Correlation between gene mutation status and molecular subtypes
Uveal Melanoma (Primary solid tumor)
21 August 2015  |  analyses__2015_08_21
Maintainer Information
Citation Information
doi:10.7908/C10K27W7
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/C10K27W7
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 8 molecular subtypes across 80 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.

  • GNAQ mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • EIF1AX mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • SF3B1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CYSLTR2 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CNMF'.

  • BAP1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • SFRS2 mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 8 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, 29 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
SF3B1 18 (22%) 62 0.00081
(0.00942) 		0.00103
(0.00942) 		0.0005
(0.00942) 		0.00173
(0.0123) 		0.00031
(0.00942) 		0.0177
(0.0565) 		0.00072
(0.00942) 		0.0111
(0.0393)
GNAQ 40 (50%) 40 0.0303
(0.0923) 		0.0405
(0.0996) 		0.0457
(0.101) 		0.0382
(0.0983) 		0.0384
(0.0983) 		0.0895
(0.159) 		0.0536
(0.11) 		0.00737
(0.0337)
EIF1AX 10 (12%) 70 0.0009
(0.00942) 		0.00193
(0.0124) 		0.00993
(0.0374) 		0.00836
(0.0357) 		0.00359
(0.0191) 		0.00518
(0.0255) 		0.0647
(0.122) 		0.171
(0.255)
BAP1 12 (15%) 68 0.00072
(0.00942) 		0.00337
(0.0191) 		0.0153
(0.0515) 		0.00126
(0.0101) 		0.0322
(0.0936) 		0.00924
(0.037) 		0.0551
(0.11) 		0.0524
(0.11)
CYSLTR2 3 (4%) 77 0.0374
(0.0983) 		1
(1.00) 		0.0433
(0.101) 		0.107
(0.181) 		0.798
(0.912) 		0.274
(0.358) 		1
(1.00) 		0.572
(0.677)
SFRS2 3 (4%) 77 1
(1.00) 		0.169
(0.255) 		0.0444
(0.101) 		0.107
(0.181) 		0.231
(0.322) 		0.382
(0.479) 		1
(1.00) 		0.232
(0.322)
GNA11 36 (45%) 44 0.0787
(0.144) 		0.0624
(0.121) 		0.191
(0.277) 		0.135
(0.216) 		0.147
(0.229) 		0.268
(0.357) 		0.237
(0.323) 		0.31
(0.397)
PRMT8 5 (6%) 75 0.857
(0.962) 		0.624
(0.726) 		0.497
(0.612) 		0.528
(0.637) 		1
(1.00) 		0.924
(1.00) 		0.127
(0.209) 		1
(1.00)
'GNAQ MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.092

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
GNAQ MUTATED 8 24 8
GNAQ WILD-TYPE 14 12 14

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

'GNAQ MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
GNAQ MUTATED 13 7 20
GNAQ WILD-TYPE 20 11 9

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

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0457 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
GNAQ MUTATED 12 5 23
GNAQ WILD-TYPE 18 10 12

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

'GNAQ MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0382 (Fisher's exact test), Q value = 0.098

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
GNAQ MUTATED 10 22 8
GNAQ WILD-TYPE 19 11 10

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.098

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
GNAQ MUTATED 13 7 20
GNAQ WILD-TYPE 21 10 9

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

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0895 (Fisher's exact test), Q value = 0.16

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
GNAQ MUTATED 5 8 18 9
GNAQ WILD-TYPE 12 5 10 13
'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0536 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
GNAQ MUTATED 12 19 6
GNAQ WILD-TYPE 20 9 8
'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 0.034

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
GNAQ MUTATED 1 2 11 12 5 6
GNAQ WILD-TYPE 4 10 5 4 10 4

Figure S6.  Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GNA11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0787 (Fisher's exact test), Q value = 0.14

Table S9.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
GNA11 MUTATED 14 12 10
GNA11 WILD-TYPE 8 24 12
'GNA11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0624 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
GNA11 MUTATED 18 10 8
GNA11 WILD-TYPE 15 8 21
'GNA11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.28

Table S11.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
GNA11 MUTATED 17 7 12
GNA11 WILD-TYPE 13 8 23
'GNA11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.22

Table S12.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
GNA11 MUTATED 17 11 8
GNA11 WILD-TYPE 12 22 10
'GNA11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.23

Table S13.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
GNA11 MUTATED 17 10 9
GNA11 WILD-TYPE 17 7 20
'GNA11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.36

Table S14.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
GNA11 MUTATED 10 4 10 12
GNA11 WILD-TYPE 7 9 18 10
'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.32

Table S15.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
GNA11 MUTATED 16 9 8
GNA11 WILD-TYPE 16 19 6
'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.4

Table S16.  Gene #2: 'GNA11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
GNA11 MUTATED 4 7 6 5 8 3
GNA11 WILD-TYPE 1 5 10 11 7 7
'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 9e-04 (Fisher's exact test), Q value = 0.0094

Table S17.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
EIF1AX MUTATED 0 10 0
EIF1AX WILD-TYPE 22 26 22

Figure S7.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00193 (Fisher's exact test), Q value = 0.012

Table S18.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
EIF1AX MUTATED 0 2 8
EIF1AX WILD-TYPE 33 16 21

Figure S8.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00993 (Fisher's exact test), Q value = 0.037

Table S19.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
EIF1AX MUTATED 0 2 8
EIF1AX WILD-TYPE 30 13 27

Figure S9.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00836 (Fisher's exact test), Q value = 0.036

Table S20.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
EIF1AX MUTATED 0 8 2
EIF1AX WILD-TYPE 29 25 16

Figure S10.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.019

Table S21.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
EIF1AX MUTATED 0 3 7
EIF1AX WILD-TYPE 34 14 22

Figure S11.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00518 (Fisher's exact test), Q value = 0.026

Table S22.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
EIF1AX MUTATED 0 3 7 0
EIF1AX WILD-TYPE 17 10 21 22

Figure S12.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0647 (Fisher's exact test), Q value = 0.12

Table S23.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
EIF1AX MUTATED 1 6 1
EIF1AX WILD-TYPE 31 22 13
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.25

Table S24.  Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
EIF1AX MUTATED 0 1 4 3 0 0
EIF1AX WILD-TYPE 5 11 12 13 15 10
'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.0094

Table S25.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
SF3B1 MUTATED 0 14 4
SF3B1 WILD-TYPE 22 22 18

Figure S13.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00103 (Fisher's exact test), Q value = 0.0094

Table S26.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
SF3B1 MUTATED 1 6 11
SF3B1 WILD-TYPE 32 12 18

Figure S14.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0094

Table S27.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
SF3B1 MUTATED 3 0 15
SF3B1 WILD-TYPE 27 15 20

Figure S15.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.012

Table S28.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
SF3B1 MUTATED 2 14 2
SF3B1 WILD-TYPE 27 19 16

Figure S16.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.0094

Table S29.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
SF3B1 MUTATED 1 5 12
SF3B1 WILD-TYPE 33 12 17

Figure S17.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.057

Table S30.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
SF3B1 MUTATED 1 5 10 2
SF3B1 WILD-TYPE 16 8 18 20

Figure S18.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0094

Table S31.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
SF3B1 MUTATED 1 11 5
SF3B1 WILD-TYPE 31 17 9

Figure S19.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.039

Table S32.  Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
SF3B1 MUTATED 0 1 6 8 2 0
SF3B1 WILD-TYPE 5 11 10 8 13 10

Figure S20.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PRMT8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 0.96

Table S33.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
PRMT8 MUTATED 1 2 2
PRMT8 WILD-TYPE 21 34 20
'PRMT8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.73

Table S34.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
PRMT8 MUTATED 3 0 2
PRMT8 WILD-TYPE 30 18 27
'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.61

Table S35.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
PRMT8 MUTATED 3 1 1
PRMT8 WILD-TYPE 27 14 34
'PRMT8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 0.64

Table S36.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
PRMT8 MUTATED 3 1 1
PRMT8 WILD-TYPE 26 32 17
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S37.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
PRMT8 MUTATED 2 1 2
PRMT8 WILD-TYPE 32 16 27
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S38.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
PRMT8 MUTATED 1 0 2 2
PRMT8 WILD-TYPE 16 13 26 20
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.21

Table S39.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
PRMT8 MUTATED 3 0 2
PRMT8 WILD-TYPE 29 28 12
'PRMT8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40.  Gene #5: 'PRMT8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
PRMT8 MUTATED 0 1 1 1 1 1
PRMT8 WILD-TYPE 5 11 15 15 14 9
'CYSLTR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.098

Table S41.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
CYSLTR2 MUTATED 0 0 3
CYSLTR2 WILD-TYPE 22 36 19

Figure S21.  Get High-res Image Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CYSLTR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S42.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
CYSLTR2 MUTATED 1 1 1
CYSLTR2 WILD-TYPE 32 17 28
'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 0.1

Table S43.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
CYSLTR2 MUTATED 1 2 0
CYSLTR2 WILD-TYPE 29 13 35

Figure S22.  Get High-res Image Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.18

Table S44.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
CYSLTR2 MUTATED 1 0 2
CYSLTR2 WILD-TYPE 28 33 16
'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 0.91

Table S45.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
CYSLTR2 MUTATED 2 0 1
CYSLTR2 WILD-TYPE 32 17 28
'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.36

Table S46.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
CYSLTR2 MUTATED 2 0 1 0
CYSLTR2 WILD-TYPE 15 13 27 22
'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S47.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
CYSLTR2 MUTATED 2 1 0
CYSLTR2 WILD-TYPE 30 27 14
'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.68

Table S48.  Gene #6: 'CYSLTR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
CYSLTR2 MUTATED 0 1 0 0 1 1
CYSLTR2 WILD-TYPE 5 11 16 16 14 9
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00072 (Fisher's exact test), Q value = 0.0094

Table S49.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
BAP1 MUTATED 6 0 6
BAP1 WILD-TYPE 16 36 16

Figure S23.  Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00337 (Fisher's exact test), Q value = 0.019

Table S50.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
BAP1 MUTATED 9 3 0
BAP1 WILD-TYPE 24 15 29

Figure S24.  Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.051

Table S51.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
BAP1 MUTATED 7 4 1
BAP1 WILD-TYPE 23 11 34

Figure S25.  Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.01

Table S52.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
BAP1 MUTATED 6 0 6
BAP1 WILD-TYPE 23 33 12

Figure S26.  Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.094

Table S53.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
BAP1 MUTATED 9 2 1
BAP1 WILD-TYPE 25 15 28

Figure S27.  Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00924 (Fisher's exact test), Q value = 0.037

Table S54.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
BAP1 MUTATED 5 0 1 6
BAP1 WILD-TYPE 12 13 27 16

Figure S28.  Get High-res Image Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0551 (Fisher's exact test), Q value = 0.11

Table S55.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
BAP1 MUTATED 8 1 2
BAP1 WILD-TYPE 24 27 12
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0524 (Fisher's exact test), Q value = 0.11

Table S56.  Gene #7: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
BAP1 MUTATED 1 3 2 0 1 4
BAP1 WILD-TYPE 4 9 14 16 14 6
'SFRS2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S57.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 22 36 22
SFRS2 MUTATED 1 1 1
SFRS2 WILD-TYPE 21 35 21
'SFRS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.25

Table S58.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 33 18 29
SFRS2 MUTATED 1 2 0
SFRS2 WILD-TYPE 32 16 29
'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.1

Table S59.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 30 15 35
SFRS2 MUTATED 1 2 0
SFRS2 WILD-TYPE 29 13 35

Figure S29.  Get High-res Image Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.18

Table S60.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
SFRS2 MUTATED 1 0 2
SFRS2 WILD-TYPE 28 33 16
'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.32

Table S61.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 34 17 29
SFRS2 MUTATED 3 0 0
SFRS2 WILD-TYPE 31 17 29
'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.48

Table S62.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 13 28 22
SFRS2 MUTATED 1 1 0 1
SFRS2 WILD-TYPE 16 12 28 21
'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S63.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 32 28 14
SFRS2 MUTATED 2 1 0
SFRS2 WILD-TYPE 30 27 14
'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.32

Table S64.  Gene #8: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 5 12 16 16 15 10
SFRS2 MUTATED 0 2 0 0 1 0
SFRS2 WILD-TYPE 5 10 16 16 14 10
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/UVM-TP/19894046/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/19785804/UVM-TP.transferedmergedcluster.txt

  • Number of patients = 80

  • Number of significantly mutated genes = 8

  • Number of Molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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