This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 8 genes and 12 clinical features across 66 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 |
PATHOLOGIC STAGE |
PATHOLOGY T STAGE |
PATHOLOGY N STAGE |
PATHOLOGY M STAGE |
GENDER |
KARNOFSKY PERFORMANCE SCORE |
NUMBER PACK YEARS SMOKED |
YEAR OF TOBACCO SMOKING ONSET |
RACE | ETHNICITY | ||
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 | Fisher's exact test | Wilcoxon-test | Wilcoxon-test | Fisher's exact test | Fisher's exact test | |
TP53 | 22 (33%) | 44 |
0.0218 (0.398) |
0.935 (1.00) |
0.307 (1.00) |
0.368 (1.00) |
0.036 (0.398) |
0.524 (1.00) |
1 (1.00) |
1 (1.00) |
0.394 (1.00) |
0.885 (1.00) |
0.194 (0.886) |
1 (1.00) |
PTEN | 6 (9%) | 60 |
0.00945 (0.326) |
0.422 (1.00) |
0.0497 (0.398) |
0.0308 (0.398) |
0.0874 (0.531) |
1 (1.00) |
0.217 (0.886) |
0.215 (0.886) |
0.213 (0.886) |
|||
ZNF814 | 3 (5%) | 63 |
0.488 (1.00) |
0.414 (1.00) |
0.589 (1.00) |
0.634 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
|||
CDC27 | 6 (9%) | 60 |
0.945 (1.00) |
0.0742 (0.531) |
0.0405 (0.398) |
0.0431 (0.398) |
1 (1.00) |
1 (1.00) |
0.682 (1.00) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||
PABPC1 | 7 (11%) | 59 |
0.0116 (0.326) |
0.252 (0.928) |
0.00426 (0.326) |
0.0461 (0.398) |
0.0874 (0.531) |
1 (1.00) |
0.226 (0.886) |
1 (1.00) |
0.0136 (0.326) |
1 (1.00) |
||
AMAC1L3 | 5 (8%) | 61 |
0.418 (1.00) |
0.799 (1.00) |
0.902 (1.00) |
0.615 (1.00) |
1 (1.00) |
0.641 (1.00) |
0.231 (0.886) |
0.331 (1.00) |
1 (1.00) |
|||
GFM1 | 3 (5%) | 63 |
0.0886 (0.531) |
0.261 (0.928) |
0.136 (0.724) |
0.193 (0.886) |
0.11 (0.618) |
1 (1.00) |
1 (1.00) |
1 (1.00) |
||||
PABPC3 | 7 (11%) | 59 |
0.658 (1.00) |
0.0327 (0.398) |
0.656 (1.00) |
0.616 (1.00) |
1 (1.00) |
1 (1.00) |
0.691 (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/KICH-TP/22569433/transformed.cor.cli.txt
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Clinical data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KICH-TP/22506450/KICH-TP.merged_data.txt
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Number of patients = 66
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Number of significantly mutated genes = 8
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Number of selected clinical features = 12
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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.