Correlation between gene mutation status and molecular subtypes
Bladder Urothelial Carcinoma (Primary solid tumor)
23 May 2013 | analyses__2013_05_23
Maintainer Information
Citation Information
doi:10.7908/C12805MK
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C12805MK
Overview
Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 3 genes and 10 molecular subtypes across 28 patients, no significant finding detected with P value < 0.05 and Q value < 0.25.

- No gene mutations related to molecuar subtypes.

Results
Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 3 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, no significant finding detected.

|  | Clinical Features | CN CNMF | METHLYATION CNMF | RPPA CNMF | RPPA CHIERARCHICAL | MRNASEQ CNMF | MRNASEQ CHIERARCHICAL | MIRSEQ CNMF | MIRSEQ CHIERARCHICAL | MIRSEQ MATURE CNMF | MIRSEQ MATURE CHIERARCHICAL
| nMutated (%) | nWild-Type | Fisher's exact 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 | Fisher's exact test | Fisher's exact test | Fisher's exact test
TP53 | 11 (39%) | 17 | 1 (1.00) | 0.179 (1.00) | 0.553 (1.00) | 0.143 (1.00) | 0.0144 (0.433) | 0.351 (1.00) | 0.886 (1.00) | 0.589 (1.00) | 0.886 (1.00) | 0.285 (1.00)
FBXW7 | 5 (18%) | 23 | 0.238 (1.00) | 0.0241 (0.7) | 0.651 (1.00) | 0.834 (1.00) | 0.379 (1.00) | 0.156 (1.00) | 0.819 (1.00) | 0.727 (1.00) | 0.546 (1.00) | 0.298 (1.00)
NFE2L2 | 4 (14%) | 24 | 0.238 (1.00) | 0.435 (1.00) | 0.212 (1.00) | 1 (1.00) | 1 (1.00) | 0.548 (1.00) | 0.533 (1.00) | 0.492 (1.00) | 1 (1.00) | 0.325 (1.00)

Methods & Data
Input

- Mutation data file = BLCA-TP.mutsig.cluster.txt

- Molecular subtypes file = BLCA-TP.transferedmergedcluster.txt

- Number of patients = 28

- Number of significantly mutated genes = 3

- Number of Molecular subtypes = 10

- Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

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

Q value calculation

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.

Download Results

This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.

- Analysis Results (MD5 checksum)

- Auxiliary Data (MD5 checksum)

- MAGE-TAB File (MD5 checksum)

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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