Correlation between gene mutation status and molecular subtypes

Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma (Primary solid tumor)

15 July 2014 | analyses__2014_07_15

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 (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C14X56HQ

Overview

Introduction

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

Summary

Testing the association between mutation status of 2 genes and 8 molecular subtypes across 38 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 2 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
NFE2L2	6 (16%)	32	0.714 (1.00)	0.503 (1.00)	0.185 (1.00)	0.282 (1.00)	0.128 (1.00)	0.57 (1.00)	0.24 (1.00)	0.103 (1.00)
PIK3CA	9 (24%)	29	0.162 (1.00)	0.439 (1.00)	0.193 (1.00)	0.303 (1.00)	0.797 (1.00)	0.875 (1.00)	0.499 (1.00)	0.255 (1.00)

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S1. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	7	15
NFE2L2 MUTATED	2	2	2
NFE2L2 WILD-TYPE	12	5	13

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S2. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	4	12	7	7	2
NFE2L2 MUTATED	0	2	2	1	1	0
NFE2L2 WILD-TYPE	6	2	10	6	6	2

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 1

Table S3. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	7	10
NFE2L2 MUTATED	4	2	0
NFE2L2 WILD-TYPE	16	5	10

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 1

Table S4. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	5	3	7
NFE2L2 MUTATED	4	2	0	0
NFE2L2 WILD-TYPE	18	3	3	7

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 1

Table S5. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	9	16
NFE2L2 MUTATED	0	2	4
NFE2L2 WILD-TYPE	13	7	12

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S6. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	6	22	10
NFE2L2 MUTATED	0	5	1
NFE2L2 WILD-TYPE	6	17	9

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S7. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	12	15
NFE2L2 MUTATED	0	2	4
NFE2L2 WILD-TYPE	11	10	11

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S8. Gene #1: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	2	8	16	6	2	3	1
NFE2L2 MUTATED	0	0	2	2	1	0	1
NFE2L2 WILD-TYPE	2	8	14	4	1	3	0

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 1

Table S9. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	14	7	15
PIK3CA MUTATED	3	0	6
PIK3CA WILD-TYPE	11	7	9

'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S10. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6
ALL	6	4	12	7	7	2
PIK3CA MUTATED	1	1	5	0	2	0
PIK3CA WILD-TYPE	5	3	7	7	5	2

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 1

Table S11. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	20	7	10
PIK3CA MUTATED	7	0	2
PIK3CA WILD-TYPE	13	7	8

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 1

Table S12. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	22	5	3	7
PIK3CA MUTATED	8	0	0	1
PIK3CA WILD-TYPE	14	5	3	6

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S13. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	13	9	16
PIK3CA MUTATED	3	3	3
PIK3CA WILD-TYPE	10	6	13

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S14. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	6	22	10
PIK3CA MUTATED	1	5	3
PIK3CA WILD-TYPE	5	17	7

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S15. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	11	12	15
PIK3CA MUTATED	3	4	2
PIK3CA WILD-TYPE	8	8	13

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 1

Table S16. Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	2	8	16	6	2	3	1
PIK3CA MUTATED	0	1	5	0	1	1	1
PIK3CA WILD-TYPE	2	7	11	6	1	2	0

Methods & Data

Input

Mutation data file = transformed.cor.cli.txt
Molecular subtypes file = CESC-TP.transferedmergedcluster.txt
Number of patients = 38
Number of significantly mutated genes = 2
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.

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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