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 20 genes and 8 molecular subtypes across 198 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CTNNB1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RB1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • ARID1A mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CNMF'.

  • AXIN1 mutation correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • BAP1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ALB mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • TSC2 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • APOB mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • PRKDC mutation correlated to 'MIRSEQ_CNMF'.

  • HNF1A mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • GNAS mutation correlated to 'MRNASEQ_CNMF'.

  • HIST1H1C mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 20 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, 36 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
CTNNB1 51 (26%) 147 0.0387
(0.194) 		0.00093
(0.0135) 		1e-05
(0.00032) 		1e-05
(0.00032) 		0.0451
(0.205) 		1e-05
(0.00032) 		0.0005
(0.00889) 		1e-05
(0.00032)
TP53 62 (31%) 136 0.00615
(0.0579) 		0.927
(0.957) 		1e-05
(0.00032) 		0.0215
(0.128) 		0.0171
(0.126) 		0.00117
(0.0156) 		0.232
(0.494) 		0.0247
(0.141)
BAP1 11 (6%) 187 0.789
(0.903) 		0.00392
(0.0482) 		0.00038
(0.0076) 		0.00012
(0.00274) 		2e-05
(0.000533) 		0.0532
(0.23) 		0.0164
(0.126) 		0.0434
(0.204)
AXIN1 9 (5%) 189 0.279
(0.51) 		0.476
(0.716) 		0.0107
(0.0925) 		0.187
(0.434) 		0.00471
(0.0538) 		0.458
(0.704) 		0.00588
(0.0579) 		0.695
(0.856)
RB1 15 (8%) 183 0.728
(0.873) 		0.00085
(0.0135) 		0.00565
(0.0579) 		0.31
(0.528) 		0.214
(0.476) 		0.391
(0.632) 		0.213
(0.476) 		0.304
(0.523)
ARID1A 17 (9%) 181 0.845
(0.92) 		0.164
(0.404) 		0.1
(0.336) 		0.046
(0.205) 		0.124
(0.378) 		0.628
(0.811) 		0.0174
(0.126) 		0.656
(0.832)
ALB 18 (9%) 180 0.041
(0.199) 		0.021
(0.128) 		0.406
(0.649) 		0.575
(0.78) 		0.821
(0.906) 		0.843
(0.92) 		0.504
(0.722) 		0.251
(0.508)
TSC2 9 (5%) 189 0.906
(0.947) 		0.0187
(0.128) 		0.101
(0.336) 		0.0199
(0.128) 		0.765
(0.9) 		0.566
(0.774) 		0.786
(0.903) 		0.11
(0.347)
APOB 25 (13%) 173 0.96
(0.979) 		0.893
(0.939) 		0.139
(0.383) 		0.133
(0.379) 		0.159
(0.404) 		0.073
(0.285) 		0.297
(0.52) 		0.0256
(0.141)
PRKDC 11 (6%) 187 0.264
(0.509) 		0.282
(0.51) 		0.502
(0.722) 		0.676
(0.845) 		0.0286
(0.153) 		0.287
(0.51) 		0.275
(0.51) 		0.103
(0.336)
HNF1A 8 (4%) 190 0.165
(0.404) 		0.664
(0.837) 		0.0724
(0.285) 		0.53
(0.744) 		0.0953
(0.336) 		0.152
(0.4) 		0.011
(0.0925) 		0.284
(0.51)
GNAS 7 (4%) 191 0.889
(0.939) 		0.238
(0.494) 		0.0305
(0.158) 		0.17
(0.406) 		0.0766
(0.292) 		0.45
(0.699) 		0.554
(0.764) 		0.724
(0.873)
HIST1H1C 5 (3%) 193 0.722
(0.873) 		0.737
(0.873) 		0.471
(0.716) 		0.349
(0.588) 		0.802
(0.904) 		0.248
(0.508) 		0.639
(0.818) 		0.0207
(0.128)
IL6ST 7 (4%) 191 0.491
(0.721) 		0.299
(0.52) 		0.167
(0.404) 		0.137
(0.383) 		0.439
(0.688) 		0.105
(0.338) 		0.479
(0.716) 		1
(1.00)
PTEN 7 (4%) 191 0.489
(0.721) 		0.264
(0.509) 		0.372
(0.619) 		0.505
(0.722) 		0.859
(0.929) 		0.276
(0.51) 		0.784
(0.903) 		0.285
(0.51)
EEF1A1 5 (3%) 193 0.0557
(0.234) 		0.734
(0.873) 		0.254
(0.508) 		0.132
(0.379) 		0.611
(0.809) 		0.26
(0.509) 		0.238
(0.494) 		0.617
(0.809)
KIF19 10 (5%) 188 0.918
(0.953) 		0.103
(0.336) 		0.234
(0.494) 		0.236
(0.494) 		0.382
(0.63) 		0.81
(0.906) 		0.153
(0.4) 		0.101
(0.336)
THADA 6 (3%) 192 0.142
(0.384) 		0.131
(0.379) 		0.0569
(0.234) 		0.202
(0.461) 		0.889
(0.939) 		0.622
(0.809) 		0.125
(0.378) 		0.547
(0.761)
F5 4 (2%) 194 0.82
(0.906) 		0.179
(0.421) 		0.799
(0.904) 		0.619
(0.809) 		0.102
(0.336) 		0.937
(0.962)
MLL4 10 (5%) 188 0.415
(0.657) 		0.163
(0.404) 		0.516
(0.731) 		0.882
(0.939) 		0.622
(0.809) 		0.391
(0.632) 		0.688
(0.853) 		0.79
(0.903)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00615 (Fisher's exact test), Q value = 0.058

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
TP53 MUTATED 9 29 23
TP53 WILD-TYPE 37 33 62

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 0.96

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
TP53 MUTATED 18 27 17
TP53 WILD-TYPE 39 56 41
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00032

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
TP53 MUTATED 30 16 3 5 7
TP53 WILD-TYPE 13 39 26 31 25

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0215 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
TP53 MUTATED 18 10 20 6 7
TP53 WILD-TYPE 16 19 47 30 22

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0171 (Fisher's exact test), Q value = 0.13

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
TP53 MUTATED 16 24 11 10
TP53 WILD-TYPE 22 44 16 50

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00117 (Fisher's exact test), Q value = 0.016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
TP53 MUTATED 14 24 6 15 2
TP53 WILD-TYPE 10 34 18 51 19

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.49

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
TP53 MUTATED 22 10 17 10
TP53 WILD-TYPE 35 31 39 11
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0247 (Fisher's exact test), Q value = 0.14

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
TP53 MUTATED 12 23 11 10 3
TP53 WILD-TYPE 20 30 39 10 17

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.19

Table S9.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
CTNNB1 MUTATED 19 13 19
CTNNB1 WILD-TYPE 27 49 66

Figure S7.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00093 (Fisher's exact test), Q value = 0.014

Table S10.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
CTNNB1 MUTATED 9 33 9
CTNNB1 WILD-TYPE 48 50 49

Figure S8.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00032

Table S11.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
CTNNB1 MUTATED 9 8 1 5 28
CTNNB1 WILD-TYPE 34 47 28 31 4

Figure S9.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00032

Table S12.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
CTNNB1 MUTATED 3 7 9 7 25
CTNNB1 WILD-TYPE 31 22 58 29 4

Figure S10.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0451 (Fisher's exact test), Q value = 0.2

Table S13.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
CTNNB1 MUTATED 9 25 7 9
CTNNB1 WILD-TYPE 29 43 20 51

Figure S11.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00032

Table S14.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
CTNNB1 MUTATED 8 11 2 11 18
CTNNB1 WILD-TYPE 16 47 22 55 3

Figure S12.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.0089

Table S15.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
CTNNB1 MUTATED 8 5 25 5
CTNNB1 WILD-TYPE 49 36 31 16

Figure S13.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00032

Table S16.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
CTNNB1 MUTATED 3 10 7 7 16
CTNNB1 WILD-TYPE 29 43 43 13 4

Figure S14.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 0.87

Table S17.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
RB1 MUTATED 3 6 5
RB1 WILD-TYPE 43 56 80
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00085 (Fisher's exact test), Q value = 0.014

Table S18.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
RB1 MUTATED 1 3 11
RB1 WILD-TYPE 56 80 47

Figure S15.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00565 (Fisher's exact test), Q value = 0.058

Table S19.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
RB1 MUTATED 3 6 6 0 0
RB1 WILD-TYPE 40 49 23 36 32

Figure S16.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.53

Table S20.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
RB1 MUTATED 3 1 8 3 0
RB1 WILD-TYPE 31 28 59 33 29
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.48

Table S21.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
RB1 MUTATED 0 6 2 6
RB1 WILD-TYPE 38 62 25 54
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.63

Table S22.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
RB1 MUTATED 1 3 2 8 0
RB1 WILD-TYPE 23 55 22 58 21
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.213 (Fisher's exact test), Q value = 0.48

Table S23.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
RB1 MUTATED 6 4 1 1
RB1 WILD-TYPE 51 37 55 20
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.52

Table S24.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
RB1 MUTATED 5 3 3 1 0
RB1 WILD-TYPE 27 50 47 19 20
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.845 (Fisher's exact test), Q value = 0.92

Table S25.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
ARID1A MUTATED 4 6 6
ARID1A WILD-TYPE 42 56 79
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.4

Table S26.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
ARID1A MUTATED 5 4 8
ARID1A WILD-TYPE 52 79 50
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.34

Table S27.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
ARID1A MUTATED 3 2 6 2 4
ARID1A WILD-TYPE 40 53 23 34 28
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.046 (Fisher's exact test), Q value = 0.2

Table S28.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
ARID1A MUTATED 2 2 2 7 4
ARID1A WILD-TYPE 32 27 65 29 25

Figure S17.  Get High-res Image Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.38

Table S29.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
ARID1A MUTATED 4 6 5 2
ARID1A WILD-TYPE 34 62 22 58
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 0.81

Table S30.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
ARID1A MUTATED 3 3 3 7 1
ARID1A WILD-TYPE 21 55 21 59 20
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.13

Table S31.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
ARID1A MUTATED 5 3 2 6
ARID1A WILD-TYPE 52 38 54 15

Figure S18.  Get High-res Image Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 0.83

Table S32.  Gene #4: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
ARID1A MUTATED 3 3 6 3 1
ARID1A WILD-TYPE 29 50 44 17 19
'AXIN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.51

Table S33.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
AXIN1 MUTATED 2 5 2
AXIN1 WILD-TYPE 44 57 83
'AXIN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.72

Table S34.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
AXIN1 MUTATED 1 4 4
AXIN1 WILD-TYPE 56 79 54
'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.092

Table S35.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
AXIN1 MUTATED 1 3 5 0 0
AXIN1 WILD-TYPE 42 52 24 36 32

Figure S19.  Get High-res Image Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.187 (Fisher's exact test), Q value = 0.43

Table S36.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
AXIN1 MUTATED 1 0 4 4 0
AXIN1 WILD-TYPE 33 29 63 32 29
'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00471 (Fisher's exact test), Q value = 0.054

Table S37.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
AXIN1 MUTATED 0 4 4 0
AXIN1 WILD-TYPE 38 64 23 60

Figure S20.  Get High-res Image Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.7

Table S38.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
AXIN1 MUTATED 1 1 2 4 0
AXIN1 WILD-TYPE 23 57 22 62 21
'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.058

Table S39.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
AXIN1 MUTATED 1 0 2 4
AXIN1 WILD-TYPE 56 41 54 17

Figure S21.  Get High-res Image Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 0.86

Table S40.  Gene #5: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
AXIN1 MUTATED 0 2 3 1 1
AXIN1 WILD-TYPE 32 51 47 19 19
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 0.9

Table S41.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
BAP1 MUTATED 2 3 6
BAP1 WILD-TYPE 44 59 79
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.048

Table S42.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
BAP1 MUTATED 5 0 6
BAP1 WILD-TYPE 52 83 52

Figure S22.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.0076

Table S43.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
BAP1 MUTATED 1 0 4 6 0
BAP1 WILD-TYPE 42 55 25 30 32

Figure S23.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0027

Table S44.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
BAP1 MUTATED 5 0 0 6 0
BAP1 WILD-TYPE 29 29 67 30 29

Figure S24.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00053

Table S45.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
BAP1 MUTATED 0 0 0 11
BAP1 WILD-TYPE 38 68 27 49

Figure S25.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0532 (Fisher's exact test), Q value = 0.23

Table S46.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
BAP1 MUTATED 0 1 2 8 0
BAP1 WILD-TYPE 24 57 22 58 21
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.13

Table S47.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
BAP1 MUTATED 4 6 0 1
BAP1 WILD-TYPE 53 35 56 20

Figure S26.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.2

Table S48.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
BAP1 MUTATED 1 2 8 0 0
BAP1 WILD-TYPE 31 51 42 20 20

Figure S27.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ALB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.041 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
ALB MUTATED 8 2 7
ALB WILD-TYPE 38 60 78

Figure S28.  Get High-res Image Gene #7: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ALB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
ALB MUTATED 5 12 1
ALB WILD-TYPE 52 71 57

Figure S29.  Get High-res Image Gene #7: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ALB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
ALB MUTATED 4 6 0 4 3
ALB WILD-TYPE 39 49 29 32 29
'ALB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.575 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
ALB MUTATED 3 4 6 1 3
ALB WILD-TYPE 31 25 61 35 26
'ALB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
ALB MUTATED 4 6 1 5
ALB WILD-TYPE 34 62 26 55
'ALB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
ALB MUTATED 3 5 2 4 2
ALB WILD-TYPE 21 53 22 62 19
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
ALB MUTATED 4 4 6 0
ALB WILD-TYPE 53 37 50 21
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
ALB MUTATED 1 5 2 3 3
ALB WILD-TYPE 31 48 48 17 17
'TSC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 0.95

Table S57.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
TSC2 MUTATED 2 2 5
TSC2 WILD-TYPE 44 60 80
'TSC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0187 (Fisher's exact test), Q value = 0.13

Table S58.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
TSC2 MUTATED 6 3 0
TSC2 WILD-TYPE 51 80 58

Figure S30.  Get High-res Image Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TSC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.34

Table S59.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
TSC2 MUTATED 5 1 2 1 0
TSC2 WILD-TYPE 38 54 27 35 32
'TSC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.13

Table S60.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
TSC2 MUTATED 5 0 4 0 0
TSC2 WILD-TYPE 29 29 63 36 29

Figure S31.  Get High-res Image Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TSC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.765 (Fisher's exact test), Q value = 0.9

Table S61.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
TSC2 MUTATED 2 4 0 3
TSC2 WILD-TYPE 36 64 27 57
'TSC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.77

Table S62.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
TSC2 MUTATED 2 2 2 2 1
TSC2 WILD-TYPE 22 56 22 64 20
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 0.9

Table S63.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
TSC2 MUTATED 4 2 3 0
TSC2 WILD-TYPE 53 39 53 21
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.35

Table S64.  Gene #8: 'TSC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
TSC2 MUTATED 4 1 1 1 2
TSC2 WILD-TYPE 28 52 49 19 18
'IL6ST MUTATION STATUS' versus 'CN_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.72

Table S65.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
IL6ST MUTATED 0 2 4
IL6ST WILD-TYPE 46 60 81
'IL6ST MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.52

Table S66.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
IL6ST MUTATED 3 1 3
IL6ST WILD-TYPE 54 82 55
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.4

Table S67.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
IL6ST MUTATED 1 1 2 0 3
IL6ST WILD-TYPE 42 54 27 36 29
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.38

Table S68.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
IL6ST MUTATED 0 1 1 2 3
IL6ST WILD-TYPE 34 28 66 34 26
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 0.69

Table S69.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
IL6ST MUTATED 0 3 2 2
IL6ST WILD-TYPE 38 65 25 58
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.34

Table S70.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
IL6ST MUTATED 0 0 1 4 2
IL6ST WILD-TYPE 24 58 23 62 19
'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.72

Table S71.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
IL6ST MUTATED 2 0 3 1
IL6ST WILD-TYPE 55 41 53 20
'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S72.  Gene #9: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
IL6ST MUTATED 1 2 2 0 1
IL6ST WILD-TYPE 31 51 48 20 19
'APOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.96 (Fisher's exact test), Q value = 0.98

Table S73.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
APOB MUTATED 6 7 10
APOB WILD-TYPE 40 55 75
'APOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 0.94

Table S74.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
APOB MUTATED 6 11 8
APOB WILD-TYPE 51 72 50
'APOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.38

Table S75.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
APOB MUTATED 3 7 4 2 8
APOB WILD-TYPE 40 48 25 34 24
'APOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.38

Table S76.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
APOB MUTATED 4 3 7 2 8
APOB WILD-TYPE 30 26 60 34 21
'APOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.4

Table S77.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
APOB MUTATED 9 6 4 6
APOB WILD-TYPE 29 62 23 54
'APOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.073 (Fisher's exact test), Q value = 0.28

Table S78.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
APOB MUTATED 3 8 0 8 6
APOB WILD-TYPE 21 50 24 58 15
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.52

Table S79.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
APOB MUTATED 6 4 11 1
APOB WILD-TYPE 51 37 45 20
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0256 (Fisher's exact test), Q value = 0.14

Table S80.  Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
APOB MUTATED 1 6 5 3 7
APOB WILD-TYPE 31 47 45 17 13

Figure S32.  Get High-res Image Gene #10: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 0.72

Table S81.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
PTEN MUTATED 0 2 4
PTEN WILD-TYPE 46 60 81
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.51

Table S82.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
PTEN MUTATED 0 4 3
PTEN WILD-TYPE 57 79 55
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.62

Table S83.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
PTEN MUTATED 1 4 0 0 1
PTEN WILD-TYPE 42 51 29 36 31
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.505 (Fisher's exact test), Q value = 0.72

Table S84.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
PTEN MUTATED 1 0 4 0 1
PTEN WILD-TYPE 33 29 63 36 28
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 0.93

Table S85.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
PTEN MUTATED 1 3 0 3
PTEN WILD-TYPE 37 65 27 57
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.51

Table S86.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
PTEN MUTATED 0 5 0 2 0
PTEN WILD-TYPE 24 53 24 64 21
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 0.9

Table S87.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
PTEN MUTATED 3 1 3 0
PTEN WILD-TYPE 54 40 53 21
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 0.51

Table S88.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
PTEN MUTATED 1 5 1 0 0
PTEN WILD-TYPE 31 48 49 20 20
'EEF1A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0557 (Fisher's exact test), Q value = 0.23

Table S89.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
EEF1A1 MUTATED 0 0 5
EEF1A1 WILD-TYPE 46 62 80
'EEF1A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 0.87

Table S90.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
EEF1A1 MUTATED 1 3 1
EEF1A1 WILD-TYPE 56 80 57
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 0.51

Table S91.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
EEF1A1 MUTATED 0 1 0 2 2
EEF1A1 WILD-TYPE 43 54 29 34 30
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.38

Table S92.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
EEF1A1 MUTATED 0 2 1 0 2
EEF1A1 WILD-TYPE 34 27 66 36 27
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 0.81

Table S93.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
EEF1A1 MUTATED 1 1 0 3
EEF1A1 WILD-TYPE 37 67 27 57
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.51

Table S94.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
EEF1A1 MUTATED 1 2 1 0 1
EEF1A1 WILD-TYPE 23 56 23 66 20
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.49

Table S95.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
EEF1A1 MUTATED 0 2 3 0
EEF1A1 WILD-TYPE 57 39 53 21
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.617 (Fisher's exact test), Q value = 0.81

Table S96.  Gene #12: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
EEF1A1 MUTATED 0 2 1 1 1
EEF1A1 WILD-TYPE 32 51 49 19 19
'KIF19 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 0.95

Table S97.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
KIF19 MUTATED 2 4 4
KIF19 WILD-TYPE 44 58 81
'KIF19 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.34

Table S98.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
KIF19 MUTATED 0 6 4
KIF19 WILD-TYPE 57 77 54
'KIF19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 0.49

Table S99.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
KIF19 MUTATED 4 3 0 0 2
KIF19 WILD-TYPE 39 52 29 36 30
'KIF19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 0.49

Table S100.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
KIF19 MUTATED 3 0 4 0 2
KIF19 WILD-TYPE 31 29 63 36 27
'KIF19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.63

Table S101.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
KIF19 MUTATED 1 6 0 3
KIF19 WILD-TYPE 37 62 27 57
'KIF19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.81 (Fisher's exact test), Q value = 0.91

Table S102.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
KIF19 MUTATED 2 3 0 4 1
KIF19 WILD-TYPE 22 55 24 62 20
'KIF19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.4

Table S103.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
KIF19 MUTATED 5 0 4 0
KIF19 WILD-TYPE 52 41 52 21
'KIF19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.34

Table S104.  Gene #13: 'KIF19 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
KIF19 MUTATED 4 3 0 1 1
KIF19 WILD-TYPE 28 50 50 19 19
'THADA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.38

Table S105.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
THADA MUTATED 0 4 2
THADA WILD-TYPE 46 58 83
'THADA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.38

Table S106.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
THADA MUTATED 0 5 1
THADA WILD-TYPE 57 78 57
'THADA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0569 (Fisher's exact test), Q value = 0.23

Table S107.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
THADA MUTATED 0 5 0 1 0
THADA WILD-TYPE 43 50 29 35 32
'THADA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.46

Table S108.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
THADA MUTATED 1 0 5 0 0
THADA WILD-TYPE 33 29 62 36 29
'THADA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 0.94

Table S109.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
THADA MUTATED 1 3 1 1
THADA WILD-TYPE 37 65 26 59
'THADA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.622 (Fisher's exact test), Q value = 0.81

Table S110.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
THADA MUTATED 1 3 1 1 0
THADA WILD-TYPE 23 55 23 65 21
'THADA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.38

Table S111.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
THADA MUTATED 0 2 4 0
THADA WILD-TYPE 57 39 52 21
'THADA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.547 (Fisher's exact test), Q value = 0.76

Table S112.  Gene #14: 'THADA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
THADA MUTATED 0 3 1 1 1
THADA WILD-TYPE 32 50 49 19 19
'PRKDC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.51

Table S113.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
PRKDC MUTATED 4 1 5
PRKDC WILD-TYPE 42 61 80
'PRKDC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.51

Table S114.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
PRKDC MUTATED 1 7 3
PRKDC WILD-TYPE 56 76 55
'PRKDC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 0.72

Table S115.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
PRKDC MUTATED 3 4 0 1 3
PRKDC WILD-TYPE 40 51 29 35 29
'PRKDC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 0.85

Table S116.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
PRKDC MUTATED 1 1 5 1 3
PRKDC WILD-TYPE 33 28 62 35 26
'PRKDC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0286 (Fisher's exact test), Q value = 0.15

Table S117.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
PRKDC MUTATED 0 7 3 1
PRKDC WILD-TYPE 38 61 24 59

Figure S33.  Get High-res Image Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'PRKDC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.51

Table S118.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
PRKDC MUTATED 0 3 2 3 3
PRKDC WILD-TYPE 24 55 22 63 18
'PRKDC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.51

Table S119.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
PRKDC MUTATED 3 1 6 0
PRKDC WILD-TYPE 54 40 50 21
'PRKDC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.34

Table S120.  Gene #15: 'PRKDC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
PRKDC MUTATED 1 2 3 0 4
PRKDC WILD-TYPE 31 51 47 20 16
'HNF1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.4

Table S121.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
HNF1A MUTATED 0 2 6
HNF1A WILD-TYPE 46 60 79
'HNF1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 0.84

Table S122.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
HNF1A MUTATED 3 4 1
HNF1A WILD-TYPE 54 79 57
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0724 (Fisher's exact test), Q value = 0.28

Table S123.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
HNF1A MUTATED 1 6 0 0 1
HNF1A WILD-TYPE 42 49 29 36 31
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.53 (Fisher's exact test), Q value = 0.74

Table S124.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
HNF1A MUTATED 1 1 5 0 1
HNF1A WILD-TYPE 33 28 62 36 28
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0953 (Fisher's exact test), Q value = 0.34

Table S125.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
HNF1A MUTATED 1 5 2 0
HNF1A WILD-TYPE 37 63 25 60
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.152 (Fisher's exact test), Q value = 0.4

Table S126.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
HNF1A MUTATED 0 6 0 2 0
HNF1A WILD-TYPE 24 52 24 64 21
'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.011 (Fisher's exact test), Q value = 0.092

Table S127.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
HNF1A MUTATED 0 0 5 2
HNF1A WILD-TYPE 57 41 51 19

Figure S34.  Get High-res Image Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.51

Table S128.  Gene #16: 'HNF1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
HNF1A MUTATED 1 5 1 0 0
HNF1A WILD-TYPE 31 48 49 20 20
'F5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 0.91

Table S129.  Gene #17: 'F5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
F5 MUTATED 1 2 1
F5 WILD-TYPE 45 60 84
'F5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.42

Table S130.  Gene #17: 'F5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
F5 MUTATED 0 1 3
F5 WILD-TYPE 57 82 55
'F5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 0.9

Table S131.  Gene #17: 'F5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
F5 MUTATED 1 2 1 0 0
F5 WILD-TYPE 42 53 28 36 32
'F5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.619 (Fisher's exact test), Q value = 0.81

Table S132.  Gene #17: 'F5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
F5 MUTATED 0 0 3 1 0
F5 WILD-TYPE 34 29 64 35 29
'F5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.34

Table S133.  Gene #17: 'F5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
F5 MUTATED 0 4 0 0
F5 WILD-TYPE 38 64 27 60
'F5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 0.96

Table S134.  Gene #17: 'F5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
F5 MUTATED 0 1 1 2 0
F5 WILD-TYPE 24 57 23 64 21
'GNAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 0.94

Table S135.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
GNAS MUTATED 1 2 4
GNAS WILD-TYPE 45 60 81
'GNAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.49

Table S136.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
GNAS MUTATED 2 1 4
GNAS WILD-TYPE 55 82 54
'GNAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.16

Table S137.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
GNAS MUTATED 0 1 2 4 0
GNAS WILD-TYPE 43 54 27 32 32

Figure S35.  Get High-res Image Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'GNAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.41

Table S138.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
GNAS MUTATED 1 3 1 2 0
GNAS WILD-TYPE 33 26 66 34 29
'GNAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 0.29

Table S139.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
GNAS MUTATED 0 1 0 5
GNAS WILD-TYPE 38 67 27 55
'GNAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.45 (Fisher's exact test), Q value = 0.7

Table S140.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
GNAS MUTATED 0 1 2 3 0
GNAS WILD-TYPE 24 57 22 63 21
'GNAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.76

Table S141.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
GNAS MUTATED 2 3 1 0
GNAS WILD-TYPE 55 38 55 21
'GNAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 0.87

Table S142.  Gene #18: 'GNAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
GNAS MUTATED 1 1 3 0 1
GNAS WILD-TYPE 31 52 47 20 19
'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 0.66

Table S143.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
MLL4 MUTATED 4 3 3
MLL4 WILD-TYPE 42 59 82
'MLL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.4

Table S144.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
MLL4 MUTATED 2 7 1
MLL4 WILD-TYPE 55 76 57
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 0.73

Table S145.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
MLL4 MUTATED 4 2 0 2 2
MLL4 WILD-TYPE 39 53 29 34 30
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 0.94

Table S146.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
MLL4 MUTATED 2 2 3 1 2
MLL4 WILD-TYPE 32 27 64 35 27
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 0.81

Table S147.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
MLL4 MUTATED 1 5 2 2
MLL4 WILD-TYPE 37 63 25 58
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.63

Table S148.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
MLL4 MUTATED 2 2 2 2 2
MLL4 WILD-TYPE 22 56 22 64 19
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.85

Table S149.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
MLL4 MUTATED 2 2 3 2
MLL4 WILD-TYPE 55 39 53 19
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.79 (Fisher's exact test), Q value = 0.9

Table S150.  Gene #19: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
MLL4 MUTATED 2 2 2 2 1
MLL4 WILD-TYPE 30 51 48 18 19
'HIST1H1C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.87

Table S151.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 46 62 85
HIST1H1C MUTATED 2 1 2
HIST1H1C WILD-TYPE 44 61 83
'HIST1H1C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.87

Table S152.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 57 83 58
HIST1H1C MUTATED 1 3 1
HIST1H1C WILD-TYPE 56 80 57
'HIST1H1C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.72

Table S153.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 55 29 36 32
HIST1H1C MUTATED 0 1 1 1 2
HIST1H1C WILD-TYPE 43 54 28 35 30
'HIST1H1C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 0.59

Table S154.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 34 29 67 36 29
HIST1H1C MUTATED 1 1 1 0 2
HIST1H1C WILD-TYPE 33 28 66 36 27
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 0.9

Table S155.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 38 68 27 60
HIST1H1C MUTATED 1 3 0 1
HIST1H1C WILD-TYPE 37 65 27 59
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.51

Table S156.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 24 58 24 66 21
HIST1H1C MUTATED 0 1 1 1 2
HIST1H1C WILD-TYPE 24 57 23 65 19
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 0.82

Table S157.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 57 41 56 21
HIST1H1C MUTATED 1 1 3 0
HIST1H1C WILD-TYPE 56 40 53 21
'HIST1H1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0207 (Fisher's exact test), Q value = 0.13

Table S158.  Gene #20: 'HIST1H1C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 32 53 50 20 20
HIST1H1C MUTATED 1 0 1 0 3
HIST1H1C WILD-TYPE 31 53 49 20 17

Figure S36.  Get High-res Image Gene #20: 'HIST1H1C 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/LIHC-TP/19897750/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/20139336/LIHC-TP.transferedmergedcluster.txt

  • Number of patients = 198

  • Number of significantly mutated genes = 20

  • 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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