Correlation between gene mutation status and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
17 October 2014  |  analyses__2014_10_17
Maintainer Information
Citation Information
doi:10.7908/C1BR8R1B
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/C1BR8R1B
Overview
Introduction

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

Summary

Testing the association between mutation status of 4 genes and 8 molecular subtypes across 66 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 4 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
TP53 22 (33%) 44 0.615
(1.00) 		0.0891
(1.00) 		0.0657
(1.00) 		0.016
(0.495) 		0.643
(1.00) 		0.662
(1.00) 		1
(1.00) 		0.688
(1.00)
PTEN 6 (9%) 60 0.0996
(1.00) 		0.322
(1.00) 		0.352
(1.00) 		0.475
(1.00) 		0.353
(1.00) 		0.0674
(1.00) 		0.372
(1.00) 		0.374
(1.00)
PABPC1 7 (11%) 59 0.489
(1.00) 		0.236
(1.00) 		0.204
(1.00) 		0.74
(1.00) 		0.61
(1.00) 		0.308
(1.00) 		0.286
(1.00) 		0.143
(1.00)
URGCP 3 (5%) 63 0.648
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.195
(1.00) 		0.542
(1.00) 		0.152
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
TP53 MUTATED 2 14 6
TP53 WILD-TYPE 3 33 8
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0891 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
TP53 MUTATED 3 16 3
TP53 WILD-TYPE 15 19 10
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0657 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
TP53 MUTATED 6 6 9 1
TP53 WILD-TYPE 13 16 6 9
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.016 (Fisher's exact test), Q value = 0.49

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
TP53 MUTATED 5 6 1 0 7 3 0
TP53 WILD-TYPE 14 10 6 6 3 1 4

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
TP53 MUTATED 5 9 8
TP53 WILD-TYPE 15 15 14
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
TP53 MUTATED 7 5 3 1 1 3 2
TP53 WILD-TYPE 11 6 9 5 4 2 7
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
TP53 MUTATED 7 11
TP53 WILD-TYPE 12 18
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
TP53 MUTATED 4 3 2 2 1 3 3 0
TP53 WILD-TYPE 6 3 3 6 3 3 2 4
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0996 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
PTEN MUTATED 2 3 1
PTEN WILD-TYPE 3 44 13
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
PTEN MUTATED 3 3 0
PTEN WILD-TYPE 15 32 13
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
PTEN MUTATED 2 1 3 0
PTEN WILD-TYPE 17 21 12 10
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.475 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
PTEN MUTATED 2 1 0 0 3 0 0
PTEN WILD-TYPE 17 15 7 6 7 4 4
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
PTEN MUTATED 1 4 1
PTEN WILD-TYPE 19 20 21
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0674 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
PTEN MUTATED 5 0 0 0 0 1 0
PTEN WILD-TYPE 13 11 12 6 5 4 9
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2
ALL 19 29
PTEN MUTATED 3 2
PTEN WILD-TYPE 16 27
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
PTEN MUTATED 3 0 1 0 0 0 1 0
PTEN WILD-TYPE 7 6 4 8 4 6 4 4
'PABPC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 1

Table S17.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
PABPC1 MUTATED 1 4 2
PABPC1 WILD-TYPE 4 43 12
'PABPC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 1

Table S18.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
PABPC1 MUTATED 2 2 3
PABPC1 WILD-TYPE 16 33 10
'PABPC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
PABPC1 MUTATED 2 1 1 3
PABPC1 WILD-TYPE 17 21 14 7
'PABPC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S20.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
PABPC1 MUTATED 2 1 2 1 1 0 0
PABPC1 WILD-TYPE 17 15 5 5 9 4 4
'PABPC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
PABPC1 MUTATED 3 3 1
PABPC1 WILD-TYPE 17 21 21
'PABPC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
PABPC1 MUTATED 2 1 0 1 0 0 3
PABPC1 WILD-TYPE 16 10 12 5 5 5 6
'PABPC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
PABPC1 MUTATED 3 1
PABPC1 WILD-TYPE 16 28
'PABPC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 10 6 5 8 4 6 5 4
PABPC1 MUTATED 0 0 1 0 0 2 1 0
PABPC1 WILD-TYPE 10 6 4 8 4 4 4 4
'URGCP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
URGCP MUTATED 0 2 1
URGCP WILD-TYPE 5 45 13
'URGCP MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S26.  Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
URGCP MUTATED 1 2 0
URGCP WILD-TYPE 17 33 13
'URGCP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S27.  Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
URGCP MUTATED 1 1 1 0
URGCP WILD-TYPE 18 21 14 10
'URGCP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S28.  Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 19 16 7 6 10 4 4
URGCP MUTATED 1 1 0 0 1 0 0
URGCP WILD-TYPE 18 15 7 6 9 4 4
'URGCP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
URGCP MUTATED 2 0 1
URGCP WILD-TYPE 18 24 21
'URGCP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.542 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 18 11 12 6 5 5 9
URGCP MUTATED 1 0 0 1 0 0 1
URGCP WILD-TYPE 17 11 12 5 5 5 8
'URGCP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'URGCP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
URGCP MUTATED 2 0
URGCP WILD-TYPE 17 29
Methods & Data
Input

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

  • Molecular subtypes file = KICH-TP.transferedmergedcluster.txt

  • Number of patients = 66

  • Number of significantly mutated genes = 4

  • 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)
Copyright © 2015 Broad Institute TCGA GDAC as part of the TCGA Research Network. All rights reserved.
Made with Nozzle