Correlation between gene mutation status and molecular subtypes
Kidney Renal Papillary Cell Carcinoma (Primary solid tumor)
15 January 2014 | analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1668BKS
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1668BKS
Overview
Introduction

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

Summary

Testing the association between 'NF2 MUTATION ANALYSIS' and 8 molecular subtypes across 112 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 1 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
NF2 | 7 (6%) | 105 | 0.0599 (0.479) | 0.0672 (0.479) | 0.237 (1.00) | 0.471 (1.00) | 0.891 (1.00) | 0.423 (1.00) | 1 (1.00) | 1 (1.00)

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0599 (Fisher's exact test), Q value = 0.48

Table S1. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 20 | 51 | 20 | 21
NF2 MUTATED | 0 | 3 | 0 | 4
NF2 WILD-TYPE | 20 | 48 | 20 | 17

'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0672 (Fisher's exact test), Q value = 0.48

Table S2. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 28 | 31 | 38
NF2 MUTATED | 0 | 5 | 2
NF2 WILD-TYPE | 28 | 26 | 36

'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3 | CLUS_4
--- | --- | --- | --- | ---
ALL | 41 | 25 | 17 | 20
NF2 MUTATED | 5 | 2 | 0 | 0
NF2 WILD-TYPE | 36 | 23 | 17 | 20

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 23 | 44 | 36
NF2 MUTATED | 3 | 2 | 2
NF2 WILD-TYPE | 20 | 42 | 34

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 41 | 45 | 26
NF2 MUTATED | 2 | 3 | 2
NF2 WILD-TYPE | 39 | 42 | 24

'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 16 | 49 | 47
NF2 MUTATED | 2 | 2 | 3
NF2 WILD-TYPE | 14 | 47 | 44

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 42 | 50 | 20
NF2 MUTATED | 3 | 3 | 1
NF2 WILD-TYPE | 39 | 47 | 19

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients | CLUS_1 | CLUS_2 | CLUS_3
--- | --- | --- | ---
ALL | 12 | 53 | 47
NF2 MUTATED | 0 | 4 | 3
NF2 WILD-TYPE | 12 | 49 | 44

Methods & Data
Input

- Mutation data file = transformed.cor.cli.txt

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

- Number of patients = 112

- Number of significantly mutated genes = 1: 'NF2 MUTATION ANALYSIS'

- 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

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

- 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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