Correlation between gene mutation status and molecular subtypes
Cervical Squamous Cell Carcinoma (Primary solid tumor)
23 May 2013  |  analyses__2013_05_23
Maintainer Information
Citation Information
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/C1NS0RWN
Overview
Introduction

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

Summary

Testing the association between mutation status of 5 genes and 8 molecular subtypes across 39 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 5 genes and 8 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
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
PIK3CA 9 (23%) 30 0.098
(1.00)
0.224
(1.00)
0.387
(1.00)
0.734
(1.00)
0.88
(1.00)
0.669
(1.00)
1
(1.00)
0.113
(1.00)
TMCC1 4 (10%) 35 1
(1.00)
0.489
(1.00)
0.0537
(1.00)
0.628
(1.00)
0.556
(1.00)
0.793
(1.00)
1
(1.00)
CDC27 5 (13%) 34 0.397
(1.00)
0.234
(1.00)
0.128
(1.00)
0.0681
(1.00)
0.456
(1.00)
0.302
(1.00)
0.389
(1.00)
0.112
(1.00)
UGT3A2 3 (8%) 36 1
(1.00)
0.0166
(0.631)
0.0517
(1.00)
0.55
(1.00)
0.556
(1.00)
1
(1.00)
0.184
(1.00)
MAPK1 3 (8%) 36 0.141
(1.00)
1
(1.00)
0.398
(1.00)
0.68
(1.00)
0.0885
(1.00)
0.556
(1.00)
0.4
(1.00)
1
(1.00)
Methods & Data
Input
  • Mutation data file = CESC-TP.mutsig.cluster.txt

  • Molecular subtypes file = CESC-TP.transferedmergedcluster.txt

  • Number of patients = 39

  • Number of significantly mutated genes = 5

  • Number of Molecular subtypes = 8

  • 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.

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)