Correlation between gene mutation status and molecular subtypes
Ovarian Serous Cystadenocarcinoma (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C1T43RJ9
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/C1T43RJ9
Overview
Introduction

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

Summary

Testing the association between mutation status of 3 genes and 14 molecular subtypes across 316 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 3 genes and 14 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 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		MIR
CNMF 		MIR
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		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 Chi-square 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 Fisher's exact test Fisher's exact test Fisher's exact test
TP53 276 (87%) 40 0.814
(1.00) 		0.407
(1.00) 		0.493
(1.00) 		0.367
(1.00) 		0.553
(1.00) 		0.79
(1.00) 		0.393
(1.00) 		0.316
(1.00) 		0.768
(1.00) 		0.882
(1.00) 		0.341
(1.00) 		0.176
(1.00) 		0.15
(1.00) 		0.727
(1.00)
TBP 4 (1%) 312 1
(1.00) 		0.837
(1.00) 		0.692
(1.00) 		0.596
(1.00) 		0.0365
(1.00) 		0.018
(0.684) 		0.131
(1.00) 		0.872
(1.00) 		1
(1.00) 		1
(1.00) 		0.689
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
SRC 4 (1%) 312 0.838
(1.00) 		0.837
(1.00) 		0.566
(1.00) 		0.16
(1.00) 		0.161
(1.00) 		0.464
(1.00) 		0.483
(1.00) 		0.325
(1.00) 		0.605
(1.00) 		0.324
(1.00)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
TP53 MUTATED 105 101 70
TP53 WILD-TYPE 14 14 12
'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.407 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 118 113
TP53 MUTATED 71 106 99
TP53 WILD-TYPE 14 12 14
'TP53 MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
TP53 MUTATED 83 81 112
TP53 WILD-TYPE 9 15 16
'TP53 MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.367 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 76 75 57 27 49
TP53 MUTATED 29 67 68 50 24 38
TP53 WILD-TYPE 3 9 7 7 3 11
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 112 103 96
TP53 MUTATED 97 93 82
TP53 WILD-TYPE 15 10 14
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
TP53 MUTATED 80 90 106
TP53 WILD-TYPE 10 15 15
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
TP53 MUTATED 65 88 33
TP53 WILD-TYPE 11 8 5
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 45 52 83
TP53 MUTATED 28 41 48 69
TP53 WILD-TYPE 2 4 4 14
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
TP53 MUTATED 60 36 46
TP53 WILD-TYPE 10 4 5
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 66 27
TP53 MUTATED 61 57 24
TP53 WILD-TYPE 7 9 3
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 1

Table S11.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
TP53 MUTATED 65 106 79
TP53 WILD-TYPE 14 13 10
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S12.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 181 102
TP53 MUTATED 3 154 93
TP53 WILD-TYPE 1 27 9
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 1

Table S13.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 124 99
TP53 MUTATED 51 111 88
TP53 WILD-TYPE 13 13 11
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S14.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 5 182
TP53 MUTATED 89 5 156
TP53 WILD-TYPE 11 0 26
'TBP MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S15.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
TBP MUTATED 2 1 1
TBP WILD-TYPE 117 114 81
'TBP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 118 113
TBP MUTATED 1 1 2
TBP WILD-TYPE 84 117 111
'TBP MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
TBP MUTATED 2 1 1
TBP WILD-TYPE 90 95 127
'TBP MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.596 (Chi-square test), Q value = 1

Table S18.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 76 75 57 27 49
TBP MUTATED 0 1 1 2 0 0
TBP WILD-TYPE 32 75 74 55 27 49
'TBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 112 103 96
TBP MUTATED 4 0 0
TBP WILD-TYPE 108 103 96

Figure S1.  Get High-res Image Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

'TBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.68

Table S20.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
TBP MUTATED 0 4 0
TBP WILD-TYPE 90 101 121

Figure S2.  Get High-res Image Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

'TBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 1

Table S21.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #7: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 76 96 38
TBP MUTATED 3 0 0
TBP WILD-TYPE 73 96 38
'TBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #8: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 30 45 52 83
TBP MUTATED 0 0 1 2
TBP WILD-TYPE 30 45 51 81
'TBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S23.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #9: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 70 40 51
TBP MUTATED 1 1 1
TBP WILD-TYPE 69 39 50
'TBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S24.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #10: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 66 27
TBP MUTATED 2 1 0
TBP WILD-TYPE 66 65 27
'TBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S25.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
TBP MUTATED 2 1 1
TBP WILD-TYPE 77 118 88
'TBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S26.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 181 102
TBP MUTATED 0 3 1
TBP WILD-TYPE 4 178 101
'TBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S27.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 124 99
TBP MUTATED 1 2 1
TBP WILD-TYPE 63 122 98
'TBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S28.  Gene #2: 'TBP MUTATION STATUS' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 5 182
TBP MUTATED 1 0 3
TBP WILD-TYPE 99 5 179
'SRC MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 115 82
SRC MUTATED 1 2 1
SRC WILD-TYPE 118 113 81
'SRC MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 118 113
SRC MUTATED 1 1 2
SRC WILD-TYPE 84 117 111
'SRC MUTATION STATUS' versus 'MIR_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S31.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #3: 'MIR_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 96 128
SRC MUTATED 0 2 2
SRC WILD-TYPE 92 94 126
'SRC MUTATION STATUS' versus 'MIR_CHIERARCHICAL'

P value = 0.16 (Chi-square test), Q value = 1

Table S32.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #4: 'MIR_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 32 76 75 57 27 49
SRC MUTATED 1 3 0 0 0 0
SRC WILD-TYPE 31 73 75 57 27 49
'SRC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 1

Table S33.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #5: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 112 103 96
SRC MUTATED 0 3 1
SRC WILD-TYPE 112 100 95
'SRC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S34.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #6: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 90 105 121
SRC MUTATED 0 1 3
SRC WILD-TYPE 90 104 118
'SRC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 119 89
SRC MUTATED 0 1 2
SRC WILD-TYPE 79 118 87
'SRC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.325 (Fisher's exact test), Q value = 1

Table S36.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 181 102
SRC MUTATED 0 1 2
SRC WILD-TYPE 4 180 100
'SRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 1

Table S37.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #13: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 64 124 99
SRC MUTATED 0 1 2
SRC WILD-TYPE 64 123 97
'SRC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S38.  Gene #3: 'SRC MUTATION STATUS' versus Molecular Subtype #14: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 100 5 182
SRC MUTATED 2 0 1
SRC WILD-TYPE 98 5 181
Methods & Data
Input

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

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

  • Number of patients = 316

  • Number of significantly mutated genes = 3

  • Number of Molecular subtypes = 14

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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