Correlation between gene mutation status and molecular subtypes
Uveal Melanoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1571BH8
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/C1571BH8
Overview
Introduction

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

Summary

Testing the association between mutation status of 7 genes and 8 molecular subtypes across 80 patients, 27 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

  • BAP1 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'.

  • SFRS2 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 7 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, 27 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 0.0364
(0.0841) 		0.00011
(0.000684) 		9e-05
(0.00063) 		0.00183
(0.00932) 		0.0325
(0.0829) 		0.0184
(0.0596) 		0.00793
(0.0313) 		0.0166
(0.0582)
BAP1 22 (28%) 58 3e-05
(0.00028) 		1e-05
(0.000112) 		1e-05
(0.000112) 		1e-05
(0.000112) 		1e-05
(0.000112) 		1e-05
(0.000112) 		0.00277
(0.0129) 		7e-05
(0.00056)
EIF1AX 10 (12%) 70 0.221
(0.326) 		0.00022
(0.00123) 		0.0192
(0.0596) 		0.00839
(0.0313) 		0.0253
(0.0746) 		0.00498
(0.0215) 		0.215
(0.325) 		0.036
(0.0841)
GNAQ 40 (50%) 40 0.373
(0.435) 		0.505
(0.555) 		0.134
(0.215) 		0.0375
(0.0841) 		0.0448
(0.0929) 		0.0899
(0.168) 		0.099
(0.179) 		0.0324
(0.0829)
CYSLTR2 3 (4%) 77 0.0275
(0.0771) 		1
(1.00) 		0.0599
(0.116) 		0.107
(0.184) 		0.24
(0.344) 		0.274
(0.357) 		0.6
(0.646) 		0.367
(0.435)
SFRS2 3 (4%) 77 0.258
(0.357) 		0.182
(0.283) 		0.0595
(0.116) 		0.109
(0.184) 		0.402
(0.45) 		0.381
(0.435) 		0.818
(0.833) 		0.0416
(0.0896)
GNA11 36 (45%) 44 0.269
(0.357) 		0.726
(0.753) 		0.35
(0.426) 		0.134
(0.215) 		0.669
(0.707) 		0.268
(0.357) 		0.324
(0.404) 		0.307
(0.391)
'GNAQ MUTATION STATUS' versus 'CN_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
GNAQ MUTATED 10 2 4 20 3 1
GNAQ WILD-TYPE 12 5 6 11 3 3
'GNAQ MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
GNAQ MUTATED 11 8 7 14
GNAQ WILD-TYPE 17 6 7 10
'GNAQ MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
GNAQ MUTATED 8 5 21 6
GNAQ WILD-TYPE 10 10 11 9
'GNAQ MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.084

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 S1.  Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.093

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
GNAQ MUTATED 2 1 7 17 10 3
GNAQ WILD-TYPE 6 7 4 8 13 2

Figure S2.  Get High-res Image Gene #1: 'GNAQ MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'GNAQ MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0899 (Fisher's exact test), Q value = 0.17

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 = 0.099 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
GNAQ MUTATED 9 0 11 5 4 5 3
GNAQ WILD-TYPE 11 7 6 4 4 2 3
'GNAQ MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.083

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
GNAQ MUTATED 7 20 5 5
GNAQ WILD-TYPE 11 8 11 7

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

'GNA11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
GNA11 MUTATED 12 5 3 11 2 3
GNA11 WILD-TYPE 10 2 7 20 4 1
'GNA11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
GNA11 MUTATED 15 6 6 9
GNA11 WILD-TYPE 13 8 8 15
'GNA11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
GNA11 MUTATED 11 7 11 7
GNA11 WILD-TYPE 7 8 21 8
'GNA11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.134 (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 = 0.669 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
GNA11 MUTATED 5 5 4 9 11 2
GNA11 WILD-TYPE 3 3 7 16 12 3
'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 = 0.324 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
GNA11 MUTATED 10 6 6 3 4 2 2
GNA11 WILD-TYPE 10 1 11 6 4 5 4
'GNA11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
GNA11 MUTATED 10 9 9 5
GNA11 WILD-TYPE 8 19 7 7
'EIF1AX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
EIF1AX MUTATED 2 0 0 8 0 0
EIF1AX WILD-TYPE 20 7 10 23 6 4
'EIF1AX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0012

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
EIF1AX MUTATED 0 6 0 4
EIF1AX WILD-TYPE 28 8 14 20

Figure S4.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.06

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
EIF1AX MUTATED 0 2 8 0
EIF1AX WILD-TYPE 18 13 24 15

Figure S5.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00839 (Fisher's exact test), Q value = 0.031

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 S6.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.075

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
EIF1AX MUTATED 0 0 3 6 0 1
EIF1AX WILD-TYPE 8 8 8 19 23 4

Figure S7.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00498 (Fisher's exact test), Q value = 0.021

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 S8.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
EIF1AX MUTATED 0 1 4 1 1 0 1
EIF1AX WILD-TYPE 20 6 13 8 7 7 5
'EIF1AX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.036 (Fisher's exact test), Q value = 0.084

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
EIF1AX MUTATED 0 6 0 2
EIF1AX WILD-TYPE 18 22 16 10

Figure S9.  Get High-res Image Gene #3: 'EIF1AX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.084

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
SF3B1 MUTATED 3 0 1 13 0 1
SF3B1 WILD-TYPE 19 7 9 18 6 3

Figure S10.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.00068

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
SF3B1 MUTATED 0 2 5 11
SF3B1 WILD-TYPE 28 12 9 13

Figure S11.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.00063

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
SF3B1 MUTATED 3 0 15 0
SF3B1 WILD-TYPE 15 15 17 15

Figure S12.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00183 (Fisher's exact test), Q value = 0.0093

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

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.083

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
SF3B1 MUTATED 1 1 3 10 1 2
SF3B1 WILD-TYPE 7 7 8 15 22 3

Figure S14.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.06

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 S15.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00793 (Fisher's exact test), Q value = 0.031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
SF3B1 MUTATED 0 0 7 3 3 2 2
SF3B1 WILD-TYPE 20 7 10 6 5 5 4

Figure S16.  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 = 0.0166 (Fisher's exact test), Q value = 0.058

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
SF3B1 MUTATED 1 12 2 2
SF3B1 WILD-TYPE 17 16 14 10

Figure S17.  Get High-res Image Gene #4: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00028

Table S33.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
BAP1 MUTATED 8 5 5 0 3 1
BAP1 WILD-TYPE 14 2 5 31 3 3

Figure S18.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S34.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
BAP1 MUTATED 14 1 7 0
BAP1 WILD-TYPE 14 13 7 24

Figure S19.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S35.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
BAP1 MUTATED 11 6 0 5
BAP1 WILD-TYPE 7 9 32 10

Figure S20.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S36.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 29 33 18
BAP1 MUTATED 14 0 8
BAP1 WILD-TYPE 15 33 10

Figure S21.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S37.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
BAP1 MUTATED 6 2 0 1 12 1
BAP1 WILD-TYPE 2 6 11 24 11 4

Figure S22.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00011

Table S38.  Gene #5: '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 9 0 1 12
BAP1 WILD-TYPE 8 13 27 10

Figure S23.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00277 (Fisher's exact test), Q value = 0.013

Table S39.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
BAP1 MUTATED 10 3 0 4 3 1 0
BAP1 WILD-TYPE 10 4 17 5 5 6 6

Figure S24.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.00056

Table S40.  Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
BAP1 MUTATED 11 1 6 3
BAP1 WILD-TYPE 7 27 10 9

Figure S25.  Get High-res Image Gene #5: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CYSLTR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.077

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
CYSLTR2 MUTATED 0 0 2 0 1 0
CYSLTR2 WILD-TYPE 22 7 8 31 5 4

Figure S26.  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 CLUS_4
ALL 28 14 14 24
CYSLTR2 MUTATED 1 0 1 1
CYSLTR2 WILD-TYPE 27 14 13 23
'CYSLTR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0599 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
CYSLTR2 MUTATED 0 2 0 1
CYSLTR2 WILD-TYPE 18 13 32 14
'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 = 0.24 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
CYSLTR2 MUTATED 1 1 0 0 1 0
CYSLTR2 WILD-TYPE 7 7 11 25 22 5
'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 = 0.6 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
CYSLTR2 MUTATED 1 0 0 1 0 1 0
CYSLTR2 WILD-TYPE 19 7 17 8 8 6 6
'CYSLTR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
CYSLTR2 MUTATED 1 0 1 1
CYSLTR2 WILD-TYPE 17 28 15 11
'SFRS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.36

Table S49.  Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 22 7 10 31 6 4
SFRS2 MUTATED 3 0 0 0 0 0
SFRS2 WILD-TYPE 19 7 10 31 6 4
'SFRS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.28

Table S50.  Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 28 14 14 24
SFRS2 MUTATED 1 2 0 0
SFRS2 WILD-TYPE 27 12 14 24
'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0595 (Fisher's exact test), Q value = 0.12

Table S51.  Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 15 32 15
SFRS2 MUTATED 0 2 0 1
SFRS2 WILD-TYPE 18 13 32 14
'SFRS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.18

Table S52.  Gene #7: '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 = 0.402 (Fisher's exact test), Q value = 0.45

Table S53.  Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 8 8 11 25 23 5
SFRS2 MUTATED 1 0 1 0 1 0
SFRS2 WILD-TYPE 7 8 10 25 22 5
'SFRS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 0.44

Table S54.  Gene #7: '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 = 0.818 (Fisher's exact test), Q value = 0.83

Table S55.  Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 20 7 17 9 8 7 6
SFRS2 MUTATED 1 1 1 0 0 0 0
SFRS2 WILD-TYPE 19 6 16 9 8 7 6
'SFRS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0416 (Fisher's exact test), Q value = 0.09

Table S56.  Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 18 28 16 12
SFRS2 MUTATED 0 0 1 2
SFRS2 WILD-TYPE 18 28 15 10

Figure S27.  Get High-res Image Gene #7: 'SFRS2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/22572046/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/UVM-TP/22542449/UVM-TP.transferedmergedcluster.txt

  • Number of patients = 80

  • Number of significantly mutated genes = 7

  • 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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