Skin Cutaneous Melanoma: Correlation between gene mutation status and molecular subtypes<BR>(WT cohort)

Skin Cutaneous Melanoma: Correlation between gene mutation status and molecular subtypes
(WT 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 8 genes and 8 molecular subtypes across 34 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 8 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	RPPA CNMF	RPPA CHIERARCHICAL	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	Fisher's exact test	Fisher's exact test
IDH1	3 (9%)	31	1 (1.00)	0.238 (1.00)	1 (1.00)		1 (1.00)	1 (1.00)	0.233 (1.00)	0.625 (1.00)
ADAMTS9	7 (21%)	27	1 (1.00)	0.672 (1.00)	1 (1.00)	0.624 (1.00)	0.0735 (1.00)	0.279 (1.00)	1 (1.00)	0.873 (1.00)
RAC1	5 (15%)	29	1 (1.00)	1 (1.00)	0.211 (1.00)	0.393 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)	1 (1.00)
SERPINI2	5 (15%)	29	1 (1.00)	1 (1.00)	0.582 (1.00)	1 (1.00)	0.626 (1.00)	0.814 (1.00)	1 (1.00)	1 (1.00)
EYA1	3 (9%)	31	0.227 (1.00)	0.238 (1.00)	1 (1.00)		0.274 (1.00)	0.359 (1.00)	1 (1.00)	0.282 (1.00)
ESRP1	6 (18%)	28	0.656 (1.00)	0.37 (1.00)	1 (1.00)	0.663 (1.00)	0.647 (1.00)	0.451 (1.00)	0.375 (1.00)	0.105 (1.00)
PCDHB5	5 (15%)	29	1 (1.00)	0.355 (1.00)	1 (1.00)		0.338 (1.00)	0.387 (1.00)	0.346 (1.00)	0.847 (1.00)
PLCB4	6 (18%)	28	1 (1.00)	1 (1.00)	1 (1.00)		0.338 (1.00)	0.387 (1.00)	0.0701 (1.00)	0.547 (1.00)

Methods & Data

Input

Mutation data file = SKCM-WT.mutsig.cluster.txt
Molecular subtypes file = SKCM-WT.transferedmergedcluster.txt
Number of patients = 34
Number of significantly mutated genes = 8
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)

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