Cervical Squamous Cell Carcinoma: Correlation between gene mutation status and molecular subtypes<BR>(primary solid tumor cohort)

Cervical Squamous Cell Carcinoma: Correlation between gene mutation status and molecular subtypes
(primary solid tumor cohort)

Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)

Overview

Introduction

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

Summary

Testing the association between mutation status of 9 genes and 6 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 9 genes and 6 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
	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
PIK3CA	9 (23%)	30	0.098 (1.00)	0.358 (1.00)	0.387 (1.00)	0.734 (1.00)	1 (1.00)	0.141 (1.00)
TMCC1	4 (10%)	35		1 (1.00)	0.489 (1.00)	0.0537 (1.00)	0.316 (1.00)	0.793 (1.00)
PRG4	5 (13%)	34	0.294 (1.00)	0.83 (1.00)	0.0205 (1.00)	0.1 (1.00)	0.152 (1.00)	0.389 (1.00)
CDC27	5 (13%)	34	0.397 (1.00)	0.221 (1.00)	0.128 (1.00)	0.0681 (1.00)	0.834 (1.00)	0.14 (1.00)
NFE2L2	6 (15%)	33	0.714 (1.00)	0.506 (1.00)	0.584 (1.00)	0.23 (1.00)	0.123 (1.00)	0.162 (1.00)
MAPK1	3 (8%)	36	0.141 (1.00)	1 (1.00)	0.398 (1.00)	0.68 (1.00)	0.29 (1.00)	1 (1.00)
SSX7	3 (8%)	36		0.762 (1.00)	0.24 (1.00)	0.0517 (1.00)	0.424 (1.00)	1 (1.00)
UGT3A2	3 (8%)	36		0.762 (1.00)	0.0166 (0.83)	0.0517 (1.00)	0.424 (1.00)	0.255 (1.00)
PRB2	4 (10%)	35		1 (1.00)	0.489 (1.00)	0.0537 (1.00)	0.174 (1.00)	0.502 (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 = 9
Number of Molecular subtypes = 6
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)

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