This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 20 genes and 11 clinical features across 220 patients, 4 significant findings detected with Q value < 0.25.
-
B2M mutation correlated to 'NEOPLASM.DISEASESTAGE'.
-
RNF43 mutation correlated to 'HISTOLOGICAL.TYPE'.
-
WSB2 mutation correlated to 'NEOPLASM.DISEASESTAGE' and 'NUMBER.OF.LYMPH.NODES'.
Clinical Features |
Time to Death |
AGE |
NEOPLASM DISEASESTAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
HISTOLOGICAL TYPE |
RADIATIONS RADIATION REGIMENINDICATION |
COMPLETENESS OF RESECTION |
NUMBER OF LYMPH NODES |
||
nMutated (%) | nWild-Type | logrank test | t-test | Chi-square test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Fisher's exact test | Chi-square test | Fisher's exact test | Fisher's exact test | t-test | |
WSB2 | 7 (3%) | 213 |
0.255 (1.00) |
0.0175 (1.00) |
6.47e-05 (0.0142) |
0.0133 (1.00) |
0.3 (1.00) |
0.347 (1.00) |
0.247 (1.00) |
0.251 (1.00) |
1 (1.00) |
0.772 (1.00) |
3.68e-07 (8.1e-05) |
B2M | 8 (4%) | 212 |
0.542 (1.00) |
0.351 (1.00) |
0.000154 (0.0337) |
0.282 (1.00) |
0.732 (1.00) |
0.395 (1.00) |
0.716 (1.00) |
0.491 (1.00) |
1 (1.00) |
0.772 (1.00) |
0.506 (1.00) |
RNF43 | 9 (4%) | 211 |
0.119 (1.00) |
0.273 (1.00) |
0.308 (1.00) |
0.0917 (1.00) |
0.155 (1.00) |
0.441 (1.00) |
0.161 (1.00) |
0.00024 (0.0521) |
1 (1.00) |
0.199 (1.00) |
0.49 (1.00) |
PIK3CA | 48 (22%) | 172 |
0.935 (1.00) |
0.464 (1.00) |
0.256 (1.00) |
0.467 (1.00) |
0.876 (1.00) |
0.337 (1.00) |
0.868 (1.00) |
0.873 (1.00) |
1 (1.00) |
0.438 (1.00) |
0.226 (1.00) |
PGM5 | 22 (10%) | 198 |
0.436 (1.00) |
0.0226 (1.00) |
0.0232 (1.00) |
0.0154 (1.00) |
0.881 (1.00) |
0.867 (1.00) |
0.00577 (1.00) |
0.924 (1.00) |
0.473 (1.00) |
0.667 (1.00) |
0.986 (1.00) |
KRAS | 25 (11%) | 195 |
0.759 (1.00) |
0.461 (1.00) |
0.0583 (1.00) |
0.748 (1.00) |
0.486 (1.00) |
1 (1.00) |
0.0491 (1.00) |
0.517 (1.00) |
1 (1.00) |
0.0307 (1.00) |
0.0772 (1.00) |
CBWD1 | 28 (13%) | 192 |
0.47 (1.00) |
0.0242 (1.00) |
0.671 (1.00) |
0.236 (1.00) |
0.625 (1.00) |
0.886 (1.00) |
0.0225 (1.00) |
0.0606 (1.00) |
0.563 (1.00) |
0.844 (1.00) |
0.066 (1.00) |
TP53 | 99 (45%) | 121 |
0.608 (1.00) |
0.699 (1.00) |
0.814 (1.00) |
0.483 (1.00) |
0.788 (1.00) |
0.0269 (1.00) |
0.68 (1.00) |
0.197 (1.00) |
0.412 (1.00) |
0.247 (1.00) |
0.639 (1.00) |
ARID1A | 41 (19%) | 179 |
0.357 (1.00) |
0.302 (1.00) |
0.228 (1.00) |
0.114 (1.00) |
0.366 (1.00) |
0.0398 (1.00) |
0.381 (1.00) |
0.244 (1.00) |
0.596 (1.00) |
0.115 (1.00) |
0.263 (1.00) |
SMAD4 | 19 (9%) | 201 |
0.187 (1.00) |
0.383 (1.00) |
0.684 (1.00) |
0.958 (1.00) |
0.768 (1.00) |
0.606 (1.00) |
0.475 (1.00) |
0.825 (1.00) |
1 (1.00) |
0.472 (1.00) |
0.438 (1.00) |
RHOA | 13 (6%) | 207 |
0.916 (1.00) |
0.296 (1.00) |
0.753 (1.00) |
0.869 (1.00) |
0.774 (1.00) |
1 (1.00) |
0.57 (1.00) |
0.422 (1.00) |
1 (1.00) |
0.783 (1.00) |
0.268 (1.00) |
IRF2 | 14 (6%) | 206 |
0.525 (1.00) |
0.593 (1.00) |
0.205 (1.00) |
0.179 (1.00) |
0.169 (1.00) |
0.637 (1.00) |
1 (1.00) |
0.793 (1.00) |
1 (1.00) |
0.022 (1.00) |
0.00134 (0.29) |
CDH1 | 18 (8%) | 202 |
0.264 (1.00) |
0.114 (1.00) |
0.4 (1.00) |
0.418 (1.00) |
0.489 (1.00) |
0.7 (1.00) |
0.623 (1.00) |
0.134 (1.00) |
1 (1.00) |
0.212 (1.00) |
0.386 (1.00) |
PTEN | 14 (6%) | 206 |
0.221 (1.00) |
0.0486 (1.00) |
0.317 (1.00) |
0.869 (1.00) |
0.421 (1.00) |
0.494 (1.00) |
0.0213 (1.00) |
0.724 (1.00) |
1 (1.00) |
0.0629 (1.00) |
0.249 (1.00) |
FBXW7 | 19 (9%) | 201 |
0.147 (1.00) |
0.306 (1.00) |
0.743 (1.00) |
0.104 (1.00) |
0.968 (1.00) |
0.856 (1.00) |
1 (1.00) |
0.56 (1.00) |
0.422 (1.00) |
0.391 (1.00) |
0.0394 (1.00) |
FAM46D | 6 (3%) | 214 |
0.125 (1.00) |
0.564 (1.00) |
0.781 (1.00) |
0.353 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.995 (1.00) |
1 (1.00) |
1 (1.00) |
0.645 (1.00) |
APC | 33 (15%) | 187 |
0.0757 (1.00) |
0.0484 (1.00) |
0.263 (1.00) |
0.398 (1.00) |
0.341 (1.00) |
0.664 (1.00) |
0.703 (1.00) |
0.507 (1.00) |
0.595 (1.00) |
0.326 (1.00) |
0.722 (1.00) |
MAP2K7 | 14 (6%) | 206 |
0.544 (1.00) |
0.117 (1.00) |
0.518 (1.00) |
0.142 (1.00) |
0.33 (1.00) |
1 (1.00) |
0.574 (1.00) |
0.816 (1.00) |
1 (1.00) |
0.695 (1.00) |
0.758 (1.00) |
TRPS1 | 30 (14%) | 190 |
0.479 (1.00) |
0.373 (1.00) |
0.151 (1.00) |
0.955 (1.00) |
0.635 (1.00) |
0.642 (1.00) |
0.43 (1.00) |
0.835 (1.00) |
1 (1.00) |
0.445 (1.00) |
0.924 (1.00) |
C13ORF33 | 6 (3%) | 214 |
0.869 (1.00) |
0.364 (1.00) |
0.00174 (0.374) |
0.133 (1.00) |
0.0406 (1.00) |
1 (1.00) |
0.685 (1.00) |
0.873 (1.00) |
0.155 (1.00) |
1 (1.00) |
0.198 (1.00) |
P value = 0.000154 (Chi-square test), Q value = 0.034
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 7 | 21 | 24 | 21 | 30 | 3 | 33 | 23 | 18 | 24 |
B2M MUTATED | 1 | 1 | 0 | 0 | 2 | 0 | 0 | 0 | 2 | 1 | 1 |
B2M WILD-TYPE | 0 | 6 | 21 | 24 | 19 | 30 | 3 | 33 | 21 | 17 | 23 |
P value = 0.00024 (Chi-square test), Q value = 0.052
nPatients | STOMACH ADENOCARCINOMA DIFFUSE TYPE | STOMACH ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA NOT OTHERWISE SPECIFIED (NOS) | STOMACH INTESTINAL ADENOCARCINOMA TUBULAR TYPE | STOMACH INTESTINAL ADENOCARCINOMA MUCINOUS TYPE | STOMACH INTESTINAL ADENOCARCINOMA PAPILLARY TYPE | STOMACH ADENOCARCINOMA SIGNET RING TYPE |
---|---|---|---|---|---|---|---|
ALL | 32 | 108 | 34 | 26 | 13 | 5 | 1 |
RNF43 MUTATED | 0 | 5 | 2 | 1 | 0 | 0 | 1 |
RNF43 WILD-TYPE | 32 | 103 | 32 | 25 | 13 | 5 | 0 |
P value = 6.47e-05 (Chi-square test), Q value = 0.014
nPatients | STAGE I | STAGE IA | STAGE IB | STAGE II | STAGE IIA | STAGE IIB | STAGE III | STAGE IIIA | STAGE IIIB | STAGE IIIC | STAGE IV |
---|---|---|---|---|---|---|---|---|---|---|---|
ALL | 1 | 7 | 21 | 24 | 21 | 30 | 3 | 33 | 23 | 18 | 24 |
WSB2 MUTATED | 1 | 1 | 1 | 2 | 1 | 0 | 0 | 0 | 1 | 0 | 0 |
WSB2 WILD-TYPE | 0 | 6 | 20 | 22 | 20 | 30 | 3 | 33 | 22 | 18 | 24 |
P value = 3.68e-07 (t-test), Q value = 8.1e-05
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 191 | 5.2 (7.5) |
WSB2 MUTATED | 7 | 1.0 (1.2) |
WSB2 WILD-TYPE | 184 | 5.3 (7.6) |
-
Mutation data file = transformed.cor.cli.txt
-
Clinical data file = STAD-TP.merged_data.txt
-
Number of patients = 220
-
Number of significantly mutated genes = 20
-
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 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 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 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.