This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 33 genes and 5 clinical features across 248 patients, 10 significant findings detected with Q value < 0.25.
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PPP2R1A mutation correlated to 'HISTOLOGICAL.TYPE'.
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CTNNB1 mutation correlated to 'HISTOLOGICAL.TYPE'.
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PIK3R1 mutation correlated to 'HISTOLOGICAL.TYPE'.
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PTEN mutation correlated to 'HISTOLOGICAL.TYPE'.
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KRAS mutation correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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TP53 mutation correlated to 'AGE' and 'HISTOLOGICAL.TYPE'.
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CTCF mutation correlated to 'HISTOLOGICAL.TYPE'.
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ARID1A mutation correlated to 'HISTOLOGICAL.TYPE'.
Clinical Features |
Time to Death |
AGE |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
||
nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | Fisher's exact test | Fisher's exact test | |
KRAS | 53 (21%) | 195 |
0.0827 (1.00) |
0.000274 (0.043) |
0.000253 (0.04) |
0.253 (1.00) |
0.388 (1.00) |
TP53 | 69 (28%) | 179 |
0.0256 (1.00) |
6.15e-06 (0.00099) |
8.52e-23 (1.4e-20) |
0.371 (1.00) |
0.18 (1.00) |
PPP2R1A | 27 (11%) | 221 |
0.831 (1.00) |
0.0374 (1.00) |
0.000478 (0.0746) |
0.52 (1.00) |
1 (1.00) |
CTNNB1 | 74 (30%) | 174 |
0.684 (1.00) |
0.0017 (0.264) |
1.99e-08 (3.24e-06) |
0.381 (1.00) |
0.291 (1.00) |
PIK3R1 | 83 (33%) | 165 |
0.955 (1.00) |
0.806 (1.00) |
1.49e-06 (0.000241) |
0.395 (1.00) |
0.935 (1.00) |
PTEN | 161 (65%) | 87 |
0.00619 (0.934) |
0.0276 (1.00) |
1.23e-23 (2.03e-21) |
0.0503 (1.00) |
0.0517 (1.00) |
CTCF | 44 (18%) | 204 |
0.152 (1.00) |
0.0349 (1.00) |
0.000179 (0.0285) |
1 (1.00) |
0.866 (1.00) |
ARID1A | 83 (33%) | 165 |
0.00573 (0.872) |
0.00721 (1.00) |
0.000113 (0.0181) |
0.673 (1.00) |
0.257 (1.00) |
PIK3CA | 132 (53%) | 116 |
0.0336 (1.00) |
0.195 (1.00) |
0.258 (1.00) |
0.593 (1.00) |
0.18 (1.00) |
PRKAR1B | 4 (2%) | 244 |
0.598 (1.00) |
0.978 (1.00) |
1 (1.00) |
0.608 (1.00) |
1 (1.00) |
FBXW7 | 39 (16%) | 209 |
0.815 (1.00) |
0.904 (1.00) |
0.00409 (0.625) |
0.855 (1.00) |
0.592 (1.00) |
SPOP | 21 (8%) | 227 |
0.375 (1.00) |
0.527 (1.00) |
0.842 (1.00) |
0.811 (1.00) |
0.408 (1.00) |
ARID5B | 29 (12%) | 219 |
0.788 (1.00) |
0.649 (1.00) |
0.00928 (1.00) |
1 (1.00) |
0.161 (1.00) |
FGFR2 | 31 (12%) | 217 |
0.532 (1.00) |
0.998 (1.00) |
0.701 (1.00) |
1 (1.00) |
0.337 (1.00) |
NFE2L2 | 15 (6%) | 233 |
0.629 (1.00) |
0.191 (1.00) |
0.14 (1.00) |
0.589 (1.00) |
0.789 (1.00) |
CCND1 | 14 (6%) | 234 |
0.567 (1.00) |
0.0694 (1.00) |
0.171 (1.00) |
0.565 (1.00) |
0.131 (1.00) |
CHD4 | 35 (14%) | 213 |
0.47 (1.00) |
0.418 (1.00) |
0.477 (1.00) |
0.565 (1.00) |
0.967 (1.00) |
FAM9A | 14 (6%) | 234 |
0.283 (1.00) |
0.913 (1.00) |
0.437 (1.00) |
1 (1.00) |
0.859 (1.00) |
MORC4 | 20 (8%) | 228 |
0.117 (1.00) |
0.0204 (1.00) |
0.269 (1.00) |
1 (1.00) |
1 (1.00) |
CASP8 | 17 (7%) | 231 |
0.497 (1.00) |
0.652 (1.00) |
0.491 (1.00) |
1 (1.00) |
0.67 (1.00) |
FOXA2 | 12 (5%) | 236 |
0.865 (1.00) |
0.531 (1.00) |
1 (1.00) |
0.229 (1.00) |
0.58 (1.00) |
ABI1 | 4 (2%) | 244 |
0.616 (1.00) |
0.0342 (1.00) |
1 (1.00) |
0.302 (1.00) |
0.282 (1.00) |
DNER | 18 (7%) | 230 |
0.499 (1.00) |
0.0414 (1.00) |
0.417 (1.00) |
0.44 (1.00) |
0.806 (1.00) |
BCOR | 30 (12%) | 218 |
0.0526 (1.00) |
0.0419 (1.00) |
0.00741 (1.00) |
1 (1.00) |
0.337 (1.00) |
BRS3 | 15 (6%) | 233 |
0.141 (1.00) |
0.133 (1.00) |
0.14 (1.00) |
0.4 (1.00) |
0.806 (1.00) |
SGK1 | 15 (6%) | 233 |
0.834 (1.00) |
0.427 (1.00) |
0.47 (1.00) |
0.158 (1.00) |
0.122 (1.00) |
NRAS | 9 (4%) | 239 |
0.245 (1.00) |
0.616 (1.00) |
1 (1.00) |
0.722 (1.00) |
1 (1.00) |
TIAL1 | 11 (4%) | 237 |
0.282 (1.00) |
0.475 (1.00) |
0.352 (1.00) |
0.753 (1.00) |
0.639 (1.00) |
SIN3A | 21 (8%) | 227 |
0.422 (1.00) |
0.256 (1.00) |
0.276 (1.00) |
0.811 (1.00) |
1 (1.00) |
SLC48A1 | 5 (2%) | 243 |
0.468 (1.00) |
0.645 (1.00) |
0.621 (1.00) |
0.663 (1.00) |
0.559 (1.00) |
RNF43 | 12 (5%) | 236 |
0.248 (1.00) |
0.644 (1.00) |
0.289 (1.00) |
0.0039 (0.601) |
0.689 (1.00) |
ZFHX3 | 44 (18%) | 204 |
0.634 (1.00) |
0.765 (1.00) |
0.0615 (1.00) |
0.73 (1.00) |
0.558 (1.00) |
RB1 | 20 (8%) | 228 |
0.333 (1.00) |
0.237 (1.00) |
0.0685 (1.00) |
0.465 (1.00) |
0.933 (1.00) |
P value = 0.000478 (Fisher's exact test), Q value = 0.075
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 200 | 4 | 44 |
PPP2R1A MUTATED | 14 | 1 | 12 |
PPP2R1A WILD-TYPE | 186 | 3 | 32 |
P value = 1.99e-08 (Fisher's exact test), Q value = 3.2e-06
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 200 | 4 | 44 |
CTNNB1 MUTATED | 74 | 0 | 0 |
CTNNB1 WILD-TYPE | 126 | 4 | 44 |
P value = 1.49e-06 (Fisher's exact test), Q value = 0.00024
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 200 | 4 | 44 |
PIK3R1 MUTATED | 80 | 1 | 2 |
PIK3R1 WILD-TYPE | 120 | 3 | 42 |
P value = 1.23e-23 (Fisher's exact test), Q value = 2e-21
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
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ALL | 200 | 4 | 44 |
PTEN MUTATED | 159 | 1 | 1 |
PTEN WILD-TYPE | 41 | 3 | 43 |
P value = 0.000274 (t-test), Q value = 0.043
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 248 | 63.1 (11.1) |
KRAS MUTATED | 53 | 58.8 (8.7) |
KRAS WILD-TYPE | 195 | 64.3 (11.4) |
P value = 0.000253 (Fisher's exact test), Q value = 0.04
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 200 | 4 | 44 |
KRAS MUTATED | 52 | 0 | 1 |
KRAS WILD-TYPE | 148 | 4 | 43 |
P value = 6.15e-06 (t-test), Q value = 0.00099
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 248 | 63.1 (11.1) |
TP53 MUTATED | 69 | 67.9 (9.4) |
TP53 WILD-TYPE | 179 | 61.3 (11.2) |
P value = 8.52e-23 (Fisher's exact test), Q value = 1.4e-20
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 200 | 4 | 44 |
TP53 MUTATED | 27 | 3 | 39 |
TP53 WILD-TYPE | 173 | 1 | 5 |
P value = 0.000179 (Fisher's exact test), Q value = 0.028
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 200 | 4 | 44 |
CTCF MUTATED | 44 | 0 | 0 |
CTCF WILD-TYPE | 156 | 4 | 44 |
P value = 0.000113 (Fisher's exact test), Q value = 0.018
nPatients | ENDOMETRIOID ENDOMETRIAL ADENOCARCINOMA | MIXED SEROUS AND ENDOMETRIOID | SEROUS ENDOMETRIAL ADENOCARCINOMA |
---|---|---|---|
ALL | 200 | 4 | 44 |
ARID1A MUTATED | 78 | 1 | 4 |
ARID1A WILD-TYPE | 122 | 3 | 40 |
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Mutation data file = transformed.cor.cli.txt
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Clinical data file = UCEC-TP.merged_data.txt
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Number of patients = 248
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Number of significantly mutated genes = 33
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Number of selected clinical features = 5
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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 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.