This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 36 genes and 17 clinical features across 492 patients, 11 significant findings detected with Q value < 0.25.
-
BRAF mutation correlated to 'PATHOLOGIC_STAGE', 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', 'EXTRATHYROIDAL_EXTENSION', and 'NUMBER_OF_LYMPH_NODES'.
-
NRAS mutation correlated to 'PATHOLOGY_N_STAGE', 'HISTOLOGICAL_TYPE', and 'NUMBER_OF_LYMPH_NODES'.
-
HRAS mutation correlated to 'HISTOLOGICAL_TYPE'.
-
RANBP9 mutation correlated to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RADIATION EXPOSURE |
EXTRATHYROIDAL EXTENSION |
RESIDUAL TUMOR |
NUMBER OF LYMPH NODES |
MULTIFOCALITY |
TUMOR SIZE |
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 | Fisher's exact test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
BRAF | 290 (59%) | 202 |
0.221 (1.00) |
0.488 (1.00) |
0.00021 (0.0184) |
0.00126 (0.0964) |
1.68e-06 (0.000839) |
0.728 (1.00) |
1 (1.00) |
0.923 (1.00) |
1e-05 (0.00122) |
0.316 (1.00) |
1e-05 (0.00122) |
0.341 (1.00) |
0.00291 (0.171) |
1 (1.00) |
0.407 (1.00) |
0.863 (1.00) |
0.118 (0.977) |
NRAS | 40 (8%) | 452 |
0.406 (1.00) |
0.279 (1.00) |
0.0507 (0.839) |
0.574 (1.00) |
5.6e-05 (0.00571) |
0.125 (0.977) |
0.853 (1.00) |
0.5 (1.00) |
1e-05 (0.00122) |
1 (1.00) |
0.206 (1.00) |
0.444 (1.00) |
0.00263 (0.171) |
0.509 (1.00) |
0.859 (1.00) |
0.483 (1.00) |
0.0309 (0.655) |
HRAS | 16 (3%) | 476 |
0.487 (1.00) |
0.413 (1.00) |
0.424 (1.00) |
0.738 (1.00) |
0.172 (1.00) |
0.254 (1.00) |
0.773 (1.00) |
0.0585 (0.867) |
0.00307 (0.171) |
1 (1.00) |
0.496 (1.00) |
0.307 (1.00) |
0.354 (1.00) |
1 (1.00) |
0.434 (1.00) |
0.101 (0.977) |
0.378 (1.00) |
RANBP9 | 3 (1%) | 489 |
2.74e-06 (0.000839) |
0.398 (1.00) |
0.0552 (0.867) |
0.159 (1.00) |
1 (1.00) |
0.0316 (0.655) |
0.172 (1.00) |
0.295 (1.00) |
1 (1.00) |
1 (1.00) |
0.134 (0.977) |
0.235 (1.00) |
0.595 (1.00) |
1 (1.00) |
|||
NUDT11 | 10 (2%) | 482 |
0.642 (1.00) |
0.787 (1.00) |
0.42 (1.00) |
0.418 (1.00) |
0.285 (1.00) |
1 (1.00) |
0.139 (0.977) |
1 (1.00) |
0.0743 (0.912) |
0.0273 (0.655) |
0.824 (1.00) |
0.804 (1.00) |
0.336 (1.00) |
0.524 (1.00) |
0.686 (1.00) |
1 (1.00) |
1 (1.00) |
RPTN | 10 (2%) | 482 |
0.663 (1.00) |
0.301 (1.00) |
0.802 (1.00) |
0.466 (1.00) |
0.337 (1.00) |
1 (1.00) |
1 (1.00) |
0.00733 (0.345) |
0.878 (1.00) |
0.306 (1.00) |
0.365 (1.00) |
0.803 (1.00) |
0.123 (0.977) |
0.356 (1.00) |
0.485 (1.00) |
0.35 (1.00) |
0.564 (1.00) |
EMG1 | 11 (2%) | 481 |
0.627 (1.00) |
0.475 (1.00) |
1 (1.00) |
0.713 (1.00) |
0.22 (1.00) |
1 (1.00) |
0.303 (1.00) |
0.222 (1.00) |
0.433 (1.00) |
1 (1.00) |
0.189 (1.00) |
0.034 (0.655) |
0.264 (1.00) |
0.56 (1.00) |
0.411 (1.00) |
0.776 (1.00) |
0.608 (1.00) |
FAM47C | 14 (3%) | 478 |
0.517 (1.00) |
0.294 (1.00) |
0.453 (1.00) |
0.92 (1.00) |
0.259 (1.00) |
1 (1.00) |
0.373 (1.00) |
0.781 (1.00) |
0.654 (1.00) |
1 (1.00) |
1 (1.00) |
0.883 (1.00) |
0.474 (1.00) |
0.425 (1.00) |
0.886 (1.00) |
0.774 (1.00) |
0.143 (0.981) |
EIF1AX | 7 (1%) | 485 |
0.0327 (0.655) |
0.031 (0.655) |
0.884 (1.00) |
1 (1.00) |
0.215 (1.00) |
1 (1.00) |
0.388 (1.00) |
0.433 (1.00) |
0.0277 (0.655) |
1 (1.00) |
0.757 (1.00) |
0.397 (1.00) |
0.393 (1.00) |
0.419 (1.00) |
0.251 (1.00) |
1 (1.00) |
|
DLX6 | 7 (1%) | 485 |
0.729 (1.00) |
0.805 (1.00) |
0.272 (1.00) |
0.615 (1.00) |
0.0672 (0.887) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.816 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.116 (0.977) |
1 (1.00) |
0.524 (1.00) |
1 (1.00) |
1 (1.00) |
GPR44 | 4 (1%) | 488 |
0.657 (1.00) |
0.965 (1.00) |
0.644 (1.00) |
0.0299 (0.655) |
0.371 (1.00) |
1 (1.00) |
0.286 (1.00) |
0.633 (1.00) |
0.705 (1.00) |
1 (1.00) |
0.0972 (0.977) |
0.0682 (0.887) |
0.129 (0.977) |
0.0196 (0.655) |
0.583 (1.00) |
1 (1.00) |
|
TMEM184A | 5 (1%) | 487 |
0.824 (1.00) |
0.403 (1.00) |
0.71 (1.00) |
0.128 (0.977) |
1 (1.00) |
1 (1.00) |
0.611 (1.00) |
1 (1.00) |
0.565 (1.00) |
1 (1.00) |
0.138 (0.977) |
0.392 (1.00) |
0.66 (1.00) |
1 (1.00) |
0.582 (1.00) |
1 (1.00) |
|
NUP93 | 4 (1%) | 488 |
0.851 (1.00) |
0.524 (1.00) |
0.736 (1.00) |
0.742 (1.00) |
0.623 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.013 (0.532) |
1 (1.00) |
1 (1.00) |
0.557 (1.00) |
0.504 (1.00) |
0.336 (1.00) |
0.988 (1.00) |
0.23 (1.00) |
1 (1.00) |
GAGE2A | 4 (1%) | 488 |
0.871 (1.00) |
0.00664 (0.339) |
0.839 (1.00) |
0.872 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.706 (1.00) |
1 (1.00) |
0.612 (1.00) |
0.454 (1.00) |
0.965 (1.00) |
1 (1.00) |
0.349 (1.00) |
0.479 (1.00) |
1 (1.00) |
ABL1 | 5 (1%) | 487 |
0.617 (1.00) |
0.0199 (0.655) |
0.58 (1.00) |
0.893 (1.00) |
1 (1.00) |
0.121 (0.977) |
0.332 (1.00) |
0.655 (1.00) |
0.74 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.857 (1.00) |
0.381 (1.00) |
0.559 (1.00) |
0.582 (1.00) |
0.404 (1.00) |
LMTK2 | 4 (1%) | 488 |
0.523 (1.00) |
0.845 (1.00) |
0.141 (0.977) |
0.168 (1.00) |
0.622 (1.00) |
0.0921 (0.977) |
1 (1.00) |
1 (1.00) |
0.455 (1.00) |
1 (1.00) |
0.154 (1.00) |
0.0696 (0.887) |
0.129 (0.977) |
0.0904 (0.977) |
1 (1.00) |
0.338 (1.00) |
|
SRPX | 4 (1%) | 488 |
0.829 (1.00) |
0.289 (1.00) |
0.556 (1.00) |
1 (1.00) |
0.248 (1.00) |
1 (1.00) |
0.577 (1.00) |
0.633 (1.00) |
0.225 (1.00) |
1 (1.00) |
0.425 (1.00) |
1 (1.00) |
0.248 (1.00) |
0.336 (1.00) |
0.421 (1.00) |
0.479 (1.00) |
0.266 (1.00) |
PPM1D | 6 (1%) | 486 |
0.684 (1.00) |
0.231 (1.00) |
0.0954 (0.977) |
0.337 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.615 (1.00) |
1 (1.00) |
0.192 (1.00) |
0.391 (1.00) |
0.744 (1.00) |
1 (1.00) |
0.744 (1.00) |
1 (1.00) |
1 (1.00) |
TG | 20 (4%) | 472 |
0.436 (1.00) |
0.301 (1.00) |
0.266 (1.00) |
0.175 (1.00) |
0.47 (1.00) |
0.325 (1.00) |
1 (1.00) |
0.817 (1.00) |
0.0407 (0.732) |
1 (1.00) |
0.214 (1.00) |
0.906 (1.00) |
0.926 (1.00) |
0.653 (1.00) |
0.789 (1.00) |
0.893 (1.00) |
0.225 (1.00) |
PTCD1 | 3 (1%) | 489 |
0.0316 (0.655) |
0.363 (1.00) |
0.416 (1.00) |
0.16 (1.00) |
0.499 (1.00) |
1 (1.00) |
1 (1.00) |
0.559 (1.00) |
0.649 (1.00) |
1 (1.00) |
0.0806 (0.948) |
0.236 (1.00) |
0.254 (1.00) |
0.123 (0.977) |
0.186 (1.00) |
||
TSC22D1 | 4 (1%) | 488 |
0.615 (1.00) |
0.547 (1.00) |
0.109 (0.977) |
0.633 (1.00) |
0.371 (1.00) |
0.121 (0.977) |
0.286 (1.00) |
0.302 (1.00) |
0.137 (0.977) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.45 (1.00) |
0.629 (1.00) |
0.578 (1.00) |
1 (1.00) |
1 (1.00) |
AKT1 | 5 (1%) | 487 |
0.837 (1.00) |
0.172 (1.00) |
0.111 (0.977) |
0.401 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.128 (0.977) |
1 (1.00) |
0.096 (0.977) |
0.0256 (0.655) |
0.715 (1.00) |
1 (1.00) |
0.594 (1.00) |
1 (1.00) |
0.404 (1.00) |
ZNF878 | 3 (1%) | 489 |
0.714 (1.00) |
0.808 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.295 (1.00) |
0.646 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.254 (1.00) |
1 (1.00) |
1 (1.00) |
||
RBM10 | 4 (1%) | 488 |
0.836 (1.00) |
0.792 (1.00) |
0.735 (1.00) |
1 (1.00) |
0.623 (1.00) |
1 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.0343 (0.655) |
1 (1.00) |
0.42 (1.00) |
0.313 (1.00) |
0.87 (1.00) |
0.0432 (0.755) |
0.139 (0.977) |
1 (1.00) |
0.266 (1.00) |
EP400 | 3 (1%) | 489 |
0.768 (1.00) |
0.647 (1.00) |
1 (1.00) |
0.159 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0821 (0.948) |
1 (1.00) |
0.552 (1.00) |
1 (1.00) |
0.631 (1.00) |
1 (1.00) |
|
ABCD1 | 4 (1%) | 488 |
0.842 (1.00) |
0.154 (1.00) |
0.476 (1.00) |
0.199 (1.00) |
0.0605 (0.867) |
1 (1.00) |
1 (1.00) |
0.633 (1.00) |
0.14 (0.977) |
1 (1.00) |
0.644 (1.00) |
0.0494 (0.839) |
0.0745 (0.912) |
0.595 (1.00) |
0.588 (1.00) |
1 (1.00) |
0.266 (1.00) |
MYH10 | 4 (1%) | 488 |
0.768 (1.00) |
0.551 (1.00) |
0.201 (1.00) |
0.453 (1.00) |
0.123 (0.977) |
1 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.703 (1.00) |
1 (1.00) |
0.153 (1.00) |
1 (1.00) |
0.662 (1.00) |
1 (1.00) |
0.479 (1.00) |
1 (1.00) |
|
NLRP6 | 4 (1%) | 488 |
0.683 (1.00) |
0.565 (1.00) |
0.4 (1.00) |
0.0613 (0.867) |
0.623 (1.00) |
1 (1.00) |
0.302 (1.00) |
1 (1.00) |
1 (1.00) |
0.423 (1.00) |
0.314 (1.00) |
0.13 (0.977) |
0.336 (1.00) |
0.0228 (0.655) |
0.0238 (0.655) |
1 (1.00) |
|
IGSF3 | 4 (1%) | 488 |
0.714 (1.00) |
0.129 (0.977) |
0.175 (1.00) |
0.0286 (0.655) |
1 (1.00) |
0.0623 (0.867) |
0.286 (1.00) |
1 (1.00) |
0.111 (0.977) |
1 (1.00) |
1 (1.00) |
0.0682 (0.887) |
0.857 (1.00) |
0.629 (1.00) |
0.982 (1.00) |
1 (1.00) |
|
PRMT8 | 3 (1%) | 489 |
0.856 (1.00) |
0.302 (1.00) |
0.508 (1.00) |
0.312 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.649 (1.00) |
1 (1.00) |
0.612 (1.00) |
1 (1.00) |
0.252 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|
ARMCX3 | 3 (1%) | 489 |
0.824 (1.00) |
0.528 (1.00) |
0.788 (1.00) |
0.313 (1.00) |
0.122 (0.977) |
1 (1.00) |
0.569 (1.00) |
0.0523 (0.842) |
0.647 (1.00) |
1 (1.00) |
0.611 (1.00) |
1 (1.00) |
1 (1.00) |
0.107 (0.977) |
1 (1.00) |
||
RYR1 | 7 (1%) | 485 |
0.647 (1.00) |
0.0389 (0.722) |
0.592 (1.00) |
0.506 (1.00) |
0.121 (0.977) |
1 (1.00) |
0.388 (1.00) |
0.204 (1.00) |
0.656 (1.00) |
1 (1.00) |
0.258 (1.00) |
0.462 (1.00) |
0.117 (0.977) |
1 (1.00) |
0.735 (1.00) |
0.539 (1.00) |
1 (1.00) |
TNRC18 | 4 (1%) | 488 |
0.786 (1.00) |
0.417 (1.00) |
0.0284 (0.655) |
0.636 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.302 (1.00) |
0.013 (0.532) |
1 (1.00) |
0.424 (1.00) |
1 (1.00) |
0.76 (1.00) |
0.336 (1.00) |
0.478 (1.00) |
0.478 (1.00) |
1 (1.00) |
TMEM90B | 3 (1%) | 489 |
0.839 (1.00) |
0.622 (1.00) |
0.416 (1.00) |
0.587 (1.00) |
0.622 (1.00) |
1 (1.00) |
0.569 (1.00) |
1 (1.00) |
0.336 (1.00) |
1 (1.00) |
0.287 (1.00) |
1 (1.00) |
0.504 (1.00) |
0.0951 (0.977) |
0.478 (1.00) |
1 (1.00) |
|
ZC3H11A | 3 (1%) | 489 |
0.885 (1.00) |
0.0791 (0.948) |
0.788 (1.00) |
0.696 (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) |
0.595 (1.00) |
0.0623 (0.867) |
1 (1.00) |
||
DGCR8 | 3 (1%) | 489 |
0.857 (1.00) |
0.287 (1.00) |
0.607 (1.00) |
0.492 (1.00) |
1 (1.00) |
1 (1.00) |
0.569 (1.00) |
0.559 (1.00) |
0.227 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.595 (1.00) |
0.664 (1.00) |
1 (1.00) |
P value = 0.00021 (Fisher's exact test), Q value = 0.018
nPatients | STAGE I | STAGE II | STAGE III | STAGE IV | STAGE IVA | STAGE IVC |
---|---|---|---|---|---|---|
ALL | 278 | 50 | 108 | 2 | 46 | 6 |
BRAF MUTATED | 157 | 19 | 74 | 0 | 35 | 4 |
BRAF WILD-TYPE | 121 | 31 | 34 | 2 | 11 | 2 |
P value = 0.00126 (Fisher's exact test), Q value = 0.096
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 141 | 162 | 164 | 23 |
BRAF MUTATED | 78 | 81 | 112 | 18 |
BRAF WILD-TYPE | 63 | 81 | 52 | 5 |
P value = 1.68e-06 (Fisher's exact test), Q value = 0.00084
nPatients | 0 | 1 |
---|---|---|
ALL | 220 | 222 |
BRAF MUTATED | 108 | 159 |
BRAF WILD-TYPE | 112 | 63 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0012
nPatients | OTHER, SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 7 | 348 | 102 | 35 |
BRAF MUTATED | 4 | 238 | 16 | 32 |
BRAF WILD-TYPE | 3 | 110 | 86 | 3 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0012
nPatients | MINIMAL (T3) | MODERATE/ADVANCED (T4A) | NONE | VERY ADVANCED (T4B) |
---|---|---|---|---|
ALL | 130 | 18 | 328 | 1 |
BRAF MUTATED | 99 | 16 | 170 | 0 |
BRAF WILD-TYPE | 31 | 2 | 158 | 1 |
P value = 0.00291 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 378 | 3.7 (6.2) |
BRAF MUTATED | 236 | 3.9 (5.9) |
BRAF WILD-TYPE | 142 | 3.5 (6.8) |
P value = 5.6e-05 (Fisher's exact test), Q value = 0.0057
nPatients | 0 | 1 |
---|---|---|
ALL | 220 | 222 |
NRAS MUTATED | 30 | 7 |
NRAS WILD-TYPE | 190 | 215 |
P value = 1e-05 (Fisher's exact test), Q value = 0.0012
nPatients | OTHER, SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 7 | 348 | 102 | 35 |
NRAS MUTATED | 0 | 14 | 26 | 0 |
NRAS WILD-TYPE | 7 | 334 | 76 | 35 |
P value = 0.00263 (Wilcoxon-test), Q value = 0.17
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 378 | 3.7 (6.2) |
NRAS MUTATED | 30 | 1.7 (3.8) |
NRAS WILD-TYPE | 348 | 3.9 (6.4) |
P value = 0.00307 (Fisher's exact test), Q value = 0.17
nPatients | OTHER, SPECIFY | THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL | THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) | THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) |
---|---|---|---|---|
ALL | 7 | 348 | 102 | 35 |
HRAS MUTATED | 0 | 6 | 10 | 0 |
HRAS WILD-TYPE | 7 | 342 | 92 | 35 |
P value = 2.74e-06 (logrank test), Q value = 0.00084
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 491 | 14 | 0.2 - 178.3 (31.1) |
RANBP9 MUTATED | 3 | 1 | 17.5 - 48.1 (17.5) |
RANBP9 WILD-TYPE | 488 | 13 | 0.2 - 178.3 (31.2) |
-
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/THCA-TP/22815544/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/THCA-TP/22507188/THCA-TP.merged_data.txt
-
Number of patients = 492
-
Number of significantly mutated genes = 36
-
Number of selected clinical features = 17
-
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.