This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 19 genes and 5 clinical features across 316 patients, no significant finding detected with Q value < 0.25.
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No gene mutations related to clinical features.
Clinical Features |
Time to Death |
AGE |
KARNOFSKY PERFORMANCE SCORE |
RACE | ETHNICITY | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
TP53 | 273 (86%) | 43 |
0.178 (1.00) |
0.7 (1.00) |
0.667 (1.00) |
0.307 (1.00) |
0.0668 (1.00) |
BRCA1 | 12 (4%) | 304 |
0.957 (1.00) |
0.597 (1.00) |
1 (1.00) |
1 (1.00) |
|
FAM86B2 | 6 (2%) | 310 |
0.867 (1.00) |
0.161 (1.00) |
1 (1.00) |
0.185 (1.00) |
|
TBP | 4 (1%) | 312 |
0.321 (1.00) |
0.4 (1.00) |
1 (1.00) |
1 (1.00) |
|
NBPF10 | 4 (1%) | 312 |
0.871 (1.00) |
0.457 (1.00) |
1 (1.00) |
1 (1.00) |
|
NF1 | 14 (4%) | 302 |
0.2 (1.00) |
0.604 (1.00) |
0.655 (1.00) |
0.34 (1.00) |
|
C10ORF140 | 5 (2%) | 311 |
0.916 (1.00) |
0.458 (1.00) |
0.0658 (1.00) |
1 (1.00) |
|
BRCA2 | 11 (3%) | 305 |
0.085 (1.00) |
0.423 (1.00) |
0.565 (1.00) |
1 (1.00) |
|
CDK12 | 8 (3%) | 308 |
0.481 (1.00) |
0.188 (1.00) |
0.452 (1.00) |
1 (1.00) |
|
OR4F21 | 3 (1%) | 313 |
0.199 (1.00) |
1 (1.00) |
1 (1.00) |
||
C9ORF171 | 5 (2%) | 311 |
0.895 (1.00) |
0.0718 (1.00) |
0.7 (1.00) |
1 (1.00) |
1 (1.00) |
HYDIN | 11 (3%) | 305 |
0.908 (1.00) |
0.839 (1.00) |
1 (1.00) |
1 (1.00) |
|
RB1 | 8 (3%) | 308 |
0.248 (1.00) |
0.176 (1.00) |
1 (1.00) |
1 (1.00) |
|
GART | 3 (1%) | 313 |
0.196 (1.00) |
0.019 (1.00) |
1 (1.00) |
1 (1.00) |
|
SRC | 4 (1%) | 312 |
0.197 (1.00) |
0.48 (1.00) |
1 (1.00) |
1 (1.00) |
|
ZNF236 | 7 (2%) | 309 |
0.613 (1.00) |
0.254 (1.00) |
0.362 (1.00) |
1 (1.00) |
|
NBPF16 | 4 (1%) | 312 |
0.972 (1.00) |
0.589 (1.00) |
1 (1.00) |
1 (1.00) |
|
CYP11B1 | 7 (2%) | 309 |
0.0926 (1.00) |
0.864 (1.00) |
0.406 (1.00) |
1 (1.00) |
|
SON | 8 (3%) | 308 |
0.483 (1.00) |
0.0746 (1.00) |
1 (1.00) |
0.157 (1.00) |
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Mutation data file = transformed.cor.cli.txt
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Clinical data file = OV-TP.merged_data.txt
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Number of patients = 316
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Number of significantly mutated genes = 19
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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 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.