This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 44 genes and 11 clinical features across 498 patients, 6 significant findings detected with Q value < 0.25.
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TP53 mutation correlated to 'PATHOLOGY_T_STAGE', 'PATHOLOGY_N_STAGE', 'NUMBER_OF_LYMPH_NODES', and 'GLEASON_SCORE'.
-
ZMYM3 mutation correlated to 'GLEASON_SCORE'.
-
ZFP36L2 mutation correlated to 'Time to Death'.
Clinical Features |
Time to Death |
YEARS TO BIRTH |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
RADIATION THERAPY |
HISTOLOGICAL TYPE |
RESIDUAL TUMOR |
NUMBER OF LYMPH NODES |
GLEASON SCORE |
PSA VALUE |
RACE | ||
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 | Wilcoxon-test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | |
TP53 | 57 (11%) | 441 |
0.294 (1.00) |
0.883 (1.00) |
0.00309 (0.249) |
0.0029 (0.249) |
0.191 (1.00) |
0.686 (1.00) |
0.0103 (0.623) |
0.000136 (0.0219) |
1.97e-09 (9.55e-07) |
0.0284 (0.888) |
1 (1.00) |
ZMYM3 | 12 (2%) | 486 |
0.445 (1.00) |
0.126 (1.00) |
0.0725 (1.00) |
0.248 (1.00) |
0.129 (1.00) |
1 (1.00) |
0.0799 (1.00) |
0.213 (1.00) |
0.00304 (0.249) |
0.453 (1.00) |
1 (1.00) |
ZFP36L2 | 4 (1%) | 494 |
7.89e-05 (0.0191) |
0.63 (1.00) |
0.224 (1.00) |
0.562 (1.00) |
0.342 (1.00) |
1 (1.00) |
0.657 (1.00) |
0.644 (1.00) |
0.728 (1.00) |
0.133 (1.00) |
|
SPOP | 57 (11%) | 441 |
0.798 (1.00) |
0.349 (1.00) |
0.348 (1.00) |
0.123 (1.00) |
1 (1.00) |
0.686 (1.00) |
0.128 (1.00) |
0.0867 (1.00) |
0.903 (1.00) |
0.208 (1.00) |
0.553 (1.00) |
PTEN | 17 (3%) | 481 |
0.619 (1.00) |
0.524 (1.00) |
1 (1.00) |
0.747 (1.00) |
1 (1.00) |
0.411 (1.00) |
0.612 (1.00) |
0.495 (1.00) |
0.362 (1.00) |
0.0127 (0.682) |
1 (1.00) |
NUDT11 | 11 (2%) | 487 |
0.688 (1.00) |
0.0964 (1.00) |
0.452 (1.00) |
0.404 (1.00) |
0.161 (1.00) |
1 (1.00) |
0.584 (1.00) |
0.371 (1.00) |
0.476 (1.00) |
0.651 (1.00) |
1 (1.00) |
MLL2 | 29 (6%) | 469 |
0.444 (1.00) |
0.185 (1.00) |
0.0792 (1.00) |
1 (1.00) |
0.762 (1.00) |
0.599 (1.00) |
0.908 (1.00) |
0.997 (1.00) |
0.0211 (0.786) |
0.222 (1.00) |
1 (1.00) |
CTNNB1 | 13 (3%) | 485 |
0.456 (1.00) |
0.423 (1.00) |
0.678 (1.00) |
0.134 (1.00) |
1 (1.00) |
0.331 (1.00) |
0.2 (1.00) |
0.0847 (1.00) |
0.197 (1.00) |
0.992 (1.00) |
1 (1.00) |
PIK3CA | 14 (3%) | 484 |
0.431 (1.00) |
0.133 (1.00) |
0.453 (1.00) |
0.698 (1.00) |
1 (1.00) |
0.352 (1.00) |
0.00674 (0.466) |
0.342 (1.00) |
0.0197 (0.786) |
0.309 (1.00) |
1 (1.00) |
KDM6A | 13 (3%) | 485 |
0.681 (1.00) |
0.145 (1.00) |
0.0838 (1.00) |
0.477 (1.00) |
0.38 (1.00) |
1 (1.00) |
0.0951 (1.00) |
0.249 (1.00) |
0.529 (1.00) |
0.454 (1.00) |
1 (1.00) |
FOXA1 | 28 (6%) | 470 |
0.378 (1.00) |
0.193 (1.00) |
0.914 (1.00) |
0.0952 (1.00) |
0.745 (1.00) |
0.586 (1.00) |
0.73 (1.00) |
0.0982 (1.00) |
0.962 (1.00) |
0.411 (1.00) |
0.0539 (1.00) |
MLL3 | 29 (6%) | 469 |
0.133 (1.00) |
0.791 (1.00) |
0.434 (1.00) |
1 (1.00) |
0.0628 (1.00) |
0.599 (1.00) |
0.728 (1.00) |
0.69 (1.00) |
0.175 (1.00) |
0.405 (1.00) |
1 (1.00) |
GAGE2A | 5 (1%) | 493 |
0.84 (1.00) |
0.518 (1.00) |
0.441 (1.00) |
1 (1.00) |
0.503 (1.00) |
1 (1.00) |
0.722 (1.00) |
0.325 (1.00) |
0.911 (1.00) |
0.544 (1.00) |
|
TNRC18 | 9 (2%) | 489 |
0.476 (1.00) |
0.264 (1.00) |
0.286 (1.00) |
0.646 (1.00) |
0.0725 (1.00) |
1 (1.00) |
0.371 (1.00) |
0.658 (1.00) |
0.243 (1.00) |
0.368 (1.00) |
|
AGAP6 | 5 (1%) | 493 |
0.783 (1.00) |
0.929 (1.00) |
0.108 (1.00) |
0.589 (1.00) |
0.503 (1.00) |
0.142 (1.00) |
0.238 (1.00) |
0.271 (1.00) |
0.151 (1.00) |
0.548 (1.00) |
|
IDH1 | 6 (1%) | 492 |
0.667 (1.00) |
0.315 (1.00) |
0.477 (1.00) |
1 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.0537 (1.00) |
0.787 (1.00) |
0.017 (0.786) |
0.526 (1.00) |
|
GATA6 | 4 (1%) | 494 |
0.837 (1.00) |
0.324 (1.00) |
0.672 (1.00) |
0.562 (1.00) |
0.428 (1.00) |
1 (1.00) |
1 (1.00) |
0.737 (1.00) |
0.728 (1.00) |
0.0385 (0.888) |
|
SMG7 | 8 (2%) | 490 |
0.645 (1.00) |
0.0879 (1.00) |
0.287 (1.00) |
0.361 (1.00) |
0.602 (1.00) |
1 (1.00) |
1 (1.00) |
0.162 (1.00) |
0.939 (1.00) |
0.271 (1.00) |
1 (1.00) |
CNTNAP1 | 9 (2%) | 489 |
0.791 (1.00) |
0.21 (1.00) |
1 (1.00) |
0.619 (1.00) |
0.279 (1.00) |
0.242 (1.00) |
0.227 (1.00) |
0.573 (1.00) |
0.233 (1.00) |
0.278 (1.00) |
|
CDKN1B | 6 (1%) | 492 |
0.689 (1.00) |
0.316 (1.00) |
0.109 (1.00) |
1 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.0723 (1.00) |
0.941 (1.00) |
0.897 (1.00) |
0.811 (1.00) |
1 (1.00) |
EOMES | 5 (1%) | 493 |
0.488 (1.00) |
0.483 (1.00) |
0.106 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.46 (1.00) |
0.325 (1.00) |
0.902 (1.00) |
0.282 (1.00) |
|
NBPF1 | 9 (2%) | 489 |
0.719 (1.00) |
0.404 (1.00) |
0.114 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0835 (1.00) |
0.763 (1.00) |
0.0383 (0.888) |
0.637 (1.00) |
1 (1.00) |
LMOD2 | 6 (1%) | 492 |
0.831 (1.00) |
0.699 (1.00) |
0.717 (1.00) |
1 (1.00) |
0.503 (1.00) |
1 (1.00) |
1 (1.00) |
0.941 (1.00) |
0.859 (1.00) |
0.0904 (1.00) |
|
EHHADH | 5 (1%) | 493 |
0.708 (1.00) |
0.431 (1.00) |
0.686 (1.00) |
1 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.721 (1.00) |
0.941 (1.00) |
0.57 (1.00) |
0.746 (1.00) |
|
MED12 | 8 (2%) | 490 |
0.737 (1.00) |
0.377 (1.00) |
0.761 (1.00) |
0.619 (1.00) |
1 (1.00) |
1 (1.00) |
0.112 (1.00) |
0.49 (1.00) |
0.304 (1.00) |
0.93 (1.00) |
1 (1.00) |
ZNF709 | 5 (1%) | 493 |
0.708 (1.00) |
0.459 (1.00) |
0.244 (1.00) |
0.589 (1.00) |
0.128 (1.00) |
1 (1.00) |
0.22 (1.00) |
0.271 (1.00) |
0.212 (1.00) |
0.468 (1.00) |
|
TCEB3 | 4 (1%) | 494 |
0.871 (1.00) |
0.384 (1.00) |
1 (1.00) |
0.461 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.467 (1.00) |
0.931 (1.00) |
|
MED15 | 7 (1%) | 491 |
0.718 (1.00) |
0.193 (1.00) |
1 (1.00) |
0.357 (1.00) |
0.568 (1.00) |
1 (1.00) |
0.764 (1.00) |
0.191 (1.00) |
0.212 (1.00) |
0.149 (1.00) |
0.164 (1.00) |
ERF | 5 (1%) | 493 |
0.72 (1.00) |
0.302 (1.00) |
0.105 (1.00) |
0.589 (1.00) |
0.503 (1.00) |
1 (1.00) |
0.459 (1.00) |
0.325 (1.00) |
0.0758 (1.00) |
0.721 (1.00) |
|
ERN1 | 4 (1%) | 494 |
0.78 (1.00) |
0.283 (1.00) |
0.675 (1.00) |
0.562 (1.00) |
1 (1.00) |
1 (1.00) |
0.238 (1.00) |
0.875 (1.00) |
0.812 (1.00) |
0.37 (1.00) |
|
MLLT10 | 5 (1%) | 493 |
0.766 (1.00) |
0.498 (1.00) |
1 (1.00) |
0.589 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.271 (1.00) |
0.704 (1.00) |
0.218 (1.00) |
1 (1.00) |
ZFHX3 | 16 (3%) | 482 |
0.641 (1.00) |
0.198 (1.00) |
1 (1.00) |
0.716 (1.00) |
0.706 (1.00) |
0.392 (1.00) |
0.354 (1.00) |
0.71 (1.00) |
0.0366 (0.888) |
0.634 (1.00) |
0.26 (1.00) |
FMN1 | 4 (1%) | 494 |
0.78 (1.00) |
0.234 (1.00) |
0.0668 (1.00) |
0.562 (1.00) |
0.0838 (1.00) |
1 (1.00) |
0.659 (1.00) |
0.633 (1.00) |
0.467 (1.00) |
0.0266 (0.888) |
|
AKT1 | 3 (1%) | 495 |
0.841 (1.00) |
0.998 (1.00) |
0.586 (1.00) |
0.461 (1.00) |
0.342 (1.00) |
1 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.944 (1.00) |
0.908 (1.00) |
|
ATM | 22 (4%) | 476 |
0.324 (1.00) |
0.563 (1.00) |
0.073 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0772 (1.00) |
0.841 (1.00) |
0.314 (1.00) |
0.804 (1.00) |
0.347 (1.00) |
STRC | 5 (1%) | 493 |
0.802 (1.00) |
0.515 (1.00) |
0.243 (1.00) |
0.159 (1.00) |
1 (1.00) |
1 (1.00) |
0.22 (1.00) |
0.12 (1.00) |
0.212 (1.00) |
0.468 (1.00) |
|
APC | 10 (2%) | 488 |
0.179 (1.00) |
0.607 (1.00) |
0.577 (1.00) |
1 (1.00) |
0.613 (1.00) |
1 (1.00) |
0.164 (1.00) |
0.559 (1.00) |
0.0377 (0.888) |
0.767 (1.00) |
|
MYOT | 5 (1%) | 493 |
0.725 (1.00) |
0.019 (0.786) |
0.244 (1.00) |
0.562 (1.00) |
1 (1.00) |
0.142 (1.00) |
0.22 (1.00) |
0.875 (1.00) |
0.0344 (0.888) |
0.409 (1.00) |
|
KIRREL | 6 (1%) | 492 |
0.725 (1.00) |
0.736 (1.00) |
0.721 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.742 (1.00) |
0.884 (1.00) |
0.605 (1.00) |
0.453 (1.00) |
1 (1.00) |
PGBD2 | 3 (1%) | 495 |
0.752 (1.00) |
0.032 (0.888) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.395 (1.00) |
0.0619 (1.00) |
0.897 (1.00) |
|
LOC100132247 | 3 (1%) | 495 |
0.887 (1.00) |
0.45 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.0878 (1.00) |
0.605 (1.00) |
0.944 (1.00) |
0.788 (1.00) |
||
EMG1 | 4 (1%) | 494 |
0.469 (1.00) |
0.736 (1.00) |
0.672 (1.00) |
1 (1.00) |
1 (1.00) |
0.115 (1.00) |
0.421 (1.00) |
0.325 (1.00) |
0.977 (1.00) |
0.295 (1.00) |
|
CDH16 | 4 (1%) | 494 |
0.811 (1.00) |
0.932 (1.00) |
0.226 (1.00) |
1 (1.00) |
0.428 (1.00) |
1 (1.00) |
0.42 (1.00) |
0.395 (1.00) |
0.188 (1.00) |
0.439 (1.00) |
|
KRT25 | 6 (1%) | 492 |
0.829 (1.00) |
0.407 (1.00) |
0.477 (1.00) |
0.233 (1.00) |
0.177 (1.00) |
1 (1.00) |
0.46 (1.00) |
0.268 (1.00) |
0.147 (1.00) |
0.645 (1.00) |
1 (1.00) |
P value = 0.00309 (Fisher's exact test), Q value = 0.25
nPatients | T2 | T3 | T4 |
---|---|---|---|
ALL | 188 | 293 | 10 |
TP53 MUTATED | 11 | 44 | 2 |
TP53 WILD-TYPE | 177 | 249 | 8 |
P value = 0.0029 (Fisher's exact test), Q value = 0.25
nPatients | 0 | 1 |
---|---|---|
ALL | 346 | 79 |
TP53 MUTATED | 37 | 19 |
TP53 WILD-TYPE | 309 | 60 |
P value = 0.000136 (Wilcoxon-test), Q value = 0.022
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 407 | 0.4 (1.4) |
TP53 MUTATED | 53 | 1.2 (2.3) |
TP53 WILD-TYPE | 354 | 0.3 (1.1) |
P value = 1.97e-09 (Wilcoxon-test), Q value = 9.5e-07
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 498 | 7.6 (1.0) |
TP53 MUTATED | 57 | 8.4 (0.9) |
TP53 WILD-TYPE | 441 | 7.5 (1.0) |
P value = 0.00304 (Wilcoxon-test), Q value = 0.25
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 498 | 7.6 (1.0) |
ZMYM3 MUTATED | 12 | 8.5 (0.9) |
ZMYM3 WILD-TYPE | 486 | 7.6 (1.0) |
P value = 7.89e-05 (logrank test), Q value = 0.019
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 498 | 10 | 0.8 - 165.2 (30.4) |
ZFP36L2 MUTATED | 4 | 1 | 25.9 - 49.9 (33.0) |
ZFP36L2 WILD-TYPE | 494 | 9 | 0.8 - 165.2 (30.4) |
-
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/PRAD-TP/22592901/transformed.cor.cli.txt
-
Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/PRAD-TP/22506989/PRAD-TP.merged_data.txt
-
Number of patients = 498
-
Number of significantly mutated genes = 44
-
Number of selected clinical features = 11
-
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.