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 33 genes and 12 molecular subtypes across 248 patients, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

  • CTNNB1 mutation correlated to 'MRNA_CNMF',  'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • PIK3R1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • KRAS mutation correlated to 'MRNA_CHIERARCHICAL' and 'MIRSEQ_CNMF'.

  • TP53 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CTCF mutation correlated to 'CN_CNMF'.

  • ARID1A mutation correlated to 'CN_CNMF'.

  • RNF43 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 33 genes and 12 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 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test Chi-square test Fisher's exact test Fisher's exact test Fisher's exact test
TP53 69 (28%) 179 3.76e-05
(0.0131) 		2.45e-07
(8.74e-05) 		4.35e-30
(1.64e-27) 		2.53e-12
(9.2e-10) 		2.01e-05
(0.00706) 		0.0014
(0.469) 		4.09e-24
(1.53e-21) 		6.53e-21
(2.44e-18) 		3.53e-17
(1.3e-14) 		1.52e-13
(5.55e-11) 		6.65e-09
(2.38e-06) 		1.24e-09
(4.45e-07)
PTEN 161 (65%) 87 0.00442
(1.00) 		0.000362
(0.125) 		1.82e-20
(6.75e-18) 		1.79e-12
(6.52e-10) 		0.0257
(1.00) 		0.183
(1.00) 		4.45e-21
(1.66e-18) 		2.86e-17
(1.06e-14) 		7.65e-16
(2.81e-13) 		1.44e-13
(5.26e-11) 		5.35e-09
(1.92e-06) 		8.55e-14
(3.14e-11)
CTNNB1 74 (30%) 174 5.68e-07
(0.000202) 		0.00115
(0.389) 		8.75e-06
(0.00309) 		0.00315
(1.00) 		1.29e-10
(4.65e-08) 		0.112
(1.00) 		1.4e-20
(5.2e-18) 		3.02e-06
(0.00107) 		1.98e-11
(7.16e-09) 		0.138
(1.00) 		0.0232
(1.00) 		0.00379
(1.00)
PIK3R1 83 (33%) 165 0.0669
(1.00) 		0.0218
(1.00) 		0.000523
(0.18) 		3.32e-05
(0.0116) 		0.649
(1.00) 		0.877
(1.00) 		0.000113
(0.0391) 		2.24e-05
(0.00787) 		0.0133
(1.00) 		0.146
(1.00) 		0.0126
(1.00) 		0.000575
(0.197)
KRAS 53 (21%) 195 0.203
(1.00) 		0.000649
(0.221) 		0.00606
(1.00) 		0.123
(1.00) 		0.297
(1.00) 		0.855
(1.00) 		0.00755
(1.00) 		0.0376
(1.00) 		0.000628
(0.215) 		0.564
(1.00) 		0.143
(1.00) 		0.457
(1.00)
CTCF 44 (18%) 204 0.149
(1.00) 		0.421
(1.00) 		0.000441
(0.152) 		0.0433
(1.00) 		0.0458
(1.00) 		1
(1.00) 		0.000834
(0.284) 		0.00121
(0.411) 		0.00949
(1.00) 		0.00316
(1.00) 		0.00792
(1.00) 		0.103
(1.00)
ARID1A 83 (33%) 165 0.266
(1.00) 		0.011
(1.00) 		7.11e-07
(0.000252) 		0.227
(1.00) 		0.0271
(1.00) 		1
(1.00) 		0.00267
(0.888) 		0.0452
(1.00) 		0.0226
(1.00) 		0.053
(1.00) 		0.0664
(1.00) 		0.0139
(1.00)
RNF43 12 (5%) 236 0.133
(1.00) 		0.151
(1.00) 		0.443
(1.00) 		0.377
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.032
(1.00) 		2.55e-05
(0.00892) 		0.129
(1.00) 		0.445
(1.00) 		0.349
(1.00) 		0.484
(1.00)
PPP2R1A 27 (11%) 221 0.076
(1.00) 		0.0518
(1.00) 		0.0121
(1.00) 		0.0129
(1.00) 		0.141
(1.00) 		0.313
(1.00) 		0.00577
(1.00) 		0.00531
(1.00) 		0.0257
(1.00) 		0.0356
(1.00) 		0.0673
(1.00) 		0.0127
(1.00)
PIK3CA 132 (53%) 116 0.834
(1.00) 		0.198
(1.00) 		0.475
(1.00) 		0.677
(1.00) 		0.366
(1.00) 		0.365
(1.00) 		0.148
(1.00) 		0.989
(1.00) 		0.746
(1.00) 		0.32
(1.00) 		0.41
(1.00) 		0.753
(1.00)
PRKAR1B 4 (2%) 244 0.988
(1.00) 		0.509
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.387
(1.00) 		0.262
(1.00) 		0.482
(1.00) 		0.37
(1.00) 		0.797
(1.00) 		0.155
(1.00)
FBXW7 39 (16%) 209 0.225
(1.00) 		0.692
(1.00) 		0.343
(1.00) 		0.0757
(1.00) 		0.106
(1.00) 		0.107
(1.00) 		0.0237
(1.00) 		0.0148
(1.00) 		0.135
(1.00) 		0.104
(1.00) 		0.351
(1.00) 		0.0228
(1.00)
SPOP 21 (8%) 227 0.349
(1.00) 		1
(1.00) 		0.85
(1.00) 		0.356
(1.00) 		0.834
(1.00) 		0.415
(1.00) 		0.352
(1.00) 		0.362
(1.00) 		0.0343
(1.00) 		0.462
(1.00) 		0.61
(1.00) 		0.692
(1.00)
ARID5B 29 (12%) 219 0.961
(1.00) 		0.459
(1.00) 		0.0427
(1.00) 		0.136
(1.00) 		0.164
(1.00) 		0.182
(1.00) 		0.0531
(1.00) 		0.0676
(1.00) 		0.0452
(1.00) 		0.346
(1.00) 		0.263
(1.00) 		0.724
(1.00)
FGFR2 31 (12%) 217 0.385
(1.00) 		0.293
(1.00) 		0.611
(1.00) 		0.914
(1.00) 		0.97
(1.00) 		0.829
(1.00) 		0.527
(1.00) 		0.565
(1.00) 		0.876
(1.00) 		0.59
(1.00) 		0.644
(1.00) 		0.82
(1.00)
NFE2L2 15 (6%) 233 0.0905
(1.00) 		0.833
(1.00) 		0.00636
(1.00) 		0.631
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.0134
(1.00) 		0.574
(1.00) 		0.392
(1.00) 		0.775
(1.00) 		0.263
(1.00) 		0.724
(1.00)
CCND1 14 (6%) 234 0.631
(1.00) 		0.833
(1.00) 		0.154
(1.00) 		0.495
(1.00) 		0.514
(1.00) 		0.509
(1.00) 		0.635
(1.00) 		0.269
(1.00) 		0.124
(1.00) 		0.612
(1.00) 		0.439
(1.00) 		0.853
(1.00)
CHD4 35 (14%) 213 0.0986
(1.00) 		0.284
(1.00) 		0.776
(1.00) 		0.852
(1.00) 		0.97
(1.00) 		0.287
(1.00) 		0.872
(1.00) 		0.479
(1.00) 		0.739
(1.00) 		0.59
(1.00) 		0.405
(1.00) 		0.97
(1.00)
FAM9A 14 (6%) 234 0.887
(1.00) 		0.27
(1.00) 		0.178
(1.00) 		0.0227
(1.00) 		0.0562
(1.00) 		0.065
(1.00) 		0.308
(1.00) 		0.0424
(1.00) 		0.0237
(1.00) 		0.149
(1.00)
MORC4 20 (8%) 228 0.583
(1.00) 		0.18
(1.00) 		0.34
(1.00) 		0.28
(1.00) 		0.212
(1.00) 		0.0332
(1.00) 		0.00821
(1.00) 		0.266
(1.00) 		0.315
(1.00) 		0.19
(1.00) 		0.322
(1.00) 		0.0396
(1.00)
CASP8 17 (7%) 231 0.381
(1.00) 		0.0595
(1.00) 		0.204
(1.00) 		0.626
(1.00) 		0.154
(1.00) 		0.269
(1.00) 		0.375
(1.00) 		0.126
(1.00) 		0.152
(1.00) 		0.189
(1.00) 		0.367
(1.00) 		0.91
(1.00)
FOXA2 12 (5%) 236 0.304
(1.00) 		0.795
(1.00) 		0.0719
(1.00) 		0.744
(1.00) 		0.506
(1.00) 		0.589
(1.00) 		0.0582
(1.00) 		0.8
(1.00) 		0.681
(1.00) 		0.332
(1.00)
ABI1 4 (2%) 244 0.821
(1.00) 		0.64
(1.00) 		0.637
(1.00) 		0.681
(1.00) 		0.262
(1.00) 		0.687
(1.00) 		0.655
(1.00)
DNER 18 (7%) 230 0.191
(1.00) 		0.0515
(1.00) 		0.013
(1.00) 		0.597
(1.00) 		0.0217
(1.00) 		0.581
(1.00) 		0.126
(1.00) 		0.0936
(1.00) 		0.785
(1.00) 		0.153
(1.00) 		0.681
(1.00) 		0.91
(1.00)
BCOR 30 (12%) 218 0.687
(1.00) 		0.405
(1.00) 		0.00577
(1.00) 		0.0246
(1.00) 		0.512
(1.00) 		0.5
(1.00) 		0.00134
(0.451) 		0.323
(1.00) 		0.0495
(1.00) 		0.0922
(1.00) 		0.866
(1.00) 		0.176
(1.00)
BRS3 15 (6%) 233 0.536
(1.00) 		0.151
(1.00) 		0.339
(1.00) 		0.519
(1.00) 		0.392
(1.00) 		0.54
(1.00) 		0.108
(1.00) 		0.00295
(0.98) 		0.393
(1.00) 		0.00527
(1.00) 		0.562
(1.00) 		0.343
(1.00)
SGK1 15 (6%) 233 0.381
(1.00) 		0.0595
(1.00) 		0.43
(1.00) 		0.625
(1.00) 		0.226
(1.00) 		0.0954
(1.00) 		0.0301
(1.00) 		0.893
(1.00) 		0.431
(1.00) 		1
(1.00) 		0.687
(1.00) 		0.853
(1.00)
NRAS 9 (4%) 239 0.749
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.56
(1.00) 		0.908
(1.00) 		0.604
(1.00) 		0.213
(1.00)
TIAL1 11 (4%) 237 0.381
(1.00) 		0.405
(1.00) 		0.362
(1.00) 		0.0634
(1.00) 		0.564
(1.00) 		0.744
(1.00) 		0.00545
(1.00) 		0.0128
(1.00) 		0.812
(1.00) 		1
(1.00) 		0.477
(1.00) 		0.724
(1.00)
SIN3A 21 (8%) 227 0.0266
(1.00) 		0.598
(1.00) 		0.00607
(1.00) 		0.129
(1.00) 		0.00261
(0.873) 		0.0226
(1.00) 		0.16
(1.00) 		0.00595
(1.00) 		0.517
(1.00) 		0.465
(1.00)
SLC48A1 5 (2%) 243 0.736
(1.00) 		0.639
(1.00) 		0.803
(1.00) 		0.372
(1.00) 		0.876
(1.00) 		0.849
(1.00) 		0.726
(1.00) 		0.686
(1.00) 		0.797
(1.00) 		0.458
(1.00)
ZFHX3 44 (18%) 204 0.375
(1.00) 		0.0291
(1.00) 		0.094
(1.00) 		0.0648
(1.00) 		0.318
(1.00) 		0.179
(1.00) 		0.592
(1.00) 		0.115
(1.00) 		0.207
(1.00) 		0.614
(1.00) 		0.847
(1.00) 		0.526
(1.00)
RB1 20 (8%) 228 0.639
(1.00) 		1
(1.00) 		0.31
(1.00) 		0.626
(1.00) 		0.12
(1.00) 		0.313
(1.00) 		0.583
(1.00) 		0.271
(1.00) 		0.955
(1.00) 		0.00126
(0.425) 		0.854
(1.00) 		1
(1.00)
'PPP2R1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.076 (Fisher's exact test), Q value = 1

Table S1.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
PPP2R1A MUTATED 3 5 0 0
PPP2R1A WILD-TYPE 9 13 11 10
'PPP2R1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0518 (Fisher's exact test), Q value = 1

Table S2.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
PPP2R1A MUTATED 4 0 4
PPP2R1A WILD-TYPE 13 18 12
'PPP2R1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0121 (Chi-square test), Q value = 1

Table S3.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
PPP2R1A MUTATED 11 0 12 2 0 0
PPP2R1A WILD-TYPE 146 12 42 6 10 1

Figure S1.  Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PPP2R1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0129 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
PPP2R1A MUTATED 10 1 5
PPP2R1A WILD-TYPE 33 40 46

Figure S2.  Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PPP2R1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.141 (Chi-square test), Q value = 1

Table S5.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
PPP2R1A MUTATED 3 7 2 0 2 4
PPP2R1A WILD-TYPE 36 29 35 10 38 20
'PPP2R1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
PPP2R1A MUTATED 9 9
PPP2R1A WILD-TYPE 106 62
'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00577 (Fisher's exact test), Q value = 1

Table S7.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
PPP2R1A MUTATED 15 2 6 4
PPP2R1A WILD-TYPE 48 34 66 70

Figure S3.  Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PPP2R1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00531 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
PPP2R1A MUTATED 17 4 6
PPP2R1A WILD-TYPE 68 44 106

Figure S4.  Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Chi-square test), Q value = 1

Table S9.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
PPP2R1A MUTATED 10 4 3 2 6
PPP2R1A WILD-TYPE 32 74 20 24 65

Figure S5.  Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
PPP2R1A MUTATED 0 8 17
PPP2R1A WILD-TYPE 4 123 88

Figure S6.  Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 1

Table S11.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
PPP2R1A MUTATED 9 3 4
PPP2R1A WILD-TYPE 27 23 50
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 1

Table S12.  Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
PPP2R1A MUTATED 6 6 4 0
PPP2R1A WILD-TYPE 17 16 61 6

Figure S7.  Get High-res Image Gene #1: 'PPP2R1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
PIK3CA MUTATED 7 8 6 6
PIK3CA WILD-TYPE 5 10 5 4
'PIK3CA MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
PIK3CA MUTATED 12 8 7
PIK3CA WILD-TYPE 5 10 9
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.475 (Chi-square test), Q value = 1

Table S15.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
PIK3CA MUTATED 86 8 24 3 6 1
PIK3CA WILD-TYPE 71 4 30 5 4 0
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
PIK3CA MUTATED 22 23 24
PIK3CA WILD-TYPE 21 18 27
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (Chi-square test), Q value = 1

Table S17.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
PIK3CA MUTATED 17 22 19 7 18 15
PIK3CA WILD-TYPE 22 14 18 3 22 9
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
PIK3CA MUTATED 64 34
PIK3CA WILD-TYPE 51 37
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 1

Table S19.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
PIK3CA MUTATED 27 24 39 40
PIK3CA WILD-TYPE 36 12 33 34
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.989 (Fisher's exact test), Q value = 1

Table S20.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
PIK3CA MUTATED 45 25 60
PIK3CA WILD-TYPE 40 23 52
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.746 (Chi-square test), Q value = 1

Table S21.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
PIK3CA MUTATED 20 46 11 13 38
PIK3CA WILD-TYPE 22 32 12 13 33
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 1

Table S22.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
PIK3CA MUTATED 3 74 51
PIK3CA WILD-TYPE 1 57 54
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 1

Table S23.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
PIK3CA MUTATED 15 14 30
PIK3CA WILD-TYPE 21 12 24
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S24.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
PIK3CA MUTATED 12 9 35 3
PIK3CA WILD-TYPE 11 13 30 3
'CTNNB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 5.68e-07 (Fisher's exact test), Q value = 2e-04

Table S25.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
CTNNB1 MUTATED 0 3 4 10
CTNNB1 WILD-TYPE 12 15 7 0

Figure S8.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00115 (Fisher's exact test), Q value = 0.39

Table S26.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
CTNNB1 MUTATED 3 12 2
CTNNB1 WILD-TYPE 14 6 14

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

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 8.75e-06 (Chi-square test), Q value = 0.0031

Table S27.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
CTNNB1 MUTATED 60 7 1 2 2 0
CTNNB1 WILD-TYPE 97 5 53 6 8 1

Figure S10.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 1

Table S28.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
CTNNB1 MUTATED 4 15 18
CTNNB1 WILD-TYPE 39 26 33

Figure S11.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1.29e-10 (Chi-square test), Q value = 4.7e-08

Table S29.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
CTNNB1 MUTATED 6 10 6 0 32 10
CTNNB1 WILD-TYPE 33 26 31 10 8 14

Figure S12.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
CTNNB1 MUTATED 45 19
CTNNB1 WILD-TYPE 70 52
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.4e-20 (Fisher's exact test), Q value = 5.2e-18

Table S31.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
CTNNB1 MUTATED 3 4 53 13
CTNNB1 WILD-TYPE 60 32 19 61

Figure S13.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3.02e-06 (Fisher's exact test), Q value = 0.0011

Table S32.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
CTNNB1 MUTATED 9 19 45
CTNNB1 WILD-TYPE 76 29 67

Figure S14.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1.98e-11 (Chi-square test), Q value = 7.2e-09

Table S33.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
CTNNB1 MUTATED 1 13 6 20 31
CTNNB1 WILD-TYPE 41 65 17 6 40

Figure S15.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 1

Table S34.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
CTNNB1 MUTATED 0 45 26
CTNNB1 WILD-TYPE 4 86 79
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 1

Table S35.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
CTNNB1 MUTATED 3 9 15
CTNNB1 WILD-TYPE 33 17 39

Figure S16.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00379 (Fisher's exact test), Q value = 1

Table S36.  Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
CTNNB1 MUTATED 4 0 22 1
CTNNB1 WILD-TYPE 19 22 43 5

Figure S17.  Get High-res Image Gene #3: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0669 (Fisher's exact test), Q value = 1

Table S37.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
PIK3R1 MUTATED 5 2 6 3
PIK3R1 WILD-TYPE 7 16 5 7
'PIK3R1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0218 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
PIK3R1 MUTATED 8 7 1
PIK3R1 WILD-TYPE 9 11 15

Figure S18.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000523 (Chi-square test), Q value = 0.18

Table S39.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
PIK3R1 MUTATED 64 2 6 5 5 0
PIK3R1 WILD-TYPE 93 10 48 3 5 1

Figure S19.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3.32e-05 (Fisher's exact test), Q value = 0.012

Table S40.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
PIK3R1 MUTATED 5 12 28
PIK3R1 WILD-TYPE 38 29 23

Figure S20.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3R1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.649 (Chi-square test), Q value = 1

Table S41.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
PIK3R1 MUTATED 13 11 18 3 16 9
PIK3R1 WILD-TYPE 26 25 19 7 24 15
'PIK3R1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S42.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
PIK3R1 MUTATED 44 26
PIK3R1 WILD-TYPE 71 45
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000113 (Fisher's exact test), Q value = 0.039

Table S43.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
PIK3R1 MUTATED 7 15 28 31
PIK3R1 WILD-TYPE 56 21 44 43

Figure S21.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.24e-05 (Fisher's exact test), Q value = 0.0079

Table S44.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
PIK3R1 MUTATED 13 24 44
PIK3R1 WILD-TYPE 72 24 68

Figure S22.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0133 (Chi-square test), Q value = 1

Table S45.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
PIK3R1 MUTATED 5 29 7 9 31
PIK3R1 WILD-TYPE 37 49 16 17 40

Figure S23.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 1

Table S46.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
PIK3R1 MUTATED 1 51 29
PIK3R1 WILD-TYPE 3 80 76
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 1

Table S47.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
PIK3R1 MUTATED 5 9 23
PIK3R1 WILD-TYPE 31 17 31

Figure S24.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.000575 (Fisher's exact test), Q value = 0.2

Table S48.  Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
PIK3R1 MUTATED 4 1 29 3
PIK3R1 WILD-TYPE 19 21 36 3

Figure S25.  Get High-res Image Gene #4: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PRKAR1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.988 (Chi-square test), Q value = 1

Table S49.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
PRKAR1B MUTATED 3 0 1 0 0 0
PRKAR1B WILD-TYPE 154 12 53 8 10 1
'PRKAR1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
PRKAR1B MUTATED 2 0 1
PRKAR1B WILD-TYPE 41 41 50
'PRKAR1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.887 (Chi-square test), Q value = 1

Table S51.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
PRKAR1B MUTATED 1 1 1 0 0 1
PRKAR1B WILD-TYPE 38 35 36 10 40 23
'PRKAR1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S52.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
PRKAR1B MUTATED 3 1
PRKAR1B WILD-TYPE 112 70
'PRKAR1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S53.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
PRKAR1B MUTATED 2 1 1 0
PRKAR1B WILD-TYPE 61 35 71 74
'PRKAR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S54.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
PRKAR1B MUTATED 1 2 1
PRKAR1B WILD-TYPE 84 46 111
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.482 (Chi-square test), Q value = 1

Table S55.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
PRKAR1B MUTATED 1 0 1 0 2
PRKAR1B WILD-TYPE 41 78 22 26 69
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 1

Table S56.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
PRKAR1B MUTATED 0 1 3
PRKAR1B WILD-TYPE 4 130 102
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S57.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
PRKAR1B MUTATED 1 1 1
PRKAR1B WILD-TYPE 35 25 53
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 1

Table S58.  Gene #5: 'PRKAR1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
PRKAR1B MUTATED 1 0 1 1
PRKAR1B WILD-TYPE 22 22 64 5
'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00442 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
PTEN MUTATED 11 6 9 7
PTEN WILD-TYPE 1 12 2 3

Figure S26.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000362 (Fisher's exact test), Q value = 0.13

Table S60.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
PTEN MUTATED 15 14 4
PTEN WILD-TYPE 2 4 12

Figure S27.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 1.82e-20 (Chi-square test), Q value = 6.8e-18

Table S61.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
PTEN MUTATED 129 7 4 6 9 1
PTEN WILD-TYPE 28 5 50 2 1 0

Figure S28.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1.79e-12 (Fisher's exact test), Q value = 6.5e-10

Table S62.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
PTEN MUTATED 7 30 44
PTEN WILD-TYPE 36 11 7

Figure S29.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0257 (Chi-square test), Q value = 1

Table S63.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
PTEN MUTATED 26 21 33 9 29 14
PTEN WILD-TYPE 13 15 4 1 11 10

Figure S30.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 1

Table S64.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
PTEN MUTATED 86 46
PTEN WILD-TYPE 29 25
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.45e-21 (Fisher's exact test), Q value = 1.7e-18

Table S65.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
PTEN MUTATED 10 25 55 68
PTEN WILD-TYPE 53 11 17 6

Figure S31.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.86e-17 (Fisher's exact test), Q value = 1.1e-14

Table S66.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
PTEN MUTATED 24 38 96
PTEN WILD-TYPE 61 10 16

Figure S32.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 7.65e-16 (Chi-square test), Q value = 2.8e-13

Table S67.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
PTEN MUTATED 6 72 12 17 51
PTEN WILD-TYPE 36 6 11 9 20

Figure S33.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.44e-13 (Fisher's exact test), Q value = 5.3e-11

Table S68.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
PTEN MUTATED 4 112 42
PTEN WILD-TYPE 0 19 63

Figure S34.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 5.35e-09 (Fisher's exact test), Q value = 1.9e-06

Table S69.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
PTEN MUTATED 11 11 48
PTEN WILD-TYPE 25 15 6

Figure S35.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 8.55e-14 (Fisher's exact test), Q value = 3.1e-11

Table S70.  Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
PTEN MUTATED 6 2 58 4
PTEN WILD-TYPE 17 20 7 2

Figure S36.  Get High-res Image Gene #6: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 1

Table S71.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
KRAS MUTATED 5 2 3 1
KRAS WILD-TYPE 7 16 8 9
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.000649 (Fisher's exact test), Q value = 0.22

Table S72.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
KRAS MUTATED 9 1 1
KRAS WILD-TYPE 8 17 15

Figure S37.  Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00606 (Chi-square test), Q value = 1

Table S73.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
KRAS MUTATED 43 3 2 0 2 0
KRAS WILD-TYPE 114 9 52 8 8 1

Figure S38.  Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 1

Table S74.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
KRAS MUTATED 6 8 16
KRAS WILD-TYPE 37 33 35
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.297 (Chi-square test), Q value = 1

Table S75.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
KRAS MUTATED 6 9 12 3 5 5
KRAS WILD-TYPE 33 27 25 7 35 19
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S76.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
KRAS MUTATED 24 16
KRAS WILD-TYPE 91 55
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00755 (Fisher's exact test), Q value = 1

Table S77.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
KRAS MUTATED 7 14 12 19
KRAS WILD-TYPE 56 22 60 55

Figure S39.  Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0376 (Fisher's exact test), Q value = 1

Table S78.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
KRAS MUTATED 12 16 24
KRAS WILD-TYPE 73 32 88

Figure S40.  Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.000628 (Chi-square test), Q value = 0.21

Table S79.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
KRAS MUTATED 3 19 9 0 21
KRAS WILD-TYPE 39 59 14 26 50

Figure S41.  Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S80.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
KRAS MUTATED 0 31 21
KRAS WILD-TYPE 4 100 84
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 1

Table S81.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
KRAS MUTATED 4 8 13
KRAS WILD-TYPE 32 18 41
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S82.  Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
KRAS MUTATED 6 3 16 0
KRAS WILD-TYPE 17 19 49 6
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 3.76e-05 (Fisher's exact test), Q value = 0.013

Table S83.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
TP53 MUTATED 2 13 1 0
TP53 WILD-TYPE 10 5 10 10

Figure S42.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 2.45e-07 (Fisher's exact test), Q value = 8.7e-05

Table S84.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
TP53 MUTATED 3 0 13
TP53 WILD-TYPE 14 18 3

Figure S43.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 4.35e-30 (Chi-square test), Q value = 1.6e-27

Table S85.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
TP53 MUTATED 11 2 50 3 2 0
TP53 WILD-TYPE 146 10 4 5 8 1

Figure S44.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2.53e-12 (Fisher's exact test), Q value = 9.2e-10

Table S86.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
TP53 MUTATED 31 4 5
TP53 WILD-TYPE 12 37 46

Figure S45.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 2.01e-05 (Chi-square test), Q value = 0.0071

Table S87.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
TP53 MUTATED 9 19 4 2 2 8
TP53 WILD-TYPE 30 17 33 8 38 16

Figure S46.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.47

Table S88.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
TP53 MUTATED 18 26
TP53 WILD-TYPE 97 45

Figure S47.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4.09e-24 (Fisher's exact test), Q value = 1.5e-21

Table S89.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
TP53 MUTATED 50 8 8 3
TP53 WILD-TYPE 13 28 64 71

Figure S48.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6.53e-21 (Fisher's exact test), Q value = 2.4e-18

Table S90.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
TP53 MUTATED 56 6 7
TP53 WILD-TYPE 29 42 105

Figure S49.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 3.53e-17 (Chi-square test), Q value = 1.3e-14

Table S91.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
TP53 MUTATED 34 5 7 4 14
TP53 WILD-TYPE 8 73 16 22 57

Figure S50.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.52e-13 (Fisher's exact test), Q value = 5.5e-11

Table S92.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
TP53 MUTATED 2 10 52
TP53 WILD-TYPE 2 121 53

Figure S51.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 6.65e-09 (Fisher's exact test), Q value = 2.4e-06

Table S93.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
TP53 MUTATED 25 6 5
TP53 WILD-TYPE 11 20 49

Figure S52.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1.24e-09 (Fisher's exact test), Q value = 4.4e-07

Table S94.  Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
TP53 MUTATED 9 18 6 3
TP53 WILD-TYPE 14 4 59 3

Figure S53.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 1

Table S95.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
FBXW7 MUTATED 3 4 4 0
FBXW7 WILD-TYPE 9 14 7 10
'FBXW7 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
FBXW7 MUTATED 5 3 3
FBXW7 WILD-TYPE 12 15 13
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.343 (Chi-square test), Q value = 1

Table S97.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
FBXW7 MUTATED 25 0 12 0 2 0
FBXW7 WILD-TYPE 132 12 42 8 8 1
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0757 (Fisher's exact test), Q value = 1

Table S98.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
FBXW7 MUTATED 11 3 8
FBXW7 WILD-TYPE 32 38 43
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.106 (Chi-square test), Q value = 1

Table S99.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
FBXW7 MUTATED 10 5 5 4 3 4
FBXW7 WILD-TYPE 29 31 32 6 37 20
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 1

Table S100.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
FBXW7 MUTATED 15 16
FBXW7 WILD-TYPE 100 55
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 1

Table S101.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
FBXW7 MUTATED 14 10 6 9
FBXW7 WILD-TYPE 49 26 66 65

Figure S54.  Get High-res Image Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 1

Table S102.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
FBXW7 MUTATED 20 9 10
FBXW7 WILD-TYPE 65 39 102

Figure S55.  Get High-res Image Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.135 (Chi-square test), Q value = 1

Table S103.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
FBXW7 MUTATED 9 9 6 1 10
FBXW7 WILD-TYPE 33 69 17 25 61
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 1

Table S104.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
FBXW7 MUTATED 1 14 20
FBXW7 WILD-TYPE 3 117 85
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 1

Table S105.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
FBXW7 MUTATED 8 4 6
FBXW7 WILD-TYPE 28 22 48
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0228 (Fisher's exact test), Q value = 1

Table S106.  Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
FBXW7 MUTATED 4 8 6 0
FBXW7 WILD-TYPE 19 14 59 6

Figure S56.  Get High-res Image Gene #9: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S107.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
CTCF MUTATED 3 1 4 1
CTCF WILD-TYPE 9 17 7 9
'CTCF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S108.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
CTCF MUTATED 4 4 1
CTCF WILD-TYPE 13 14 15
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.000441 (Chi-square test), Q value = 0.15

Table S109.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
CTCF MUTATED 38 0 0 0 3 0
CTCF WILD-TYPE 119 12 54 8 7 1

Figure S57.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0433 (Fisher's exact test), Q value = 1

Table S110.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
CTCF MUTATED 3 11 7
CTCF WILD-TYPE 40 30 44

Figure S58.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0458 (Chi-square test), Q value = 1

Table S111.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
CTCF MUTATED 9 3 5 5 9 3
CTCF WILD-TYPE 30 33 32 5 31 21

Figure S59.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S112.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
CTCF MUTATED 21 13
CTCF WILD-TYPE 94 58
'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.000834 (Fisher's exact test), Q value = 0.28

Table S113.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
CTCF MUTATED 2 7 15 20
CTCF WILD-TYPE 61 29 57 54

Figure S60.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00121 (Fisher's exact test), Q value = 0.41

Table S114.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
CTCF MUTATED 6 8 30
CTCF WILD-TYPE 79 40 82

Figure S61.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00949 (Chi-square test), Q value = 1

Table S115.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
CTCF MUTATED 1 21 2 4 16
CTCF WILD-TYPE 41 57 21 22 55

Figure S62.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00316 (Fisher's exact test), Q value = 1

Table S116.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
CTCF MUTATED 0 34 10
CTCF WILD-TYPE 4 97 95

Figure S63.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 1

Table S117.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
CTCF MUTATED 1 1 12
CTCF WILD-TYPE 35 25 42

Figure S64.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 1

Table S118.  Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
CTCF MUTATED 2 0 12 0
CTCF WILD-TYPE 21 22 53 6
'ARID1A MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 1

Table S119.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
ARID1A MUTATED 5 3 4 5
ARID1A WILD-TYPE 7 15 7 5
'ARID1A MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.011 (Fisher's exact test), Q value = 1

Table S120.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
ARID1A MUTATED 9 7 1
ARID1A WILD-TYPE 8 11 15

Figure S65.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 7.11e-07 (Chi-square test), Q value = 0.00025

Table S121.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
ARID1A MUTATED 68 2 3 0 6 1
ARID1A WILD-TYPE 89 10 51 8 4 0

Figure S66.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 1

Table S122.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
ARID1A MUTATED 10 16 19
ARID1A WILD-TYPE 33 25 32
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0271 (Chi-square test), Q value = 1

Table S123.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
ARID1A MUTATED 12 13 18 3 18 2
ARID1A WILD-TYPE 27 23 19 7 22 22

Figure S67.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
ARID1A MUTATED 41 25
ARID1A WILD-TYPE 74 46
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00267 (Fisher's exact test), Q value = 0.89

Table S125.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
ARID1A MUTATED 10 11 30 31
ARID1A WILD-TYPE 53 25 42 43

Figure S68.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 1

Table S126.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
ARID1A MUTATED 20 20 42
ARID1A WILD-TYPE 65 28 70

Figure S69.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0226 (Chi-square test), Q value = 1

Table S127.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
ARID1A MUTATED 6 34 9 7 24
ARID1A WILD-TYPE 36 44 14 19 47

Figure S70.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.053 (Fisher's exact test), Q value = 1

Table S128.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
ARID1A MUTATED 2 51 27
ARID1A WILD-TYPE 2 80 78
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0664 (Fisher's exact test), Q value = 1

Table S129.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
ARID1A MUTATED 7 10 23
ARID1A WILD-TYPE 29 16 31
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0139 (Fisher's exact test), Q value = 1

Table S130.  Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
ARID1A MUTATED 8 3 29 0
ARID1A WILD-TYPE 15 19 36 6

Figure S71.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SPOP MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S131.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
SPOP MUTATED 2 1 0 2
SPOP WILD-TYPE 10 17 11 8
'SPOP MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S132.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
SPOP MUTATED 2 2 1
SPOP WILD-TYPE 15 16 15
'SPOP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.85 (Chi-square test), Q value = 1

Table S133.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
SPOP MUTATED 16 1 3 0 1 0
SPOP WILD-TYPE 141 11 51 8 9 1
'SPOP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 1

Table S134.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
SPOP MUTATED 4 1 5
SPOP WILD-TYPE 39 40 46
'SPOP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.834 (Chi-square test), Q value = 1

Table S135.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
SPOP MUTATED 5 3 2 1 3 1
SPOP WILD-TYPE 34 33 35 9 37 23
'SPOP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 1

Table S136.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
SPOP MUTATED 11 4
SPOP WILD-TYPE 104 67
'SPOP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 1

Table S137.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
SPOP MUTATED 4 5 8 4
SPOP WILD-TYPE 59 31 64 70
'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 1

Table S138.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
SPOP MUTATED 8 6 7
SPOP WILD-TYPE 77 42 105
'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0343 (Chi-square test), Q value = 1

Table S139.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
SPOP MUTATED 1 4 4 1 11
SPOP WILD-TYPE 41 74 19 25 60

Figure S72.  Get High-res Image Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S140.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
SPOP MUTATED 0 9 12
SPOP WILD-TYPE 4 122 93
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S141.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
SPOP MUTATED 4 2 3
SPOP WILD-TYPE 32 24 51
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.692 (Fisher's exact test), Q value = 1

Table S142.  Gene #12: 'SPOP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
SPOP MUTATED 3 2 4 0
SPOP WILD-TYPE 20 20 61 6
'ARID5B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S143.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
ARID5B MUTATED 3 3 2 2
ARID5B WILD-TYPE 9 15 9 8
'ARID5B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 1

Table S144.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
ARID5B MUTATED 5 3 2
ARID5B WILD-TYPE 12 15 14
'ARID5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0427 (Chi-square test), Q value = 1

Table S145.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
ARID5B MUTATED 25 2 0 0 1 0
ARID5B WILD-TYPE 132 10 54 8 9 1

Figure S73.  Get High-res Image Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ARID5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 1

Table S146.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
ARID5B MUTATED 1 1 6
ARID5B WILD-TYPE 42 40 45
'ARID5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.164 (Chi-square test), Q value = 1

Table S147.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
ARID5B MUTATED 4 5 5 4 3 3
ARID5B WILD-TYPE 35 31 32 6 37 21
'ARID5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 1

Table S148.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
ARID5B MUTATED 18 6
ARID5B WILD-TYPE 97 65
'ARID5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0531 (Fisher's exact test), Q value = 1

Table S149.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
ARID5B MUTATED 3 8 7 11
ARID5B WILD-TYPE 60 28 65 63
'ARID5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0676 (Fisher's exact test), Q value = 1

Table S150.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
ARID5B MUTATED 6 10 13
ARID5B WILD-TYPE 79 38 99
'ARID5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0452 (Chi-square test), Q value = 1

Table S151.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
ARID5B MUTATED 0 11 3 1 12
ARID5B WILD-TYPE 42 67 20 25 59

Figure S74.  Get High-res Image Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARID5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 1

Table S152.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
ARID5B MUTATED 1 16 10
ARID5B WILD-TYPE 3 115 95
'ARID5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 1

Table S153.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
ARID5B MUTATED 1 0 5
ARID5B WILD-TYPE 35 26 49
'ARID5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S154.  Gene #13: 'ARID5B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
ARID5B MUTATED 1 0 5 0
ARID5B WILD-TYPE 22 22 60 6
'FGFR2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 1

Table S155.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
FGFR2 MUTATED 3 2 1 0
FGFR2 WILD-TYPE 9 16 10 10
'FGFR2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 1

Table S156.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
FGFR2 MUTATED 4 1 1
FGFR2 WILD-TYPE 13 17 15
'FGFR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.611 (Chi-square test), Q value = 1

Table S157.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
FGFR2 MUTATED 22 2 3 1 2 0
FGFR2 WILD-TYPE 135 10 51 7 8 1
'FGFR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S158.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
FGFR2 MUTATED 5 6 6
FGFR2 WILD-TYPE 38 35 45
'FGFR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.97 (Chi-square test), Q value = 1

Table S159.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
FGFR2 MUTATED 6 5 6 1 4 3
FGFR2 WILD-TYPE 33 31 31 9 36 21
'FGFR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S160.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
FGFR2 MUTATED 15 10
FGFR2 WILD-TYPE 100 61
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S161.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
FGFR2 MUTATED 6 7 8 9
FGFR2 WILD-TYPE 57 29 64 65
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S162.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
FGFR2 MUTATED 9 8 13
FGFR2 WILD-TYPE 76 40 99
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.876 (Chi-square test), Q value = 1

Table S163.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
FGFR2 MUTATED 5 11 2 2 10
FGFR2 WILD-TYPE 37 67 21 24 61
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S164.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
FGFR2 MUTATED 1 16 13
FGFR2 WILD-TYPE 3 115 92
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S165.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
FGFR2 MUTATED 6 2 8
FGFR2 WILD-TYPE 30 24 46
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S166.  Gene #14: 'FGFR2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
FGFR2 MUTATED 3 4 8 1
FGFR2 WILD-TYPE 20 18 57 5
'NFE2L2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0905 (Fisher's exact test), Q value = 1

Table S167.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
NFE2L2 MUTATED 0 1 3 0
NFE2L2 WILD-TYPE 12 17 8 10
'NFE2L2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S168.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
NFE2L2 MUTATED 2 1 1
NFE2L2 WILD-TYPE 15 17 15
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00636 (Chi-square test), Q value = 1

Table S169.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
NFE2L2 MUTATED 10 2 0 0 3 0
NFE2L2 WILD-TYPE 147 10 54 8 7 1

Figure S75.  Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S170.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
NFE2L2 MUTATED 1 3 3
NFE2L2 WILD-TYPE 42 38 48
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.248 (Chi-square test), Q value = 1

Table S171.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
NFE2L2 MUTATED 3 2 4 2 0 2
NFE2L2 WILD-TYPE 36 34 33 8 40 22
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S172.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
NFE2L2 MUTATED 8 5
NFE2L2 WILD-TYPE 107 66
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0134 (Fisher's exact test), Q value = 1

Table S173.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
NFE2L2 MUTATED 1 4 1 8
NFE2L2 WILD-TYPE 62 32 71 66

Figure S76.  Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S174.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
NFE2L2 MUTATED 3 3 8
NFE2L2 WILD-TYPE 82 45 104
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.392 (Chi-square test), Q value = 1

Table S175.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
NFE2L2 MUTATED 1 7 2 0 5
NFE2L2 WILD-TYPE 41 71 21 26 66
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S176.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
NFE2L2 MUTATED 0 9 6
NFE2L2 WILD-TYPE 4 122 99
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 1

Table S177.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
NFE2L2 MUTATED 1 0 5
NFE2L2 WILD-TYPE 35 26 49
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S178.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
NFE2L2 MUTATED 1 0 5 0
NFE2L2 WILD-TYPE 22 22 60 6
'CCND1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S179.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
CCND1 MUTATED 2 1 0 1
CCND1 WILD-TYPE 10 17 11 9
'CCND1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S180.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
CCND1 MUTATED 2 1 1
CCND1 WILD-TYPE 15 17 15
'CCND1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Chi-square test), Q value = 1

Table S181.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
CCND1 MUTATED 14 0 0 0 0 0
CCND1 WILD-TYPE 143 12 54 8 10 1
'CCND1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S182.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
CCND1 MUTATED 1 2 4
CCND1 WILD-TYPE 42 39 47
'CCND1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.514 (Chi-square test), Q value = 1

Table S183.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
CCND1 MUTATED 4 3 1 0 1 1
CCND1 WILD-TYPE 35 33 36 10 39 23
'CCND1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S184.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
CCND1 MUTATED 5 5
CCND1 WILD-TYPE 110 66
'CCND1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.635 (Fisher's exact test), Q value = 1

Table S185.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
CCND1 MUTATED 2 2 6 4
CCND1 WILD-TYPE 61 34 66 70
'CCND1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S186.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
CCND1 MUTATED 3 5 6
CCND1 WILD-TYPE 82 43 106
'CCND1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.124 (Chi-square test), Q value = 1

Table S187.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
CCND1 MUTATED 0 3 1 2 8
CCND1 WILD-TYPE 42 75 22 24 63
'CCND1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S188.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
CCND1 MUTATED 0 9 5
CCND1 WILD-TYPE 4 122 100
'CCND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S189.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
CCND1 MUTATED 0 1 3
CCND1 WILD-TYPE 36 25 51
'CCND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S190.  Gene #16: 'CCND1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
CCND1 MUTATED 1 0 3 0
CCND1 WILD-TYPE 22 22 62 6
'CHD4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 1

Table S191.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
CHD4 MUTATED 1 6 0 2
CHD4 WILD-TYPE 11 12 11 8
'CHD4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 1

Table S192.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
CHD4 MUTATED 2 2 5
CHD4 WILD-TYPE 15 16 11
'CHD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.776 (Chi-square test), Q value = 1

Table S193.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
CHD4 MUTATED 25 1 7 0 2 0
CHD4 WILD-TYPE 132 11 47 8 8 1
'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S194.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
CHD4 MUTATED 7 5 7
CHD4 WILD-TYPE 36 36 44
'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.97 (Chi-square test), Q value = 1

Table S195.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
CHD4 MUTATED 7 6 5 1 5 3
CHD4 WILD-TYPE 32 30 32 9 35 21
'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S196.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
CHD4 MUTATED 14 13
CHD4 WILD-TYPE 101 58
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S197.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
CHD4 MUTATED 10 6 10 9
CHD4 WILD-TYPE 53 30 62 65
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 1

Table S198.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
CHD4 MUTATED 15 7 13
CHD4 WILD-TYPE 70 41 99
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.739 (Chi-square test), Q value = 1

Table S199.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
CHD4 MUTATED 4 8 3 3 12
CHD4 WILD-TYPE 38 70 20 23 59
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S200.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
CHD4 MUTATED 1 16 13
CHD4 WILD-TYPE 3 115 92
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S201.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
CHD4 MUTATED 4 2 10
CHD4 WILD-TYPE 32 24 44
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.97 (Fisher's exact test), Q value = 1

Table S202.  Gene #17: 'CHD4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
CHD4 MUTATED 3 3 10 0
CHD4 WILD-TYPE 20 19 55 6
'FAM9A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.887 (Chi-square test), Q value = 1

Table S203.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
FAM9A MUTATED 10 0 3 0 1 0
FAM9A WILD-TYPE 147 12 51 8 9 1
'FAM9A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 1

Table S204.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
FAM9A MUTATED 5 1 4
FAM9A WILD-TYPE 38 40 47
'FAM9A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.178 (Chi-square test), Q value = 1

Table S205.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
FAM9A MUTATED 3 5 2 0 0 1
FAM9A WILD-TYPE 36 31 35 10 40 23
'FAM9A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0227 (Fisher's exact test), Q value = 1

Table S206.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
FAM9A MUTATED 3 8
FAM9A WILD-TYPE 112 63

Figure S77.  Get High-res Image Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'FAM9A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 1

Table S207.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
FAM9A MUTATED 3 5 5 1
FAM9A WILD-TYPE 60 31 67 73
'FAM9A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.065 (Fisher's exact test), Q value = 1

Table S208.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
FAM9A MUTATED 9 2 3
FAM9A WILD-TYPE 76 46 109
'FAM9A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.308 (Chi-square test), Q value = 1

Table S209.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
FAM9A MUTATED 5 2 1 1 5
FAM9A WILD-TYPE 37 76 22 25 66
'FAM9A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0424 (Fisher's exact test), Q value = 1

Table S210.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
FAM9A MUTATED 1 4 9
FAM9A WILD-TYPE 3 127 96

Figure S78.  Get High-res Image Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAM9A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 1

Table S211.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
FAM9A MUTATED 6 0 2
FAM9A WILD-TYPE 30 26 52

Figure S79.  Get High-res Image Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'FAM9A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 1

Table S212.  Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
FAM9A MUTATED 3 3 2 0
FAM9A WILD-TYPE 20 19 63 6
'MORC4 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S213.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
MORC4 MUTATED 1 3 0 1
MORC4 WILD-TYPE 11 15 11 9
'MORC4 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 1

Table S214.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
MORC4 MUTATED 3 0 2
MORC4 WILD-TYPE 14 18 14
'MORC4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.34 (Chi-square test), Q value = 1

Table S215.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
MORC4 MUTATED 16 2 1 0 1 0
MORC4 WILD-TYPE 141 10 53 8 9 1
'MORC4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 1

Table S216.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
MORC4 MUTATED 2 6 4
MORC4 WILD-TYPE 41 35 47
'MORC4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.212 (Chi-square test), Q value = 1

Table S217.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
MORC4 MUTATED 6 5 1 1 4 0
MORC4 WILD-TYPE 33 31 36 9 36 24
'MORC4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 1

Table S218.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
MORC4 MUTATED 6 11
MORC4 WILD-TYPE 109 60

Figure S80.  Get High-res Image Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MORC4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00821 (Fisher's exact test), Q value = 1

Table S219.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
MORC4 MUTATED 2 6 10 2
MORC4 WILD-TYPE 61 30 62 72

Figure S81.  Get High-res Image Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MORC4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.266 (Fisher's exact test), Q value = 1

Table S220.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
MORC4 MUTATED 8 6 6
MORC4 WILD-TYPE 77 42 106
'MORC4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.315 (Chi-square test), Q value = 1

Table S221.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
MORC4 MUTATED 2 3 3 3 8
MORC4 WILD-TYPE 40 75 20 23 63
'MORC4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 1

Table S222.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
MORC4 MUTATED 0 7 12
MORC4 WILD-TYPE 4 124 93
'MORC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S223.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
MORC4 MUTATED 2 4 3
MORC4 WILD-TYPE 34 22 51
'MORC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0396 (Fisher's exact test), Q value = 1

Table S224.  Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
MORC4 MUTATED 5 0 4 0
MORC4 WILD-TYPE 18 22 61 6

Figure S82.  Get High-res Image Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S225.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
CASP8 MUTATED 2 1 0 0
CASP8 WILD-TYPE 10 17 11 10
'CASP8 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S226.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
CASP8 MUTATED 3 0 0
CASP8 WILD-TYPE 14 18 16
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.204 (Chi-square test), Q value = 1

Table S227.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
CASP8 MUTATED 14 0 1 0 2 0
CASP8 WILD-TYPE 143 12 53 8 8 1
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S228.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
CASP8 MUTATED 2 2 5
CASP8 WILD-TYPE 41 39 46
'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.154 (Chi-square test), Q value = 1

Table S229.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
CASP8 MUTATED 3 6 2 2 1 1
CASP8 WILD-TYPE 36 30 35 8 39 23
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 1

Table S230.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
CASP8 MUTATED 7 8
CASP8 WILD-TYPE 108 63
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 1

Table S231.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
CASP8 MUTATED 3 5 5 4
CASP8 WILD-TYPE 60 31 67 70
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S232.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
CASP8 MUTATED 9 4 4
CASP8 WILD-TYPE 76 44 108
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.152 (Chi-square test), Q value = 1

Table S233.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
CASP8 MUTATED 2 4 1 0 9
CASP8 WILD-TYPE 40 74 22 26 62
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 1

Table S234.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
CASP8 MUTATED 1 7 8
CASP8 WILD-TYPE 3 124 97
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 1

Table S235.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
CASP8 MUTATED 3 0 4
CASP8 WILD-TYPE 33 26 50
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S236.  Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
CASP8 MUTATED 2 1 4 0
CASP8 WILD-TYPE 21 21 61 6
'FOXA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.304 (Chi-square test), Q value = 1

Table S237.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
FOXA2 MUTATED 7 0 3 0 2 0
FOXA2 WILD-TYPE 150 12 51 8 8 1
'FOXA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S238.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
FOXA2 MUTATED 2 3 2
FOXA2 WILD-TYPE 41 38 49
'FOXA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0719 (Chi-square test), Q value = 1

Table S239.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
FOXA2 MUTATED 0 4 2 2 2 0
FOXA2 WILD-TYPE 39 32 35 8 38 24
'FOXA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S240.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
FOXA2 MUTATED 7 3
FOXA2 WILD-TYPE 108 68
'FOXA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S241.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
FOXA2 MUTATED 3 0 4 5
FOXA2 WILD-TYPE 60 36 68 69
'FOXA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S242.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
FOXA2 MUTATED 4 1 7
FOXA2 WILD-TYPE 81 47 105
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0582 (Chi-square test), Q value = 1

Table S243.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
FOXA2 MUTATED 2 6 0 3 0
FOXA2 WILD-TYPE 40 72 23 23 71
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S244.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
FOXA2 MUTATED 0 7 4
FOXA2 WILD-TYPE 4 124 101
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S245.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
FOXA2 MUTATED 1 2 4
FOXA2 WILD-TYPE 35 24 50
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 1

Table S246.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
FOXA2 MUTATED 1 0 5 1
FOXA2 WILD-TYPE 22 22 60 5
'ABI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.821 (Chi-square test), Q value = 1

Table S247.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
ABI1 MUTATED 4 0 0 0 0 0
ABI1 WILD-TYPE 153 12 54 8 10 1
'ABI1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.64 (Chi-square test), Q value = 1

Table S248.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
ABI1 MUTATED 2 1 1 0 0 0
ABI1 WILD-TYPE 37 35 36 10 40 24
'ABI1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S249.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
ABI1 MUTATED 2 2
ABI1 WILD-TYPE 113 69
'ABI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S250.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
ABI1 MUTATED 0 1 1 2
ABI1 WILD-TYPE 63 35 71 72
'ABI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S251.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
ABI1 MUTATED 1 2 1
ABI1 WILD-TYPE 84 46 111
'ABI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.687 (Chi-square test), Q value = 1

Table S252.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
ABI1 MUTATED 0 2 0 1 1
ABI1 WILD-TYPE 42 76 23 25 70
'ABI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S253.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
ABI1 MUTATED 0 3 1
ABI1 WILD-TYPE 4 128 104
'DNER MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 1

Table S254.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
DNER MUTATED 3 2 0 0
DNER WILD-TYPE 9 16 11 10
'DNER MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0515 (Fisher's exact test), Q value = 1

Table S255.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
DNER MUTATED 4 0 1
DNER WILD-TYPE 13 18 15
'DNER MUTATION STATUS' versus 'CN_CNMF'

P value = 0.013 (Chi-square test), Q value = 1

Table S256.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
DNER MUTATED 15 0 0 0 3 0
DNER WILD-TYPE 142 12 54 8 7 1

Figure S83.  Get High-res Image Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'DNER MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S257.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
DNER MUTATED 3 1 4
DNER WILD-TYPE 40 40 47
'DNER MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0217 (Chi-square test), Q value = 1

Table S258.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
DNER MUTATED 4 4 4 3 0 0
DNER WILD-TYPE 35 32 33 7 40 24

Figure S84.  Get High-res Image Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'DNER MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S259.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
DNER MUTATED 8 7
DNER WILD-TYPE 107 64
'DNER MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 1

Table S260.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
DNER MUTATED 2 6 5 5
DNER WILD-TYPE 61 30 67 69
'DNER MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0936 (Fisher's exact test), Q value = 1

Table S261.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
DNER MUTATED 6 7 5
DNER WILD-TYPE 79 41 107
'DNER MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.785 (Chi-square test), Q value = 1

Table S262.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
DNER MUTATED 2 5 2 1 7
DNER WILD-TYPE 40 73 21 25 64
'DNER MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 1

Table S263.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
DNER MUTATED 1 7 9
DNER WILD-TYPE 3 124 96
'DNER MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S264.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
DNER MUTATED 1 2 4
DNER WILD-TYPE 35 24 50
'DNER MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S265.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
DNER MUTATED 2 1 4 0
DNER WILD-TYPE 21 21 61 6
'BCOR MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S266.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
BCOR MUTATED 1 2 0 0
BCOR WILD-TYPE 11 16 11 10
'BCOR MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S267.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
BCOR MUTATED 2 0 1
BCOR WILD-TYPE 15 18 15
'BCOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00577 (Chi-square test), Q value = 1

Table S268.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
BCOR MUTATED 26 0 0 0 3 0
BCOR WILD-TYPE 131 12 54 8 7 1

Figure S85.  Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BCOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 1

Table S269.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
BCOR MUTATED 1 4 10
BCOR WILD-TYPE 42 37 41

Figure S86.  Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BCOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.512 (Chi-square test), Q value = 1

Table S270.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
BCOR MUTATED 5 6 3 3 5 2
BCOR WILD-TYPE 34 30 34 7 35 22
'BCOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.5 (Fisher's exact test), Q value = 1

Table S271.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
BCOR MUTATED 13 11
BCOR WILD-TYPE 102 60
'BCOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.45

Table S272.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
BCOR MUTATED 2 8 15 5
BCOR WILD-TYPE 61 28 57 69

Figure S87.  Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S273.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
BCOR MUTATED 9 9 12
BCOR WILD-TYPE 76 39 100
'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0495 (Chi-square test), Q value = 1

Table S274.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
BCOR MUTATED 2 8 3 1 15
BCOR WILD-TYPE 40 70 20 25 56

Figure S88.  Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0922 (Fisher's exact test), Q value = 1

Table S275.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
BCOR MUTATED 2 14 13
BCOR WILD-TYPE 2 117 92
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S276.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
BCOR MUTATED 3 3 7
BCOR WILD-TYPE 33 23 47
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 1

Table S277.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
BCOR MUTATED 2 0 10 1
BCOR WILD-TYPE 21 22 55 5
'BRS3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S278.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
BRS3 MUTATED 2 2 0 0
BRS3 WILD-TYPE 10 16 11 10
'BRS3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S279.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
BRS3 MUTATED 3 0 1
BRS3 WILD-TYPE 14 18 15
'BRS3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.339 (Chi-square test), Q value = 1

Table S280.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
BRS3 MUTATED 13 1 0 0 1 0
BRS3 WILD-TYPE 144 11 54 8 9 1
'BRS3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S281.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
BRS3 MUTATED 3 1 1
BRS3 WILD-TYPE 40 40 50
'BRS3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.392 (Chi-square test), Q value = 1

Table S282.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
BRS3 MUTATED 4 4 2 1 1 0
BRS3 WILD-TYPE 35 32 35 9 39 24
'BRS3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 1

Table S283.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
BRS3 MUTATED 6 6
BRS3 WILD-TYPE 109 65
'BRS3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 1

Table S284.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
BRS3 MUTATED 3 3 7 1
BRS3 WILD-TYPE 60 33 65 73
'BRS3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00295 (Fisher's exact test), Q value = 0.98

Table S285.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
BRS3 MUTATED 7 6 1
BRS3 WILD-TYPE 78 42 111

Figure S89.  Get High-res Image Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'BRS3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.393 (Chi-square test), Q value = 1

Table S286.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
BRS3 MUTATED 1 3 2 1 7
BRS3 WILD-TYPE 41 75 21 25 64
'BRS3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00527 (Fisher's exact test), Q value = 1

Table S287.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
BRS3 MUTATED 2 4 8
BRS3 WILD-TYPE 2 127 97

Figure S90.  Get High-res Image Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BRS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S288.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
BRS3 MUTATED 2 1 1
BRS3 WILD-TYPE 34 25 53
'BRS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 1

Table S289.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
BRS3 MUTATED 2 1 1 0
BRS3 WILD-TYPE 21 21 64 6
'SGK1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S290.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
SGK1 MUTATED 2 1 0 0
SGK1 WILD-TYPE 10 17 11 10
'SGK1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 1

Table S291.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
SGK1 MUTATED 3 0 0
SGK1 WILD-TYPE 14 18 16
'SGK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.43 (Chi-square test), Q value = 1

Table S292.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
SGK1 MUTATED 10 2 1 1 1 0
SGK1 WILD-TYPE 147 10 53 7 9 1
'SGK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S293.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
SGK1 MUTATED 1 1 3
SGK1 WILD-TYPE 42 40 48
'SGK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.226 (Chi-square test), Q value = 1

Table S294.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
SGK1 MUTATED 4 5 1 2 1 2
SGK1 WILD-TYPE 35 31 36 8 39 22
'SGK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0954 (Fisher's exact test), Q value = 1

Table S295.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
SGK1 MUTATED 6 9
SGK1 WILD-TYPE 109 62
'SGK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 1

Table S296.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
SGK1 MUTATED 1 6 5 3
SGK1 WILD-TYPE 62 30 67 71

Figure S91.  Get High-res Image Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SGK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S297.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
SGK1 MUTATED 6 3 6
SGK1 WILD-TYPE 79 45 106
'SGK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.431 (Chi-square test), Q value = 1

Table S298.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
SGK1 MUTATED 1 3 1 2 7
SGK1 WILD-TYPE 41 75 22 24 64
'SGK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S299.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
SGK1 MUTATED 0 8 6
SGK1 WILD-TYPE 4 123 99
'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S300.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
SGK1 MUTATED 1 0 3
SGK1 WILD-TYPE 35 26 51
'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S301.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
SGK1 MUTATED 1 0 3 0
SGK1 WILD-TYPE 22 22 62 6
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.749 (Chi-square test), Q value = 1

Table S302.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
NRAS MUTATED 7 0 1 0 1 0
NRAS WILD-TYPE 150 12 53 8 9 1
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.316 (Chi-square test), Q value = 1

Table S303.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
NRAS MUTATED 0 2 0 0 2 2
NRAS WILD-TYPE 39 34 37 10 38 22
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S304.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
NRAS MUTATED 4 2
NRAS WILD-TYPE 111 69
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S305.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
NRAS MUTATED 3 0 4 2
NRAS WILD-TYPE 60 36 68 72
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S306.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
NRAS MUTATED 3 1 5
NRAS WILD-TYPE 82 47 107
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.604 (Chi-square test), Q value = 1

Table S307.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
NRAS MUTATED 2 3 0 0 4
NRAS WILD-TYPE 40 75 23 26 67
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 1

Table S308.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
NRAS MUTATED 1 4 4
NRAS WILD-TYPE 3 127 101
'TIAL1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S309.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
TIAL1 MUTATED 2 1 0 0
TIAL1 WILD-TYPE 10 17 11 10
'TIAL1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 1

Table S310.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
TIAL1 MUTATED 2 0 1
TIAL1 WILD-TYPE 15 18 15
'TIAL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.362 (Chi-square test), Q value = 1

Table S311.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
TIAL1 MUTATED 10 0 0 0 1 0
TIAL1 WILD-TYPE 147 12 54 8 9 1
'TIAL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0634 (Fisher's exact test), Q value = 1

Table S312.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
TIAL1 MUTATED 1 0 5
TIAL1 WILD-TYPE 42 41 46
'TIAL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.564 (Chi-square test), Q value = 1

Table S313.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
TIAL1 MUTATED 1 2 4 1 1 1
TIAL1 WILD-TYPE 38 34 33 9 39 23
'TIAL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S314.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
TIAL1 MUTATED 7 3
TIAL1 WILD-TYPE 108 68
'TIAL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00545 (Fisher's exact test), Q value = 1

Table S315.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
TIAL1 MUTATED 0 4 6 1
TIAL1 WILD-TYPE 63 32 66 73

Figure S92.  Get High-res Image Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TIAL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0128 (Fisher's exact test), Q value = 1

Table S316.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
TIAL1 MUTATED 5 5 1
TIAL1 WILD-TYPE 80 43 111

Figure S93.  Get High-res Image Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TIAL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.812 (Chi-square test), Q value = 1

Table S317.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
TIAL1 MUTATED 1 3 1 1 5
TIAL1 WILD-TYPE 41 75 22 25 66
'TIAL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S318.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
TIAL1 MUTATED 0 6 5
TIAL1 WILD-TYPE 4 125 100
'TIAL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 1

Table S319.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
TIAL1 MUTATED 2 0 4
TIAL1 WILD-TYPE 34 26 50
'TIAL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S320.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
TIAL1 MUTATED 1 0 5 0
TIAL1 WILD-TYPE 22 22 60 6
'SIN3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0266 (Chi-square test), Q value = 1

Table S321.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
SIN3A MUTATED 16 1 0 0 3 0
SIN3A WILD-TYPE 141 11 54 8 7 1

Figure S94.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SIN3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S322.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
SIN3A MUTATED 4 3 7
SIN3A WILD-TYPE 39 38 44
'SIN3A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00607 (Chi-square test), Q value = 1

Table S323.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
SIN3A MUTATED 3 9 3 2 0 1
SIN3A WILD-TYPE 36 27 34 8 40 23

Figure S95.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'SIN3A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 1

Table S324.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
SIN3A MUTATED 8 10
SIN3A WILD-TYPE 107 61
'SIN3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00261 (Fisher's exact test), Q value = 0.87

Table S325.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
SIN3A MUTATED 3 5 12 1
SIN3A WILD-TYPE 60 31 60 73

Figure S96.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SIN3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0226 (Fisher's exact test), Q value = 1

Table S326.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
SIN3A MUTATED 10 7 4
SIN3A WILD-TYPE 75 41 108

Figure S97.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SIN3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.16 (Chi-square test), Q value = 1

Table S327.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
SIN3A MUTATED 4 2 2 4 9
SIN3A WILD-TYPE 38 76 21 22 62
'SIN3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00595 (Fisher's exact test), Q value = 1

Table S328.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
SIN3A MUTATED 1 5 15
SIN3A WILD-TYPE 3 126 90

Figure S98.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SIN3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S329.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
SIN3A MUTATED 4 3 3
SIN3A WILD-TYPE 32 23 51
'SIN3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 1

Table S330.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
SIN3A MUTATED 3 2 4 1
SIN3A WILD-TYPE 20 20 61 5
'SLC48A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.736 (Chi-square test), Q value = 1

Table S331.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
SLC48A1 MUTATED 5 0 0 0 0 0
SLC48A1 WILD-TYPE 152 12 54 8 10 1
'SLC48A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S332.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
SLC48A1 MUTATED 0 1 2
SLC48A1 WILD-TYPE 43 40 49
'SLC48A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.803 (Chi-square test), Q value = 1

Table S333.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
SLC48A1 MUTATED 1 1 0 0 2 1
SLC48A1 WILD-TYPE 38 35 37 10 38 23
'SLC48A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S334.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
SLC48A1 MUTATED 2 3
SLC48A1 WILD-TYPE 113 68
'SLC48A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S335.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
SLC48A1 MUTATED 1 1 2 1
SLC48A1 WILD-TYPE 62 35 70 73
'SLC48A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S336.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
SLC48A1 MUTATED 1 1 3
SLC48A1 WILD-TYPE 84 47 109
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.726 (Chi-square test), Q value = 1

Table S337.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
SLC48A1 MUTATED 0 2 0 1 2
SLC48A1 WILD-TYPE 42 76 23 25 69
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S338.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
SLC48A1 MUTATED 0 2 3
SLC48A1 WILD-TYPE 4 129 102
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S339.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
SLC48A1 MUTATED 1 1 1
SLC48A1 WILD-TYPE 35 25 53
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S340.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
SLC48A1 MUTATED 1 1 1 0
SLC48A1 WILD-TYPE 22 21 64 6
'RNF43 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 1

Table S341.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
RNF43 MUTATED 3 1 0 0
RNF43 WILD-TYPE 9 17 11 10
'RNF43 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 1

Table S342.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
RNF43 MUTATED 3 0 1
RNF43 WILD-TYPE 14 18 15
'RNF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.443 (Chi-square test), Q value = 1

Table S343.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
RNF43 MUTATED 10 1 0 0 1 0
RNF43 WILD-TYPE 147 11 54 8 9 1
'RNF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 1

Table S344.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
RNF43 MUTATED 2 0 3
RNF43 WILD-TYPE 41 41 48
'RNF43 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.296 (Chi-square test), Q value = 1

Table S345.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
RNF43 MUTATED 3 2 5 1 1 0
RNF43 WILD-TYPE 36 34 32 9 39 24
'RNF43 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S346.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
RNF43 MUTATED 8 4
RNF43 WILD-TYPE 107 67
'RNF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.032 (Fisher's exact test), Q value = 1

Table S347.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
RNF43 MUTATED 1 4 6 1
RNF43 WILD-TYPE 62 32 66 73

Figure S99.  Get High-res Image Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RNF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2.55e-05 (Fisher's exact test), Q value = 0.0089

Table S348.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
RNF43 MUTATED 2 9 1
RNF43 WILD-TYPE 83 39 111

Figure S100.  Get High-res Image Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RNF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.129 (Chi-square test), Q value = 1

Table S349.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
RNF43 MUTATED 1 1 2 1 7
RNF43 WILD-TYPE 41 77 21 25 64
'RNF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 1

Table S350.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
RNF43 MUTATED 0 5 7
RNF43 WILD-TYPE 4 126 98
'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 1

Table S351.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
RNF43 MUTATED 1 2 1
RNF43 WILD-TYPE 35 24 53
'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S352.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
RNF43 MUTATED 2 0 2 0
RNF43 WILD-TYPE 21 22 63 6
'ZFHX3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 1

Table S353.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
ZFHX3 MUTATED 6 6 2 2
ZFHX3 WILD-TYPE 6 12 9 8
'ZFHX3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0291 (Fisher's exact test), Q value = 1

Table S354.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
ZFHX3 MUTATED 9 2 5
ZFHX3 WILD-TYPE 8 16 11

Figure S101.  Get High-res Image Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ZFHX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.094 (Chi-square test), Q value = 1

Table S355.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
ZFHX3 MUTATED 34 1 3 1 3 0
ZFHX3 WILD-TYPE 123 11 51 7 7 1
'ZFHX3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0648 (Fisher's exact test), Q value = 1

Table S356.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
ZFHX3 MUTATED 5 2 11
ZFHX3 WILD-TYPE 38 39 40
'ZFHX3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.318 (Chi-square test), Q value = 1

Table S357.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
ZFHX3 MUTATED 7 11 5 3 5 4
ZFHX3 WILD-TYPE 32 25 32 7 35 20
'ZFHX3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 1

Table S358.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
ZFHX3 MUTATED 18 17
ZFHX3 WILD-TYPE 97 54
'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S359.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
ZFHX3 MUTATED 9 9 12 13
ZFHX3 WILD-TYPE 54 27 60 61
'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 1

Table S360.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
ZFHX3 MUTATED 15 13 15
ZFHX3 WILD-TYPE 70 35 97
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.207 (Chi-square test), Q value = 1

Table S361.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
ZFHX3 MUTATED 3 14 4 3 17
ZFHX3 WILD-TYPE 39 64 19 23 54
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S362.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
ZFHX3 MUTATED 1 21 19
ZFHX3 WILD-TYPE 3 110 86
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S363.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
ZFHX3 MUTATED 4 4 8
ZFHX3 WILD-TYPE 32 22 46
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S364.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
ZFHX3 MUTATED 4 1 10 1
ZFHX3 WILD-TYPE 19 21 55 5
'RB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S365.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 12 18 11 10
RB1 MUTATED 1 3 2 0
RB1 WILD-TYPE 11 15 9 10
'RB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S366.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 17 18 16
RB1 MUTATED 2 2 2
RB1 WILD-TYPE 15 16 14
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.31 (Chi-square test), Q value = 1

Table S367.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 157 12 54 8 10 1
RB1 MUTATED 16 0 2 0 2 0
RB1 WILD-TYPE 141 12 52 8 8 1
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S368.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 43 41 51
RB1 MUTATED 2 2 5
RB1 WILD-TYPE 41 39 46
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.12 (Chi-square test), Q value = 1

Table S369.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 39 36 37 10 40 24
RB1 MUTATED 3 6 2 3 3 1
RB1 WILD-TYPE 36 30 35 7 37 23
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 1

Table S370.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2
ALL 115 71
RB1 MUTATED 9 9
RB1 WILD-TYPE 106 62
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

Table S371.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 36 72 74
RB1 MUTATED 6 2 8 4
RB1 WILD-TYPE 57 34 64 70
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.271 (Fisher's exact test), Q value = 1

Table S372.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 85 48 112
RB1 MUTATED 10 4 6
RB1 WILD-TYPE 75 44 106
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.955 (Chi-square test), Q value = 1

Table S373.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 42 78 23 26 71
RB1 MUTATED 3 5 2 2 7
RB1 WILD-TYPE 39 73 21 24 64
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00126 (Fisher's exact test), Q value = 0.43

Table S374.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 4 131 105
RB1 MUTATED 3 7 9
RB1 WILD-TYPE 1 124 96

Figure S102.  Get High-res Image Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 1

Table S375.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 36 26 54
RB1 MUTATED 1 1 3
RB1 WILD-TYPE 35 25 51
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S376.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 23 22 65 6
RB1 MUTATED 1 1 3 0
RB1 WILD-TYPE 22 21 62 6
Methods & Data
Input

  • Mutation data file = transformed.cor.cli.txt

  • Molecular subtypes file = UCEC-TP.transferedmergedcluster.txt

  • Number of patients = 248

  • Number of significantly mutated genes = 33

  • Number of Molecular subtypes = 12

  • 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

Chi-square test

For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.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] Greenwood and Nikulin, A guide to chi-squared testing, Wiley, New York. ISBN 047155779X (1996)
[3] 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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