Correlation between gene mutation status and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
15 January 2014  |  analyses__2014_01_15
Maintainer Information
Citation Information
doi:10.7908/C12R3Q5B
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/C12R3Q5B
Overview
Introduction

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

Summary

Testing the association between mutation status of 6 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 6 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 Chi-square test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test
MUC2 8 (12%) 58 1
(1.00) 		0.276
(1.00) 		0.745
(1.00) 		0.71
(1.00) 		0.572
(1.00) 		0.586
(1.00) 		0.49
(1.00) 		0.481
(1.00)
MUC6 21 (32%) 45 0.178
(1.00) 		0.634
(1.00) 		0.253
(1.00) 		0.174
(1.00) 		0.306
(1.00) 		0.252
(1.00) 		0.205
(1.00) 		0.267
(1.00)
TP53 22 (33%) 44 0.615
(1.00) 		0.0856
(1.00) 		0.0665
(1.00) 		0.0593
(1.00) 		0.655
(1.00) 		0.706
(1.00) 		0.76
(1.00) 		0.86
(1.00)
PTEN 6 (9%) 60 0.0988
(1.00) 		0.321
(1.00) 		0.351
(1.00) 		0.13
(1.00) 		0.354
(1.00) 		0.585
(1.00) 		0.00617
(0.296) 		0.0812
(1.00)
PRSS3 7 (11%) 59 0.386
(1.00) 		0.668
(1.00) 		0.0182
(0.855) 		0.252
(1.00) 		0.0815
(1.00) 		0.581
(1.00) 		0.61
(1.00) 		0.159
(1.00)
HLA-C 7 (11%) 59 0.49
(1.00) 		0.574
(1.00) 		0.714
(1.00) 		0.569
(1.00) 		0.158
(1.00) 		0.581
(1.00) 		0.401
(1.00) 		0.561
(1.00)
'MUC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S1.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
MUC2 MUTATED 0 6 2
MUC2 WILD-TYPE 5 41 12
'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
MUC2 MUTATED 2 6 0
MUC2 WILD-TYPE 16 29 13
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
MUC2 MUTATED 3 3 2 0
MUC2 WILD-TYPE 16 19 13 10
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.71 (Chi-square test), Q value = 1

Table S4.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
MUC2 MUTATED 1 0 2 1 4
MUC2 WILD-TYPE 9 10 15 5 19
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
MUC2 MUTATED 1 4 3
MUC2 WILD-TYPE 19 20 19
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
MUC2 MUTATED 0 8
MUC2 WILD-TYPE 9 49
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.49 (Chi-square test), Q value = 1

Table S7.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 16 16 10 14
MUC2 MUTATED 1 1 4 1 1
MUC2 WILD-TYPE 9 15 12 9 13
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
MUC2 MUTATED 0 1 3 4
MUC2 WILD-TYPE 12 7 22 17
'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 1

Table S9.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
MUC6 MUTATED 2 12 7
MUC6 WILD-TYPE 3 35 7
'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S10.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
MUC6 MUTATED 7 11 3
MUC6 WILD-TYPE 11 24 10
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 1

Table S11.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
MUC6 MUTATED 6 10 4 1
MUC6 WILD-TYPE 13 12 11 9
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.174 (Chi-square test), Q value = 1

Table S12.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
MUC6 MUTATED 2 1 9 2 7
MUC6 WILD-TYPE 8 9 8 4 16
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
MUC6 MUTATED 4 10 7
MUC6 WILD-TYPE 16 14 15
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
MUC6 MUTATED 1 20
MUC6 WILD-TYPE 8 37
'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.205 (Chi-square test), Q value = 1

Table S15.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 16 16 10 14
MUC6 MUTATED 6 5 3 4 3
MUC6 WILD-TYPE 4 11 13 6 11
'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.267 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
MUC6 MUTATED 1 3 9 8
MUC6 WILD-TYPE 11 5 16 13
'TP53 MUTATION STATUS' versus 'CN_CNMF'

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

Table S17.  Gene #3: '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 = 0.0856 (Fisher's exact test), Q value = 1

Table S18.  Gene #3: '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 = 0.0665 (Fisher's exact test), Q value = 1

Table S19.  Gene #3: '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 = 0.0593 (Chi-square test), Q value = 1

Table S20.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
TP53 MUTATED 7 1 6 2 6
TP53 WILD-TYPE 3 9 11 4 17
'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: '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 = 0.706 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
TP53 MUTATED 2 20
TP53 WILD-TYPE 7 37
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.76 (Chi-square test), Q value = 1

Table S23.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 16 16 10 14
TP53 MUTATED 5 5 4 3 5
TP53 WILD-TYPE 5 11 12 7 9
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
TP53 MUTATED 3 3 8 8
TP53 WILD-TYPE 9 5 17 13
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0988 (Fisher's exact test), Q value = 1

Table S25.  Gene #4: '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 = 0.321 (Fisher's exact test), Q value = 1

Table S26.  Gene #4: '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 = 0.351 (Fisher's exact test), Q value = 1

Table S27.  Gene #4: '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 = 0.13 (Chi-square test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
PTEN MUTATED 3 0 1 0 2
PTEN WILD-TYPE 7 10 16 6 21
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 1

Table S29.  Gene #4: '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 = 0.585 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2
ALL 9 57
PTEN MUTATED 0 6
PTEN WILD-TYPE 9 51
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00617 (Chi-square test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 16 16 10 14
PTEN MUTATED 4 0 1 0 1
PTEN WILD-TYPE 6 16 15 10 13

Figure S1.  Get High-res Image Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0812 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
PTEN MUTATED 0 0 1 5
PTEN WILD-TYPE 12 8 24 16
'PRSS3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S33.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
PRSS3 MUTATED 0 4 3
PRSS3 WILD-TYPE 5 43 11
'PRSS3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S34.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
PRSS3 MUTATED 1 4 2
PRSS3 WILD-TYPE 17 31 11
'PRSS3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.86

Table S35.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
PRSS3 MUTATED 0 6 1 0
PRSS3 WILD-TYPE 19 16 14 10

Figure S2.  Get High-res Image Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PRSS3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.252 (Chi-square test), Q value = 1

Table S36.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
PRSS3 MUTATED 1 0 4 1 1
PRSS3 WILD-TYPE 9 10 13 5 22
'PRSS3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0815 (Fisher's exact test), Q value = 1

Table S37.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
PRSS3 MUTATED 3 0 4
PRSS3 WILD-TYPE 17 24 18
'PRSS3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
PRSS3 MUTATED 0 7
PRSS3 WILD-TYPE 9 50
'PRSS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.61 (Chi-square test), Q value = 1

Table S39.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 16 16 10 14
PRSS3 MUTATED 0 2 1 2 2
PRSS3 WILD-TYPE 10 14 15 8 12
'PRSS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'PRSS3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
PRSS3 MUTATED 2 1 4 0
PRSS3 WILD-TYPE 10 7 21 21
'HLA-C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S41.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

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

P value = 0.574 (Fisher's exact test), Q value = 1

Table S42.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
HLA-C MUTATED 3 3 1
HLA-C WILD-TYPE 15 32 12
'HLA-C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S43.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
HLA-C MUTATED 3 3 1 0
HLA-C WILD-TYPE 16 19 14 10
'HLA-C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.569 (Chi-square test), Q value = 1

Table S44.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 10 17 6 23
HLA-C MUTATED 1 0 3 0 3
HLA-C WILD-TYPE 9 10 14 6 20
'HLA-C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 1

Table S45.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
HLA-C MUTATED 0 3 4
HLA-C WILD-TYPE 20 21 18
'HLA-C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S46.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 9 57
HLA-C MUTATED 0 7
HLA-C WILD-TYPE 9 50
'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.401 (Chi-square test), Q value = 1

Table S47.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 10 16 16 10 14
HLA-C MUTATED 1 1 3 2 0
HLA-C WILD-TYPE 9 15 13 8 14
'HLA-C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S48.  Gene #6: 'HLA-C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 8 25 21
HLA-C MUTATED 0 1 4 2
HLA-C WILD-TYPE 12 7 21 19
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 = 6

  • 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

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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