This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 13 genes and 3 clinical features across 57 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 | RACE | ||
nMutated (%) | nWild-Type | logrank test | Wilcoxon-test | Fisher's exact test | |
TP53 | 51 (89%) | 6 |
0.331 (1.00) |
0.0288 (1.00) |
0.217 (1.00) |
FBXW7 | 22 (39%) | 35 |
0.607 (1.00) |
0.407 (1.00) |
1 (1.00) |
PPP2R1A | 16 (28%) | 41 |
0.759 (1.00) |
0.631 (1.00) |
0.533 (1.00) |
PTEN | 11 (19%) | 46 |
0.279 (1.00) |
0.504 (1.00) |
0.677 (1.00) |
KRAS | 7 (12%) | 50 |
0.403 (1.00) |
0.576 (1.00) |
0.556 (1.00) |
ZBTB7B | 6 (11%) | 51 |
0.115 (1.00) |
0.649 (1.00) |
0.22 (1.00) |
CHD4 | 10 (18%) | 47 |
0.486 (1.00) |
0.223 (1.00) |
0.231 (1.00) |
PIK3R1 | 6 (11%) | 51 |
0.691 (1.00) |
0.207 (1.00) |
0.219 (1.00) |
ARHGAP35 | 6 (11%) | 51 |
0.469 (1.00) |
0.0983 (1.00) |
0.0395 (1.00) |
PIK3CA | 20 (35%) | 37 |
0.186 (1.00) |
0.136 (1.00) |
0.757 (1.00) |
MAMLD1 | 4 (7%) | 53 |
0.848 (1.00) |
0.364 (1.00) |
0.306 (1.00) |
RB1 | 6 (11%) | 51 |
0.173 (1.00) |
0.355 (1.00) |
0.329 (1.00) |
LYPLA2 | 3 (5%) | 54 |
0.951 (1.00) |
0.138 (1.00) |
1 (1.00) |
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Mutation data file = transformed.cor.cli.txt
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Clinical data file = UCS-TP.merged_data.txt
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Number of patients = 57
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Number of significantly mutated genes = 13
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Number of selected clinical features = 3
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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.