This pipeline computes the correlation between significantly recurrent gene mutations and selected clinical features.
Testing the association between mutation status of 7 genes and 9 clinical features across 21 patients, no significant finding detected with Q value < 0.25.
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No gene mutations related to clinical features.
Table 1. Get Full Table Overview of the association between mutation status of 7 genes and 9 clinical features. Shown in the table are P values (Q values). Thresholded by Q value < 0.25, no significant finding detected.
Clinical Features |
Time to Death |
AGE |
RADIATIONS RADIATION REGIMENINDICATION |
NUMBERPACKYEARSSMOKED | TOBACCOSMOKINGHISTORYINDICATOR |
DISTANT METASTASIS |
LYMPH NODE METASTASIS |
NUMBER OF LYMPH NODES |
TUMOR STAGECODE |
||
nMutated (%) | nWild-Type | logrank test | t-test | Fisher's exact test | t-test | t-test | Fisher's exact test | Fisher's exact test | t-test | t-test | |
PIK3CA | 4 (19%) | 17 |
0.277 (1.00) |
0.462 (1.00) |
1 (1.00) |
0.0368 (1.00) |
1 (1.00) |
0.559 (1.00) |
0.479 (1.00) |
||
TMCC1 | 3 (14%) | 18 |
0.207 (1.00) |
0.408 (1.00) |
0.586 (1.00) |
0.364 (1.00) |
1 (1.00) |
1 (1.00) |
0.933 (1.00) |
||
PRG4 | 4 (19%) | 17 |
0.173 (1.00) |
0.814 (1.00) |
0.0351 (1.00) |
0.313 (1.00) |
1 (1.00) |
1 (1.00) |
|||
CDC27 | 4 (19%) | 17 |
0.182 (1.00) |
0.333 (1.00) |
0.311 (1.00) |
0.313 (1.00) |
1 (1.00) |
0.275 (1.00) |
0.185 (1.00) |
||
NFE2L2 | 4 (19%) | 17 |
0.736 (1.00) |
0.687 (1.00) |
1 (1.00) |
0.679 (1.00) |
0.522 (1.00) |
0.0686 (1.00) |
0.885 (1.00) |
||
UGT3A2 | 3 (14%) | 18 |
0.207 (1.00) |
0.72 (1.00) |
0.586 (1.00) |
0.364 (1.00) |
0.522 (1.00) |
0.559 (1.00) |
0.518 (1.00) |
||
PRB2 | 3 (14%) | 18 |
0.207 (1.00) |
0.919 (1.00) |
0.0902 (1.00) |
0.364 (1.00) |
0.522 (1.00) |
1 (1.00) |
0.933 (1.00) |
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Mutation data file = CESC-TP.mutsig.cluster.txt
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Clinical data file = CESC-TP.clin.merged.picked.txt
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Number of patients = 21
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Number of significantly mutated genes = 7
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Number of selected clinical features = 9
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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 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.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.