Correlation between gene mutation status and molecular subtypes
Thymoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1K35T5F
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1K35T5F
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 120 patients, 24 significant findings detected with P value < 0.05 and Q value < 0.25.

  • GTF2I mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • HRAS mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TP53 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • PLEKHG4B mutation correlated to 'CN_CNMF'.

  • UNC93B1 mutation correlated to 'CN_CNMF'.

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, 24 significant findings 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
GTF2I 49 (41%) 71 1e-05
(6.67e-05) 		1e-05
(6.67e-05) 		3e-05
(0.000171) 		1e-05
(6.67e-05) 		1e-05
(6.67e-05) 		1e-05
(6.67e-05) 		1e-05
(6.67e-05) 		1e-05
(6.67e-05) 		1e-05
(6.67e-05) 		1e-05
(6.67e-05)
HRAS 10 (8%) 110 0.00094
(0.0047) 		2e-05
(0.000123) 		0.0273
(0.101) 		5e-05
(0.000267) 		1e-05
(6.67e-05) 		1e-05
(6.67e-05) 		0.0409
(0.142) 		1e-05
(6.67e-05) 		0.017
(0.0682) 		0.00257
(0.0121)
TP53 4 (3%) 116 0.467
(0.748) 		0.221
(0.431) 		1
(1.00) 		0.11
(0.283) 		0.0517
(0.165) 		0.0279
(0.101) 		0.446
(0.729) 		0.00854
(0.038) 		0.0767
(0.212) 		0.784
(1.00)
PLEKHG4B 3 (2%) 117 0.0154
(0.0647) 		0.12
(0.301) 		0.503
(0.773) 		0.197
(0.395) 		0.648
(0.899) 		0.294
(0.547) 		0.609
(0.899) 		0.79
(1.00)
UNC93B1 5 (4%) 115 0.0463
(0.154) 		0.178
(0.385) 		0.676
(0.917) 		0.185
(0.39) 		0.149
(0.351) 		0.155
(0.355) 		0.084
(0.224) 		0.145
(0.351) 		0.0762
(0.212) 		0.0557
(0.171)
CAPNS1 3 (2%) 117 0.652
(0.899) 		0.946
(1.00) 		0.648
(0.899) 		0.844
(1.00) 		1
(1.00) 		0.935
(1.00) 		0.446
(0.729) 		1
(1.00)
ATRN 3 (2%) 117 0.902
(1.00) 		0.434
(0.729) 		0.365
(0.648) 		0.0633
(0.187) 		0.338
(0.615) 		0.161
(0.359) 		0.251
(0.478) 		0.493
(0.773)
NRAS 3 (2%) 117 0.903
(1.00) 		0.397
(0.691) 		1
(1.00) 		0.197
(0.395) 		0.645
(0.899) 		0.721
(0.961) 		0.609
(0.899) 		0.892
(1.00)
'GTF2I MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S1.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
GTF2I MUTATED 4 22 8 11 4
GTF2I WILD-TYPE 31 5 11 18 6

Figure S1.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'GTF2I MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S2.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
GTF2I MUTATED 2 22 0 0 17 5 1 2
GTF2I WILD-TYPE 32 1 19 10 1 3 1 4

Figure S2.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'GTF2I MUTATION STATUS' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00017

Table S3.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 31
GTF2I MUTATED 10 21 8
GTF2I WILD-TYPE 21 4 23

Figure S3.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'GTF2I MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S4.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 28 20
GTF2I MUTATED 8 22 9 0
GTF2I WILD-TYPE 8 1 19 20

Figure S4.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'GTF2I MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S5.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
GTF2I MUTATED 0 16 28 2
GTF2I WILD-TYPE 42 14 2 12

Figure S5.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'GTF2I MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S6.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
GTF2I MUTATED 0 27 19 0
GTF2I WILD-TYPE 44 15 1 10

Figure S6.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'GTF2I MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S7.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
GTF2I MUTATED 3 46 0
GTF2I WILD-TYPE 51 15 5

Figure S7.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'GTF2I MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S8.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
GTF2I MUTATED 1 16 2 0 15 15
GTF2I WILD-TYPE 25 2 24 7 1 12

Figure S8.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'GTF2I MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S9.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
GTF2I MUTATED 0 45 4 0
GTF2I WILD-TYPE 25 6 39 1

Figure S9.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'GTF2I MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S10.  Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
GTF2I MUTATED 1 30 2 16
GTF2I WILD-TYPE 25 3 31 12

Figure S10.  Get High-res Image Gene #1: 'GTF2I MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00094 (Fisher's exact test), Q value = 0.0047

Table S11.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
HRAS MUTATED 0 7 2 0 1
HRAS WILD-TYPE 35 20 17 29 9

Figure S11.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00012

Table S12.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
HRAS MUTATED 0 10 0 0 0 0 0 0
HRAS WILD-TYPE 34 13 19 10 18 8 2 6

Figure S12.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0273 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 31
HRAS MUTATED 3 5 0
HRAS WILD-TYPE 28 20 31

Figure S13.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 28 20
HRAS MUTATED 0 8 0 0
HRAS WILD-TYPE 16 15 28 20

Figure S14.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S15.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
HRAS MUTATED 0 0 10 0
HRAS WILD-TYPE 42 30 20 14

Figure S15.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S16.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
HRAS MUTATED 0 0 10 0
HRAS WILD-TYPE 44 42 10 10

Figure S16.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.14

Table S17.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
HRAS MUTATED 1 9 0
HRAS WILD-TYPE 53 52 5

Figure S17.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 6.7e-05

Table S18.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
HRAS MUTATED 0 0 1 0 8 1
HRAS WILD-TYPE 26 18 25 7 8 26

Figure S18.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.068

Table S19.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
HRAS MUTATED 0 9 1 0
HRAS WILD-TYPE 25 42 42 1

Figure S19.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00257 (Fisher's exact test), Q value = 0.012

Table S20.  Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
HRAS MUTATED 0 8 1 1
HRAS WILD-TYPE 26 25 32 27

Figure S20.  Get High-res Image Gene #2: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CAPNS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.9

Table S21.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
CAPNS1 MUTATED 0 1 1 1 0
CAPNS1 WILD-TYPE 35 26 18 28 10
'CAPNS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
CAPNS1 MUTATED 1 1 0 0 1 0 0 0
CAPNS1 WILD-TYPE 33 22 19 10 17 8 2 6
'CAPNS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 0.9

Table S23.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
CAPNS1 MUTATED 1 2 0 0
CAPNS1 WILD-TYPE 41 28 30 14
'CAPNS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
CAPNS1 MUTATED 1 2 0 0
CAPNS1 WILD-TYPE 43 40 20 10
'CAPNS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S25.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
CAPNS1 MUTATED 1 2 0
CAPNS1 WILD-TYPE 53 59 5
'CAPNS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.935 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
CAPNS1 MUTATED 0 1 1 0 0 1
CAPNS1 WILD-TYPE 26 17 25 7 16 26
'CAPNS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.73

Table S27.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
CAPNS1 MUTATED 1 2 0 0
CAPNS1 WILD-TYPE 24 49 43 1
'CAPNS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S28.  Gene #3: 'CAPNS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
CAPNS1 MUTATED 0 1 1 1
CAPNS1 WILD-TYPE 26 32 32 27
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.75

Table S29.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
TP53 MUTATED 1 1 1 0 1
TP53 WILD-TYPE 34 26 18 29 9
'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.43

Table S30.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
TP53 MUTATED 1 0 1 2 0 0 0 0
TP53 WILD-TYPE 33 23 18 8 18 8 2 6
'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S31.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 31
TP53 MUTATED 1 1 1
TP53 WILD-TYPE 30 24 30
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.28

Table S32.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 28 20
TP53 MUTATED 1 0 0 2
TP53 WILD-TYPE 15 23 28 18
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0517 (Fisher's exact test), Q value = 0.17

Table S33.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
TP53 MUTATED 2 0 0 2
TP53 WILD-TYPE 40 30 30 12
'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.1

Table S34.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
TP53 MUTATED 2 0 0 2
TP53 WILD-TYPE 42 42 20 8

Figure S21.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.73

Table S35.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
TP53 MUTATED 3 1 0
TP53 WILD-TYPE 51 60 5
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00854 (Fisher's exact test), Q value = 0.038

Table S36.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
TP53 MUTATED 1 0 0 2 1 0
TP53 WILD-TYPE 25 18 26 5 15 27

Figure S22.  Get High-res Image Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0767 (Fisher's exact test), Q value = 0.21

Table S37.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
TP53 MUTATED 0 0 4 0
TP53 WILD-TYPE 25 51 39 1
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
TP53 MUTATED 1 1 2 0
TP53 WILD-TYPE 25 32 31 28
'ATRN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
ATRN MUTATED 1 0 1 1 0
ATRN WILD-TYPE 34 27 18 28 10
'ATRN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.73

Table S40.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
ATRN MUTATED 0 2 0 0 1 0 0 0
ATRN WILD-TYPE 34 21 19 10 17 8 2 6
'ATRN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.65

Table S41.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
ATRN MUTATED 0 2 1 0
ATRN WILD-TYPE 42 28 29 14
'ATRN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0633 (Fisher's exact test), Q value = 0.19

Table S42.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
ATRN MUTATED 0 1 2 0
ATRN WILD-TYPE 44 41 18 10
'ATRN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.62

Table S43.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
ATRN MUTATED 0 3 0
ATRN WILD-TYPE 54 58 5
'ATRN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.36

Table S44.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
ATRN MUTATED 0 0 0 0 2 1
ATRN WILD-TYPE 26 18 26 7 14 26
'ATRN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.48

Table S45.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
ATRN MUTATED 0 3 0 0
ATRN WILD-TYPE 25 48 43 1
'ATRN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 0.77

Table S46.  Gene #5: 'ATRN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
ATRN MUTATED 0 2 0 1
ATRN WILD-TYPE 26 31 33 27
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S47.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
NRAS MUTATED 1 0 1 1 0
NRAS WILD-TYPE 34 27 18 28 10
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.69

Table S48.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
NRAS MUTATED 0 1 1 1 0 0 0 0
NRAS WILD-TYPE 34 22 18 9 18 8 2 6
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S49.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
NRAS MUTATED 1 1 1 0
NRAS WILD-TYPE 41 29 29 14
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.39

Table S50.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
NRAS MUTATED 1 0 1 1
NRAS WILD-TYPE 43 42 19 9
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 0.9

Table S51.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
NRAS MUTATED 2 1 0
NRAS WILD-TYPE 52 60 5
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 0.96

Table S52.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
NRAS MUTATED 1 0 1 0 1 0
NRAS WILD-TYPE 25 18 25 7 15 27
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.609 (Fisher's exact test), Q value = 0.9

Table S53.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
NRAS MUTATED 0 1 2 0
NRAS WILD-TYPE 25 50 41 1
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S54.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
NRAS MUTATED 1 1 1 0
NRAS WILD-TYPE 25 32 32 28
'PLEKHG4B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.065

Table S55.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
PLEKHG4B MUTATED 0 0 0 1 2
PLEKHG4B WILD-TYPE 35 27 19 28 8

Figure S23.  Get High-res Image Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PLEKHG4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.3

Table S56.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
PLEKHG4B MUTATED 0 1 0 1 0 0 0 1
PLEKHG4B WILD-TYPE 34 22 19 9 18 8 2 5
'PLEKHG4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.503 (Fisher's exact test), Q value = 0.77

Table S57.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
PLEKHG4B MUTATED 1 0 1 1
PLEKHG4B WILD-TYPE 41 30 29 13
'PLEKHG4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.39

Table S58.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
PLEKHG4B MUTATED 1 0 1 1
PLEKHG4B WILD-TYPE 43 42 19 9
'PLEKHG4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 0.9

Table S59.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
PLEKHG4B MUTATED 2 1 0
PLEKHG4B WILD-TYPE 52 60 5
'PLEKHG4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 0.55

Table S60.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
PLEKHG4B MUTATED 1 0 0 1 0 1
PLEKHG4B WILD-TYPE 25 18 26 6 16 26
'PLEKHG4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.609 (Fisher's exact test), Q value = 0.9

Table S61.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
PLEKHG4B MUTATED 0 1 2 0
PLEKHG4B WILD-TYPE 25 50 41 1
'PLEKHG4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S62.  Gene #7: 'PLEKHG4B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
PLEKHG4B MUTATED 1 0 1 1
PLEKHG4B WILD-TYPE 25 33 32 27
'UNC93B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.15

Table S63.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 35 27 19 29 10
UNC93B1 MUTATED 0 4 0 1 0
UNC93B1 WILD-TYPE 35 23 19 28 10

Figure S24.  Get High-res Image Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'UNC93B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.39

Table S64.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8
ALL 34 23 19 10 18 8 2 6
UNC93B1 MUTATED 0 3 0 0 1 1 0 0
UNC93B1 WILD-TYPE 34 20 19 10 17 7 2 6
'UNC93B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.92

Table S65.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 31 25 31
UNC93B1 MUTATED 1 2 1
UNC93B1 WILD-TYPE 30 23 30
'UNC93B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.39

Table S66.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 16 23 28 20
UNC93B1 MUTATED 0 3 1 0
UNC93B1 WILD-TYPE 16 20 27 20
'UNC93B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.35

Table S67.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 42 30 30 14
UNC93B1 MUTATED 0 2 3 0
UNC93B1 WILD-TYPE 42 28 27 14
'UNC93B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.36

Table S68.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 44 42 20 10
UNC93B1 MUTATED 0 3 2 0
UNC93B1 WILD-TYPE 44 39 18 10
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.084 (Fisher's exact test), Q value = 0.22

Table S69.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 61 5
UNC93B1 MUTATED 0 5 0
UNC93B1 WILD-TYPE 54 56 5
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.35

Table S70.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 26 18 26 7 16 27
UNC93B1 MUTATED 0 2 0 0 2 1
UNC93B1 WILD-TYPE 26 16 26 7 14 26
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0762 (Fisher's exact test), Q value = 0.21

Table S71.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 25 51 43 1
UNC93B1 MUTATED 0 5 0 0
UNC93B1 WILD-TYPE 25 46 43 1
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0557 (Fisher's exact test), Q value = 0.17

Table S72.  Gene #8: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 26 33 33 28
UNC93B1 MUTATED 0 4 0 1
UNC93B1 WILD-TYPE 26 29 33 27
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/THYM-TP/22571832/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/THYM-TP/22541006/THYM-TP.transferedmergedcluster.txt

  • Number of patients = 120

  • 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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