This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 21 genes and 7 clinical features across 465 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 |
YEARS TO BIRTH |
TUMOR TISSUE SITE |
RADIATION THERAPY |
KARNOFSKY PERFORMANCE SCORE |
RESIDUAL TUMOR |
ETHNICITY | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
TP53 | 384 (83%) | 81 |
0.18 (1.00) |
0.419 (1.00) |
0.437 (1.00) |
0.524 (1.00) |
0.33 (1.00) |
0.284 (1.00) |
0.0539 (1.00) |
RB1 | 15 (3%) | 450 |
0.399 (1.00) |
0.238 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
BRCA1 | 18 (4%) | 447 |
0.442 (1.00) |
0.555 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
NF1 | 24 (5%) | 441 |
0.615 (1.00) |
0.219 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
0.396 (1.00) |
|
CDK12 | 15 (3%) | 450 |
0.761 (1.00) |
0.461 (1.00) |
1 (1.00) |
1 (1.00) |
0.508 (1.00) |
1 (1.00) |
|
KRAS | 5 (1%) | 460 |
0.582 (1.00) |
0.576 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
HNF1B | 5 (1%) | 460 |
0.378 (1.00) |
0.141 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
PTEN | 5 (1%) | 460 |
0.876 (1.00) |
0.916 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
LARP1 | 4 (1%) | 461 |
0.222 (1.00) |
0.688 (1.00) |
1 (1.00) |
0.0352 (1.00) |
1 (1.00) |
||
BRCA2 | 13 (3%) | 452 |
0.00596 (0.876) |
0.588 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
EFEMP1 | 7 (2%) | 458 |
0.623 (1.00) |
0.0712 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
NRAS | 4 (1%) | 461 |
0.977 (1.00) |
0.124 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
MTA2 | 4 (1%) | 461 |
0.063 (1.00) |
0.126 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
ERCC6 | 4 (1%) | 461 |
0.49 (1.00) |
0.41 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
IL21R | 8 (2%) | 457 |
0.119 (1.00) |
0.815 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
PKD1L1 | 6 (1%) | 459 |
0.503 (1.00) |
0.0761 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
SAMD9L | 9 (2%) | 456 |
0.313 (1.00) |
0.203 (1.00) |
1 (1.00) |
1 (1.00) |
0.152 (1.00) |
||
AQP2 | 3 (1%) | 462 |
0.315 (1.00) |
0.217 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
CREBBP | 11 (2%) | 454 |
0.0801 (1.00) |
0.296 (1.00) |
1 (1.00) |
1 (1.00) |
0.207 (1.00) |
||
C9ORF171 | 5 (1%) | 460 |
0.405 (1.00) |
0.0961 (1.00) |
1 (1.00) |
1 (1.00) |
0.705 (1.00) |
1 (1.00) |
|
NCOA3 | 5 (1%) | 460 |
0.0425 (1.00) |
0.628 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
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Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
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Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/OV-TP/22572516/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/OV-TP/22507289/OV-TP.merged_data.txt
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Number of patients = 465
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Number of significantly mutated genes = 21
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Number of selected clinical features = 7
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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.