1 (1.00) |
USP6 | 7 (1%) | 508 |
0.0846 (0.682) |
0.522 (1.00) |
1 (1.00) |
0.258 (0.9) |
0.0725 (0.668) |
0.306 (0.916) |
0.351 (0.921) |
1 (1.00) |
RBBP6 | 6 (1%) | 509 |
0.194 (0.836) |
0.321 (0.921) |
1 (1.00) |
0.681 (1.00) |
0.774 (1.00) |
0.124 (0.761) |
1 (1.00) |
|
SLFN11 | 6 (1%) | 509 |
0.0895 (0.682) |
0.0583 (0.668) |
0.696 (1.00) |
1 (1.00) |
0.471 (0.99) |
0.35 (0.921) |
1 (1.00) |
0.34 (0.921) |
ASXL2 | 3 (1%) | 512 |
0.118 (0.75) |
0.413 (0.936) |
0.589 (1.00) |
1 (1.00) |
0.628 (1.00) |
1 (1.00) |
1 (1.00) |
|
KRT15 | 6 (1%) | 509 |
0.75 (1.00) |
0.116 (0.746) |
0.696 (1.00) |
0.211 (0.864) |
0.412 (0.936) |
0.888 (1.00) |
0.309 (0.916) |
1 (1.00) |
FMR1 | 5 (1%) | 510 |
0.0687 (0.668) |
0.181 (0.817) |
1 (1.00) |
0.653 (1.00) |
0.356 (0.921) |
0.125 (0.761) |
1 (1.00) |
1 (1.00) |
DDX5 | 5 (1%) | 510 |
0.331 (0.921) |
0.854 (1.00) |
1 (1.00) |
1 (1.00) |
0.292 (0.916) |
0.852 (1.00) |
1 (1.00) |
0.241 (0.9) |
SCN4A | 6 (1%) | 509 |
0.182 (0.817) |
0.26 (0.9) |
0.415 (0.936) |
0.681 (1.00) |
0.34 (0.921) |
0.774 (1.00) |
1 (1.00) |
1 (1.00) |
CCDC135 | 7 (1%) | 508 |
0.233 (0.9) |
0.755 (1.00) |
0.251 (0.9) |
1 (1.00) |
0.705 (1.00) |
1 (1.00) |
0.384 (0.921) |
|
MYOCD | 9 (2%) | 506 |
0.146 (0.803) |
0.41 (0.936) |
1 (1.00) |
0.163 (0.803) |
0.503 (1.00) |
0.0143 (0.319) |
0.426 (0.95) |
1 (1.00) |
KTELC1 | 5 (1%) | 510 |
0.308 (0.916) |
0.661 (1.00) |
0.387 (0.921) |
0.653 (1.00) |
0.849 (1.00) |
1 (1.00) |
1 (1.00) |
|
GPR133 | 4 (1%) | 511 |
0.271 (0.916) |
0.514 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.241 (0.9) |
|
CDH3 | 3 (1%) | 512 |
0.294 (0.916) |
0.627 (1.00) |
0.0884 (0.682) |
1 (1.00) |
0.632 (1.00) |
1 (1.00) |
1 (1.00) |
|
SLC25A5 | 4 (1%) | 511 |
0.0231 (0.414) |
0.577 (1.00) |
0.329 (0.921) |
1 (1.00) |
0.255 (0.9) |
0.84 (1.00) |
0.218 (0.875) |
1 (1.00) |
LAMA4 | 4 (1%) | 511 |
0.792 (1.00) |
0.355 (0.921) |
0.132 (0.787) |
1 (1.00) |
0.753 (1.00) |
0.0666 (0.668) |
0.0785 (0.682) |
0.241 (0.9) |
NKD2 | 4 (1%) | 511 |
0.968 (1.00) |
0.689 (1.00) |
1 (1.00) |
0.162 (0.803) |
0.457 (0.982) |
1 (1.00) |
1 (1.00) |
|
PHF3 | 8 (2%) | 507 |
0.693 (1.00) |
0.608 (1.00) |
1 (1.00) |
0.16 (0.803) |
0.12 (0.75) |
0.606 (1.00) |
0.387 (0.921) |
0.384 (0.921) |
AGBL1 | 5 (1%) | 510 |
0.241 (0.9) |
0.205 (0.856) |
0.387 (0.921) |
1 (1.00) |
0.19 (0.836) |
1 (1.00) |
1 (1.00) |
|
ZNF148 | 4 (1%) | 511 |
0.101 (0.718) |
0.668 (1.00) |
1 (1.00) |
0.162 (0.803) |
0.378 (0.921) |
0.0797 (0.682) |
1 (1.00) |
P value = 0 (logrank test), Q value = 0
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
IDH1 MUTATED | 396 | 73 | 0.0 - 182.3 (25.7) |
IDH1 WILD-TYPE | 115 | 52 | 0.1 - 211.2 (16.2) |
P value = 9.81e-09 (Wilcoxon-test), Q value = 1.2e-06
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
IDH1 MUTATED | 399 | 41.0 (12.3) |
IDH1 WILD-TYPE | 115 | 49.6 (14.6) |
P value = 0.00286 (Wilcoxon-test), Q value = 0.091
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 307 | 86.6 (12.6) |
IDH1 MUTATED | 241 | 87.7 (12.0) |
IDH1 WILD-TYPE | 66 | 82.7 (13.8) |
P value = 0.00555 (Fisher's exact test), Q value = 0.15
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
IDH1 MUTATED | 136 | 109 | 155 |
IDH1 WILD-TYPE | 58 | 21 | 36 |
P value = 3.07e-12 (Wilcoxon-test), Q value = 7.5e-10
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
TP53 MUTATED | 250 | 38.6 (11.3) |
TP53 WILD-TYPE | 264 | 47.0 (13.9) |
P value = 0.000182 (Fisher's exact test), Q value = 0.0079
nPatients | NO | YES |
---|---|---|
ALL | 186 | 296 |
TP53 MUTATED | 71 | 165 |
TP53 WILD-TYPE | 115 | 131 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00061
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
TP53 MUTATED | 131 | 74 | 45 |
TP53 WILD-TYPE | 63 | 56 | 146 |
P value = 2.71e-12 (Wilcoxon-test), Q value = 7.5e-10
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
ATRX MUTATED | 197 | 37.9 (11.9) |
ATRX WILD-TYPE | 317 | 46.1 (13.3) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00061
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
ATRX MUTATED | 98 | 64 | 35 |
ATRX WILD-TYPE | 96 | 66 | 156 |
P value = 8.16e-05 (logrank test), Q value = 0.0043
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
CIC MUTATED | 107 | 12 | 0.1 - 211.2 (24.6) |
CIC WILD-TYPE | 404 | 113 | 0.0 - 172.8 (21.3) |
P value = 6.82e-06 (Fisher's exact test), Q value = 0.00061
nPatients | NO | YES |
---|---|---|
ALL | 186 | 296 |
CIC MUTATED | 60 | 43 |
CIC WILD-TYPE | 126 | 253 |
P value = 1e-05 (Fisher's exact test), Q value = 0.00061
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
CIC MUTATED | 3 | 23 | 82 |
CIC WILD-TYPE | 191 | 107 | 109 |
P value = 5e-05 (Fisher's exact test), Q value = 0.0028
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
NOTCH1 MUTATED | 6 | 7 | 29 |
NOTCH1 WILD-TYPE | 188 | 123 | 162 |
P value = 0.00093 (Fisher's exact test), Q value = 0.036
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
IDH2 MUTATED | 1 | 5 | 14 |
IDH2 WILD-TYPE | 193 | 125 | 177 |
P value = 0.00305 (Wilcoxon-test), Q value = 0.093
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
FUBP1 MUTATED | 47 | 47.4 (9.5) |
FUBP1 WILD-TYPE | 467 | 42.5 (13.6) |
P value = 1e-05 (Fisher's exact test), Q value = 0.00061
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
FUBP1 MUTATED | 2 | 9 | 36 |
FUBP1 WILD-TYPE | 192 | 121 | 155 |
P value = 9.59e-05 (logrank test), Q value = 0.0047
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
NF1 MUTATED | 33 | 15 | 0.2 - 211.2 (18.6) |
NF1 WILD-TYPE | 478 | 110 | 0.0 - 182.3 (23.4) |
P value = 0.000127 (logrank test), Q value = 0.0058
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
PTEN MUTATED | 24 | 12 | 0.5 - 211.2 (17.1) |
PTEN WILD-TYPE | 487 | 113 | 0.0 - 182.3 (23.2) |
P value = 0.00176 (Wilcoxon-test), Q value = 0.065
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
PTEN MUTATED | 24 | 51.0 (12.0) |
PTEN WILD-TYPE | 490 | 42.5 (13.3) |
P value = 0.00276 (Fisher's exact test), Q value = 0.091
nPatients | ASTROCYTOMA | OLIGOASTROCYTOMA | OLIGODENDROGLIOMA |
---|---|---|---|
ALL | 194 | 130 | 191 |
PTEN MUTATED | 17 | 4 | 3 |
PTEN WILD-TYPE | 177 | 126 | 188 |
P value = 1.88e-11 (logrank test), Q value = 3.5e-09
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
EGFR MUTATED | 35 | 21 | 0.5 - 211.2 (13.8) |
EGFR WILD-TYPE | 476 | 104 | 0.0 - 182.3 (23.6) |
P value = 4.92e-11 (Wilcoxon-test), Q value = 7.2e-09
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
EGFR MUTATED | 35 | 57.7 (9.1) |
EGFR WILD-TYPE | 479 | 41.9 (13.0) |
P value = 0.00535 (Wilcoxon-test), Q value = 0.15
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 307 | 86.6 (12.6) |
EGFR MUTATED | 22 | 78.2 (16.8) |
EGFR WILD-TYPE | 285 | 87.3 (12.0) |
P value = 0.00516 (logrank test), Q value = 0.15
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
SMARCA4 MUTATED | 26 | 1 | 0.2 - 211.2 (29.1) |
SMARCA4 WILD-TYPE | 485 | 124 | 0.0 - 182.3 (21.5) |
P value = 0.00654 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
ZNF292 MUTATED | 14 | 52.6 (12.3) |
ZNF292 WILD-TYPE | 500 | 42.7 (13.3) |
P value = 1.08e-07 (logrank test), Q value = 1.1e-05
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
PLCG1 MUTATED | 6 | 4 | 6.7 - 23.7 (11.3) |
PLCG1 WILD-TYPE | 505 | 121 | 0.0 - 211.2 (22.5) |
P value = 0.00798 (Wilcoxon-test), Q value = 0.2
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 514 | 42.9 (13.4) |
SETD2 MUTATED | 10 | 54.0 (10.9) |
SETD2 WILD-TYPE | 504 | 42.7 (13.3) |
P value = 0.000469 (logrank test), Q value = 0.019
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 511 | 125 | 0.0 - 211.2 (22.3) |
TMEM184A MUTATED | 3 | 1 | 0.3 - 9.2 (6.5) |
TMEM184A WILD-TYPE | 508 | 124 | 0.0 - 211.2 (22.5) |
P value = 0.00245 (Fisher's exact test), Q value = 0.086
nPatients | HISPANIC OR LATINO | NOT HISPANIC OR LATINO |
---|---|---|
ALL | 32 | 449 |
WRN MUTATED | 3 | 2 |
WRN WILD-TYPE | 29 | 447 |
-
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/LGG-TP/22813356/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/LGG-TP/22506744/LGG-TP.merged_data.txt
-
Number of patients = 515
-
Number of significantly mutated genes = 92
-
Number of selected clinical features = 8
-
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.