Correlation between gene mutation status and molecular subtypes
Kidney Chromophobe (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C13F4NV2
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C13F4NV2
Overview
Introduction

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

Summary

Testing the association between mutation status of 8 genes and 10 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 8 genes and 10 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 		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 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 0.613
(0.991) 		0.0885
(0.731) 		0.167
(0.851) 		0.0558
(0.731) 		0.063
(0.731) 		0.0153
(0.731) 		0.644
(0.991) 		0.66
(0.991) 		1
(1.00) 		0.69
(1.00)
PTEN 6 (9%) 60 0.0995
(0.731) 		0.32
(0.851) 		0.307
(0.851) 		0.846
(1.00) 		0.352
(0.851) 		0.474
(0.991) 		0.353
(0.851) 		0.068
(0.731) 		0.372
(0.851) 		0.372
(0.851)
ZNF814 3 (5%) 63 0.647
(0.991) 		0.586
(0.991) 		1
(1.00) 		1
(1.00) 		0.0902
(0.731) 		0.0781
(0.731) 		0.196
(0.851) 		0.284
(0.851) 		0.152
(0.851)
CDC27 6 (9%) 60 0.766
(1.00) 		0.857
(1.00) 		0.557
(0.991) 		0.755
(1.00) 		0.3
(0.851) 		0.368
(0.851) 		1
(1.00) 		0.86
(1.00) 		1
(1.00) 		0.36
(0.851)
PABPC1 7 (11%) 59 0.489
(0.991) 		0.238
(0.851) 		0.535
(0.991) 		0.669
(0.991) 		0.205
(0.851) 		0.744
(1.00) 		0.61
(0.991) 		0.308
(0.851) 		0.286
(0.851) 		0.145
(0.851)
AMAC1L3 5 (8%) 61 0.55
(0.991) 		0.387
(0.86) 		0.554
(0.991) 		0.809
(1.00) 		0.118
(0.784) 		0.0429
(0.731) 		0.727
(1.00) 		0.1
(0.731) 		1
(1.00) 		0.326
(0.851)
GFM1 3 (5%) 63 1
(1.00) 		1
(1.00) 		0.615
(0.991) 		0.59
(0.991) 		1
(1.00) 		1
(1.00) 		0.768
(1.00) 		0.606
(0.991) 		1
(1.00)
PABPC3 7 (11%) 59 0.0411
(0.731) 		0.366
(0.851) 		0.88
(1.00) 		0.215
(0.851) 		0.895
(1.00) 		0.708
(1.00) 		0.48
(0.991) 		0.293
(0.851) 		0.669
(0.991) 		0.299
(0.851)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.613 (Fisher's exact test), Q value = 0.99

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 = 0.0885 (Fisher's exact test), Q value = 0.73

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 'RPPA_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
TP53 MUTATED 12 6 4
TP53 WILD-TYPE 14 11 16
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0558 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
TP53 MUTATED 14 3 5
TP53 WILD-TYPE 15 17 9
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.063 (Fisher's exact test), Q value = 0.73

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0153 (Fisher's exact test), Q value = 0.73

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 0.99

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.66 (Fisher's exact test), Q value = 0.99

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: '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 S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.69 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0995 (Fisher's exact test), Q value = 0.73

Table S11.  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 = 0.32 (Fisher's exact test), Q value = 0.85

Table S12.  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 'RPPA_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.85

Table S13.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
PTEN MUTATED 3 2 0
PTEN WILD-TYPE 23 15 20
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
PTEN MUTATED 3 1 1
PTEN WILD-TYPE 26 19 13
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.85

Table S15.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.474 (Fisher's exact test), Q value = 0.99

Table S16.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.85

Table S17.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.068 (Fisher's exact test), Q value = 0.73

Table S18.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.85

Table S19.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.372 (Fisher's exact test), Q value = 0.85

Table S20.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: '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
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 0.99

Table S21.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
ZNF814 MUTATED 0 2 1
ZNF814 WILD-TYPE 5 45 13
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 0.99

Table S22.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
ZNF814 MUTATED 0 2 1
ZNF814 WILD-TYPE 18 33 12
'ZNF814 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S23.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
ZNF814 MUTATED 1 1 1
ZNF814 WILD-TYPE 25 16 19
'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S24.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
ZNF814 MUTATED 1 1 1
ZNF814 WILD-TYPE 28 19 13
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0902 (Fisher's exact test), Q value = 0.73

Table S25.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
ZNF814 MUTATED 0 1 0 2
ZNF814 WILD-TYPE 19 21 15 8
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0781 (Fisher's exact test), Q value = 0.73

Table S26.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: '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
ZNF814 MUTATED 0 1 0 2 0 0 0
ZNF814 WILD-TYPE 19 15 7 4 10 4 4
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.85

Table S27.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
ZNF814 MUTATED 2 0 1
ZNF814 WILD-TYPE 18 24 21
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.85

Table S28.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: '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
ZNF814 MUTATED 0 0 1 0 1 0 1
ZNF814 WILD-TYPE 18 11 11 6 4 5 8
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.85

Table S29.  Gene #3: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
ZNF814 MUTATED 2 0
ZNF814 WILD-TYPE 17 29
'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S30.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
CDC27 MUTATED 0 4 2
CDC27 WILD-TYPE 5 43 12
'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S31.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
CDC27 MUTATED 1 4 1
CDC27 WILD-TYPE 17 31 12
'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 0.99

Table S32.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
CDC27 MUTATED 4 1 1
CDC27 WILD-TYPE 22 16 19
'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S33.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
CDC27 MUTATED 4 1 1
CDC27 WILD-TYPE 25 19 13
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.85

Table S34.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
CDC27 MUTATED 1 4 0 1
CDC27 WILD-TYPE 18 18 15 9
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.85

Table S35.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: '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
CDC27 MUTATED 1 4 1 0 0 0 0
CDC27 WILD-TYPE 18 12 6 6 10 4 4
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S36.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
CDC27 MUTATED 2 2 2
CDC27 WILD-TYPE 18 22 20
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S37.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: '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
CDC27 MUTATED 1 1 2 0 0 1 1
CDC27 WILD-TYPE 17 10 10 6 5 4 8
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S38.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
CDC27 MUTATED 1 3
CDC27 WILD-TYPE 18 26
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 0.85

Table S39.  Gene #4: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: '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
CDC27 MUTATED 0 2 0 1 0 1 0 0
CDC27 WILD-TYPE 10 4 5 7 4 5 5 4
'PABPC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 0.99

Table S40.  Gene #5: '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 = 0.238 (Fisher's exact test), Q value = 0.85

Table S41.  Gene #5: '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 'RPPA_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 0.99

Table S42.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
PABPC1 MUTATED 4 2 1
PABPC1 WILD-TYPE 22 15 19
'PABPC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.669 (Fisher's exact test), Q value = 0.99

Table S43.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
PABPC1 MUTATED 4 1 2
PABPC1 WILD-TYPE 25 19 12
'PABPC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.85

Table S44.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.744 (Fisher's exact test), Q value = 1

Table S45.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.99

Table S46.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.85

Table S47.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.85

Table S48.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.145 (Fisher's exact test), Q value = 0.85

Table S49.  Gene #5: 'PABPC1 MUTATION STATUS' versus Molecular Subtype #10: '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
'AMAC1L3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.99

Table S50.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
AMAC1L3 MUTATED 0 3 2
AMAC1L3 WILD-TYPE 5 44 12
'AMAC1L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.86

Table S51.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
AMAC1L3 MUTATED 0 4 1
AMAC1L3 WILD-TYPE 18 31 12
'AMAC1L3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.99

Table S52.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
AMAC1L3 MUTATED 2 0 2
AMAC1L3 WILD-TYPE 24 17 18
'AMAC1L3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
AMAC1L3 MUTATED 2 2 0
AMAC1L3 WILD-TYPE 27 18 14
'AMAC1L3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.78

Table S54.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
AMAC1L3 MUTATED 0 1 3 1
AMAC1L3 WILD-TYPE 19 21 12 9
'AMAC1L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.73

Table S55.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #6: '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
AMAC1L3 MUTATED 0 1 0 1 1 2 0
AMAC1L3 WILD-TYPE 19 15 7 5 9 2 4

Figure S2.  Get High-res Image Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S56.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
AMAC1L3 MUTATED 2 1 2
AMAC1L3 WILD-TYPE 18 23 20
'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.73

Table S57.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #8: '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
AMAC1L3 MUTATED 0 2 1 2 0 0 0
AMAC1L3 WILD-TYPE 18 9 11 4 5 5 9
'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S58.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
AMAC1L3 MUTATED 1 2
AMAC1L3 WILD-TYPE 18 27
'AMAC1L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.85

Table S59.  Gene #6: 'AMAC1L3 MUTATION STATUS' versus Molecular Subtype #10: '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
AMAC1L3 MUTATED 0 0 1 0 0 1 1 0
AMAC1L3 WILD-TYPE 10 6 4 8 4 5 4 4
'GFM1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S60.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
GFM1 MUTATED 0 3 0
GFM1 WILD-TYPE 5 44 14
'GFM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S61.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
GFM1 MUTATED 1 2 0
GFM1 WILD-TYPE 17 33 13
'GFM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 0.99

Table S62.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
GFM1 MUTATED 2 1 0
GFM1 WILD-TYPE 24 16 20
'GFM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 0.99

Table S63.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
GFM1 MUTATED 2 0 1
GFM1 WILD-TYPE 27 20 13
'GFM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S64.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
GFM1 MUTATED 1 1 1 0
GFM1 WILD-TYPE 18 21 14 10
'GFM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S65.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #6: '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
GFM1 MUTATED 1 1 0 0 1 0 0
GFM1 WILD-TYPE 18 15 7 6 9 4 4
'GFM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S66.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
GFM1 MUTATED 0 2 1
GFM1 WILD-TYPE 20 22 21
'GFM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 0.99

Table S67.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #8: '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
GFM1 MUTATED 1 1 0 0 0 1 0
GFM1 WILD-TYPE 17 10 12 6 5 4 9
'GFM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S68.  Gene #7: 'GFM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
GFM1 MUTATED 1 1
GFM1 WILD-TYPE 18 28
'PABPC3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0411 (Fisher's exact test), Q value = 0.73

Table S69.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 5 47 14
PABPC3 MUTATED 2 3 2
PABPC3 WILD-TYPE 3 44 12

Figure S3.  Get High-res Image Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PABPC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.85

Table S70.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 18 35 13
PABPC3 MUTATED 3 2 2
PABPC3 WILD-TYPE 15 33 11
'PABPC3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 26 17 20
PABPC3 MUTATED 3 1 3
PABPC3 WILD-TYPE 23 16 17
'PABPC3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.85

Table S72.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 20 14
PABPC3 MUTATED 3 4 0
PABPC3 WILD-TYPE 26 16 14
'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 19 22 15 10
PABPC3 MUTATED 3 2 1 1
PABPC3 WILD-TYPE 16 20 14 9
'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S74.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #6: '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
PABPC3 MUTATED 3 2 1 0 0 1 0
PABPC3 WILD-TYPE 16 14 6 6 10 3 4
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.99

Table S75.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 20 24 22
PABPC3 MUTATED 2 4 1
PABPC3 WILD-TYPE 18 20 21
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 0.85

Table S76.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #8: '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
PABPC3 MUTATED 3 1 0 0 2 0 1
PABPC3 WILD-TYPE 15 10 12 6 3 5 8
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.669 (Fisher's exact test), Q value = 0.99

Table S77.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2
ALL 19 29
PABPC3 MUTATED 3 3
PABPC3 WILD-TYPE 16 26
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.85

Table S78.  Gene #8: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #10: '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
PABPC3 MUTATED 0 0 2 1 1 1 1 0
PABPC3 WILD-TYPE 10 6 3 7 3 5 4 4
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KICH-TP/19893432/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KICH-TP/20147307/KICH-TP.transferedmergedcluster.txt

  • Number of patients = 66

  • Number of significantly mutated genes = 8

  • Number of Molecular subtypes = 10

  • 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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