Correlation between gene mutation status and molecular subtypes
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.

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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