This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 9 genes and 2 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 | ||
nMutated (%) | nWild-Type | logrank test | t-test | |
FBXW7 | 22 (39%) | 35 |
0.567 (1.00) |
0.572 (1.00) |
KRAS | 7 (12%) | 50 |
0.434 (1.00) |
0.782 (1.00) |
TP53 | 51 (89%) | 6 |
0.545 (1.00) |
0.0428 (0.771) |
PIK3CA | 20 (35%) | 37 |
0.183 (1.00) |
0.211 (1.00) |
PPP2R1A | 16 (28%) | 41 |
0.777 (1.00) |
0.8 (1.00) |
PTEN | 11 (19%) | 46 |
0.239 (1.00) |
0.618 (1.00) |
PIK3R1 | 6 (11%) | 51 |
0.705 (1.00) |
0.079 (1.00) |
ZBTB7B | 6 (11%) | 51 |
0.0731 (1.00) |
0.444 (1.00) |
RB1 | 6 (11%) | 51 |
0.23 (1.00) |
0.417 (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 = 9
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Number of selected clinical features = 2
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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 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 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.