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.

- 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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