Correlation between gene mutation status and molecular subtypes
Uterine Corpus Endometrioid Carcinoma (Primary solid tumor)
16 April 2014  |  analyses__2014_04_16
Maintainer Information
Citation Information
doi:10.7908/C1125RBJ
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2014): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1125RBJ
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, 34 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 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_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'.

  • 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' and 'MRNASEQ_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'CN_CNMF'.

  • DNER mutation correlated to 'CN_CNMF'.

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, 34 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 Fisher's exact 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
(8.71e-05) 		1.08e-30
(4.05e-28) 		2.53e-12
(9.2e-10) 		2.01e-05
(0.00706) 		0.0014
(0.474) 		1.07e-26
(4.02e-24) 		8.1e-23
(3.03e-20) 		2.33e-18
(8.62e-16) 		1.2e-13
(4.41e-11) 		2.13e-09
(7.6e-07) 		8.53e-10
(3.07e-07)
PTEN 161 (65%) 87 0.00442
(1.00) 		0.000362
(0.125) 		1.69e-21
(6.29e-19) 		1.79e-12
(6.52e-10) 		0.0257
(1.00) 		0.183
(1.00) 		2.48e-21
(9.22e-19) 		7.38e-19
(2.74e-16) 		1.28e-16
(4.72e-14) 		4.32e-12
(1.56e-09) 		1.97e-09
(7.04e-07) 		4.78e-13
(1.76e-10)
CTNNB1 74 (30%) 174 5.68e-07
(0.000201) 		0.00115
(0.389) 		4.43e-06
(0.00156) 		0.00315
(1.00) 		1.29e-10
(4.65e-08) 		0.112
(1.00) 		1.62e-09
(5.81e-07) 		6.58e-13
(2.41e-10) 		8.41e-13
(3.07e-10) 		0.18
(1.00) 		0.0282
(1.00) 		0.00114
(0.389)
PIK3R1 83 (33%) 165 0.0669
(1.00) 		0.0218
(1.00) 		0.00164
(0.549) 		3.32e-05
(0.0116) 		0.649
(1.00) 		0.877
(1.00) 		0.000126
(0.044) 		2.67e-05
(0.00937) 		0.0107
(1.00) 		0.31
(1.00) 		0.0181
(1.00) 		0.000779
(0.266)
CTCF 44 (18%) 204 0.149
(1.00) 		0.421
(1.00) 		0.000349
(0.121) 		0.0433
(1.00) 		0.0458
(1.00) 		1
(1.00) 		0.000847
(0.289) 		0.000449
(0.155) 		0.0154
(1.00) 		0.00699
(1.00) 		0.01
(1.00) 		0.0582
(1.00)
KRAS 53 (21%) 195 0.203
(1.00) 		0.000649
(0.223) 		0.00685
(1.00) 		0.123
(1.00) 		0.297
(1.00) 		0.855
(1.00) 		0.138
(1.00) 		0.0497
(1.00) 		0.0192
(1.00) 		0.794
(1.00) 		0.0568
(1.00) 		0.855
(1.00)
ARID1A 83 (33%) 165 0.266
(1.00) 		0.011
(1.00) 		3.93e-07
(0.000139) 		0.227
(1.00) 		0.0271
(1.00) 		1
(1.00) 		0.0215
(1.00) 		0.0164
(1.00) 		0.0374
(1.00) 		0.0577
(1.00) 		0.0281
(1.00) 		0.0622
(1.00)
DNER 18 (7%) 230 0.191
(1.00) 		0.0515
(1.00) 		0.000461
(0.158) 		0.597
(1.00) 		0.0217
(1.00) 		0.581
(1.00) 		0.864
(1.00) 		1
(1.00) 		0.56
(1.00) 		0.217
(1.00) 		0.682
(1.00) 		1
(1.00)
PPP2R1A 27 (11%) 221 0.076
(1.00) 		0.0518
(1.00) 		0.0248
(1.00) 		0.0129
(1.00) 		0.141
(1.00) 		0.313
(1.00) 		0.00233
(0.782) 		0.00456
(1.00) 		0.00613
(1.00) 		0.0379
(1.00) 		0.0549
(1.00) 		0.00398
(1.00)
PIK3CA 132 (53%) 116 0.834
(1.00) 		0.198
(1.00) 		0.388
(1.00) 		0.677
(1.00) 		0.366
(1.00) 		0.365
(1.00) 		0.719
(1.00) 		0.956
(1.00) 		0.321
(1.00) 		0.109
(1.00) 		0.299
(1.00) 		0.157
(1.00)
PRKAR1B 4 (2%) 244 0.961
(1.00) 		0.509
(1.00) 		0.887
(1.00) 		1
(1.00) 		0.472
(1.00) 		0.848
(1.00) 		0.825
(1.00) 		1
(1.00) 		0.795
(1.00) 		0.208
(1.00)
FBXW7 39 (16%) 209 0.225
(1.00) 		0.692
(1.00) 		0.576
(1.00) 		0.0757
(1.00) 		0.106
(1.00) 		0.107
(1.00) 		0.0683
(1.00) 		0.174
(1.00) 		0.724
(1.00) 		0.112
(1.00) 		0.3
(1.00) 		0.0393
(1.00)
SPOP 21 (8%) 227 0.349
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.356
(1.00) 		0.834
(1.00) 		0.415
(1.00) 		0.229
(1.00) 		0.927
(1.00) 		0.84
(1.00) 		0.367
(1.00) 		0.55
(1.00) 		0.688
(1.00)
ARID5B 29 (12%) 219 0.961
(1.00) 		0.459
(1.00) 		0.0316
(1.00) 		0.136
(1.00) 		0.164
(1.00) 		0.182
(1.00) 		0.159
(1.00) 		0.111
(1.00) 		0.219
(1.00) 		0.762
(1.00) 		0.304
(1.00) 		0.565
(1.00)
FGFR2 31 (12%) 217 0.385
(1.00) 		0.293
(1.00) 		0.317
(1.00) 		0.914
(1.00) 		0.97
(1.00) 		0.829
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.484
(1.00) 		0.648
(1.00) 		0.587
(1.00) 		0.879
(1.00)
NFE2L2 15 (6%) 233 0.0905
(1.00) 		0.833
(1.00) 		0.0207
(1.00) 		0.631
(1.00) 		0.248
(1.00) 		1
(1.00) 		0.014
(1.00) 		0.0456
(1.00) 		0.314
(1.00) 		0.722
(1.00) 		0.304
(1.00) 		0.565
(1.00)
CCND1 14 (6%) 234 0.631
(1.00) 		0.833
(1.00) 		0.0848
(1.00) 		0.495
(1.00) 		0.514
(1.00) 		0.509
(1.00) 		0.458
(1.00) 		0.591
(1.00) 		0.0747
(1.00) 		0.542
(1.00) 		0.441
(1.00) 		0.709
(1.00)
CHD4 35 (14%) 213 0.0986
(1.00) 		0.284
(1.00) 		0.438
(1.00) 		0.852
(1.00) 		0.97
(1.00) 		0.287
(1.00) 		0.37
(1.00) 		0.442
(1.00) 		0.609
(1.00) 		0.648
(1.00) 		0.415
(1.00) 		0.733
(1.00)
FAM9A 14 (6%) 234 0.63
(1.00) 		0.27
(1.00) 		0.178
(1.00) 		0.0227
(1.00) 		0.0733
(1.00) 		0.147
(1.00) 		0.612
(1.00) 		0.151
(1.00) 		0.022
(1.00) 		0.135
(1.00)
MORC4 20 (8%) 228 0.583
(1.00) 		0.18
(1.00) 		0.371
(1.00) 		0.28
(1.00) 		0.212
(1.00) 		0.0332
(1.00) 		0.144
(1.00) 		0.179
(1.00) 		0.0606
(1.00) 		0.236
(1.00) 		0.348
(1.00) 		1
(1.00)
CASP8 17 (7%) 231 0.381
(1.00) 		0.0595
(1.00) 		0.0407
(1.00) 		0.626
(1.00) 		0.154
(1.00) 		0.269
(1.00) 		0.626
(1.00) 		0.239
(1.00) 		0.379
(1.00) 		0.257
(1.00) 		0.363
(1.00) 		1
(1.00)
FOXA2 12 (5%) 236 0.867
(1.00) 		0.795
(1.00) 		0.0719
(1.00) 		0.744
(1.00) 		0.817
(1.00) 		0.712
(1.00) 		0.391
(1.00) 		0.411
(1.00) 		0.682
(1.00) 		0.179
(1.00)
ABI1 4 (2%) 244 0.691
(1.00) 		0.64
(1.00) 		0.637
(1.00) 		0.551
(1.00) 		0.697
(1.00) 		0.565
(1.00) 		0.642
(1.00)
BCOR 30 (12%) 218 0.687
(1.00) 		0.405
(1.00) 		0.00145
(0.489) 		0.0246
(1.00) 		0.512
(1.00) 		0.5
(1.00) 		0.0328
(1.00) 		0.143
(1.00) 		0.781
(1.00) 		0.558
(1.00) 		0.928
(1.00) 		0.0902
(1.00)
BRS3 15 (6%) 233 0.536
(1.00) 		0.151
(1.00) 		0.211
(1.00) 		0.519
(1.00) 		0.392
(1.00) 		0.54
(1.00) 		0.0818
(1.00) 		0.329
(1.00) 		0.233
(1.00) 		0.236
(1.00) 		0.56
(1.00) 		0.441
(1.00)
SGK1 15 (6%) 233 0.381
(1.00) 		0.0595
(1.00) 		0.338
(1.00) 		0.625
(1.00) 		0.226
(1.00) 		0.0954
(1.00) 		0.302
(1.00) 		0.944
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.811
(1.00) 		0.709
(1.00)
NRAS 9 (4%) 239 0.415
(1.00) 		0.316
(1.00) 		1
(1.00) 		0.706
(1.00) 		0.645
(1.00) 		0.481
(1.00) 		0.754
(1.00)
TIAL1 11 (4%) 237 0.381
(1.00) 		0.405
(1.00) 		0.162
(1.00) 		0.0634
(1.00) 		0.564
(1.00) 		0.744
(1.00) 		0.0444
(1.00) 		0.593
(1.00) 		0.796
(1.00) 		0.298
(1.00) 		0.304
(1.00) 		0.187
(1.00)
SIN3A 21 (8%) 227 0.0463
(1.00) 		0.598
(1.00) 		0.00607
(1.00) 		0.129
(1.00) 		0.0216
(1.00) 		0.0421
(1.00) 		0.0226
(1.00) 		0.0876
(1.00) 		0.514
(1.00) 		0.358
(1.00)
SLC48A1 5 (2%) 243 0.589
(1.00) 		0.639
(1.00) 		0.803
(1.00) 		0.372
(1.00) 		0.624
(1.00) 		0.747
(1.00) 		0.0697
(1.00) 		0.674
(1.00) 		0.795
(1.00) 		0.634
(1.00)
RNF43 12 (5%) 236 0.133
(1.00) 		0.151
(1.00) 		0.295
(1.00) 		0.377
(1.00) 		0.296
(1.00) 		1
(1.00) 		0.0478
(1.00) 		0.0112
(1.00) 		0.0445
(1.00) 		0.211
(1.00) 		0.346
(1.00) 		1
(1.00)
ZFHX3 44 (18%) 204 0.375
(1.00) 		0.0291
(1.00) 		0.0686
(1.00) 		0.0648
(1.00) 		0.318
(1.00) 		0.179
(1.00) 		0.924
(1.00) 		0.959
(1.00) 		0.127
(1.00) 		0.568
(1.00) 		0.575
(1.00) 		0.258
(1.00)
RB1 20 (8%) 228 0.639
(1.00) 		1
(1.00) 		0.177
(1.00) 		0.626
(1.00) 		0.12
(1.00) 		0.313
(1.00) 		0.478
(1.00) 		0.383
(1.00) 		0.137
(1.00) 		0.0872
(1.00) 		1
(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 = 0.0248 (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
ALL 156 23 54 7 2
PPP2R1A MUTATED 11 2 12 0 0
PPP2R1A WILD-TYPE 145 21 42 7 2

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 = 0.00233 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
PPP2R1A MUTATED 17 6 4
PPP2R1A WILD-TYPE 62 79 77

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 = 0.00456 (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 80 82 83
PPP2R1A MUTATED 4 6 17
PPP2R1A WILD-TYPE 76 76 66

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 = 0.00613 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
PPP2R1A MUTATED 14 5 6
PPP2R1A WILD-TYPE 53 91 71

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 = 0.0379 (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 2 131 107
PPP2R1A MUTATED 0 8 17
PPP2R1A WILD-TYPE 2 123 90

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 = 0.0549 (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 35 55 26
PPP2R1A MUTATED 9 4 3
PPP2R1A WILD-TYPE 26 51 23
'PPP2R1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00398 (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
ALL 6 46 64
PPP2R1A MUTATED 1 12 3
PPP2R1A WILD-TYPE 5 34 61

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 = 0.388 (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
ALL 156 23 54 7 2
PIK3CA MUTATED 87 11 24 4 2
PIK3CA WILD-TYPE 69 12 30 3 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 = 0.719 (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
ALL 79 85 81
PIK3CA MUTATED 39 46 45
PIK3CA WILD-TYPE 40 39 36
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.956 (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 80 82 83
PIK3CA MUTATED 43 44 43
PIK3CA WILD-TYPE 37 38 40
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
PIK3CA MUTATED 31 56 41
PIK3CA WILD-TYPE 36 40 36
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.109 (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 2 131 107
PIK3CA MUTATED 1 77 50
PIK3CA WILD-TYPE 1 54 57
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.299 (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 35 55 26
PIK3CA MUTATED 14 31 14
PIK3CA WILD-TYPE 21 24 12
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.157 (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
ALL 6 46 64
PIK3CA MUTATED 5 20 34
PIK3CA WILD-TYPE 1 26 30
'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 = 4.43e-06 (Chi-square test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
CTNNB1 MUTATED 59 11 1 1 0
CTNNB1 WILD-TYPE 97 12 53 6 2

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 = 1.62e-09 (Fisher's exact test), Q value = 5.8e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
CTNNB1 MUTATED 10 47 16
CTNNB1 WILD-TYPE 69 38 65

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 = 6.58e-13 (Fisher's exact test), Q value = 2.4e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 82 83
CTNNB1 MUTATED 13 50 10
CTNNB1 WILD-TYPE 67 32 73

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 = 8.41e-13 (Fisher's exact test), Q value = 3.1e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
CTNNB1 MUTATED 3 23 45
CTNNB1 WILD-TYPE 64 73 32

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 = 0.18 (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 2 131 107
CTNNB1 MUTATED 0 45 26
CTNNB1 WILD-TYPE 2 86 81
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0282 (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 35 55 26
CTNNB1 MUTATED 3 15 9
CTNNB1 WILD-TYPE 32 40 17

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 = 0.00114 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 46 64
CTNNB1 MUTATED 0 4 23
CTNNB1 WILD-TYPE 6 42 41

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 = 0.00164 (Chi-square test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
PIK3R1 MUTATED 63 8 6 4 1
PIK3R1 WILD-TYPE 93 15 48 3 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 = 0.000126 (Fisher's exact test), Q value = 0.044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
PIK3R1 MUTATED 12 36 33
PIK3R1 WILD-TYPE 67 49 48

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 = 2.67e-05 (Fisher's exact test), Q value = 0.0094

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 82 83
PIK3R1 MUTATED 34 35 12
PIK3R1 WILD-TYPE 46 47 71

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 = 0.0107 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
PIK3R1 MUTATED 13 39 29
PIK3R1 WILD-TYPE 54 57 48

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 = 0.31 (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 2 131 107
PIK3R1 MUTATED 0 49 32
PIK3R1 WILD-TYPE 2 82 75
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0181 (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 35 55 26
PIK3R1 MUTATED 5 23 9
PIK3R1 WILD-TYPE 30 32 17

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 = 0.000779 (Fisher's exact test), Q value = 0.27

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 46 64
PIK3R1 MUTATED 2 6 29
PIK3R1 WILD-TYPE 4 40 35

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 = 0.961 (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
ALL 156 23 54 7 2
PRKAR1B MUTATED 3 0 1 0 0
PRKAR1B WILD-TYPE 153 23 53 7 2
'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 = 0.472 (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
ALL 79 85 81
PRKAR1B MUTATED 2 2 0
PRKAR1B WILD-TYPE 77 83 81
'PRKAR1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.848 (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 80 82 83
PRKAR1B MUTATED 1 2 1
PRKAR1B WILD-TYPE 79 80 82
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
PRKAR1B MUTATED 1 1 2
PRKAR1B WILD-TYPE 66 95 75
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (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 2 131 107
PRKAR1B MUTATED 0 2 2
PRKAR1B WILD-TYPE 2 129 105
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.795 (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 35 55 26
PRKAR1B MUTATED 1 1 1
PRKAR1B WILD-TYPE 34 54 25
'PRKAR1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.208 (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
ALL 6 46 64
PRKAR1B MUTATED 1 1 1
PRKAR1B WILD-TYPE 5 45 63
'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 = 1.69e-21 (Chi-square test), Q value = 6.3e-19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
PTEN MUTATED 130 14 4 6 2
PTEN WILD-TYPE 26 9 50 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 = 2.48e-21 (Fisher's exact test), Q value = 9.2e-19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
PTEN MUTATED 18 66 74
PTEN WILD-TYPE 61 19 7

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 = 7.38e-19 (Fisher's exact test), Q value = 2.7e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 82 83
PTEN MUTATED 72 64 22
PTEN WILD-TYPE 8 18 61

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 = 1.28e-16 (Fisher's exact test), Q value = 4.7e-14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
PTEN MUTATED 17 85 56
PTEN WILD-TYPE 50 11 21

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 = 4.32e-12 (Fisher's exact test), Q value = 1.6e-09

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 131 107
PTEN MUTATED 2 111 45
PTEN WILD-TYPE 0 20 62

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 = 1.97e-09 (Fisher's exact test), Q value = 7e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 55 26
PTEN MUTATED 10 49 11
PTEN WILD-TYPE 25 6 15

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 = 4.78e-13 (Fisher's exact test), Q value = 1.8e-10

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 46 64
PTEN MUTATED 3 10 57
PTEN WILD-TYPE 3 36 7

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 = 0.00685 (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
ALL 156 23 54 7 2
KRAS MUTATED 42 4 2 2 0
KRAS WILD-TYPE 114 19 52 5 2

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 = 0.138 (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
ALL 79 85 81
KRAS MUTATED 11 20 21
KRAS WILD-TYPE 68 65 60
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0497 (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 80 82 83
KRAS MUTATED 23 18 11
KRAS WILD-TYPE 57 64 72

Figure S39.  Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
KRAS MUTATED 7 27 18
KRAS WILD-TYPE 60 69 59

Figure S40.  Get High-res Image Gene #7: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.794 (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 2 131 107
KRAS MUTATED 0 30 22
KRAS WILD-TYPE 2 101 85
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0568 (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 35 55 26
KRAS MUTATED 3 14 8
KRAS WILD-TYPE 32 41 18
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.855 (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
ALL 6 46 64
KRAS MUTATED 1 9 15
KRAS WILD-TYPE 5 37 49
'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 S41.  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 S42.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1.08e-30 (Chi-square test), Q value = 4.1e-28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
TP53 MUTATED 11 5 50 2 0
TP53 WILD-TYPE 145 18 4 5 2

Figure S43.  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 S44.  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 S45.  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 S46.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1.07e-26 (Fisher's exact test), Q value = 4e-24

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
TP53 MUTATED 58 8 3
TP53 WILD-TYPE 21 77 78

Figure S47.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 8.1e-23 (Fisher's exact test), Q value = 3e-20

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 82 83
TP53 MUTATED 7 5 57
TP53 WILD-TYPE 73 77 26

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2.33e-18 (Fisher's exact test), Q value = 8.6e-16

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
TP53 MUTATED 46 7 11
TP53 WILD-TYPE 21 89 66

Figure S49.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1.2e-13 (Fisher's exact test), Q value = 4.4e-11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 131 107
TP53 MUTATED 1 10 53
TP53 WILD-TYPE 1 121 54

Figure S50.  Get High-res Image Gene #8: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2.13e-09 (Fisher's exact test), Q value = 7.6e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 35 55 26
TP53 MUTATED 25 5 6
TP53 WILD-TYPE 10 50 20

Figure S51.  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 = 8.53e-10 (Fisher's exact test), Q value = 3.1e-07

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 6 46 64
TP53 MUTATED 2 29 5
TP53 WILD-TYPE 4 17 59

Figure S52.  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 = 0.576 (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
ALL 156 23 54 7 2
FBXW7 MUTATED 24 2 12 1 0
FBXW7 WILD-TYPE 132 21 42 6 2
'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 = 0.0683 (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
ALL 79 85 81
FBXW7 MUTATED 19 10 10
FBXW7 WILD-TYPE 60 75 71
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.174 (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 80 82 83
FBXW7 MUTATED 12 9 18
FBXW7 WILD-TYPE 68 73 65
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
FBXW7 MUTATED 11 12 12
FBXW7 WILD-TYPE 56 84 65
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.112 (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 2 131 107
FBXW7 MUTATED 0 14 21
FBXW7 WILD-TYPE 2 117 86
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.3 (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 35 55 26
FBXW7 MUTATED 8 6 4
FBXW7 WILD-TYPE 27 49 22
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0393 (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
ALL 6 46 64
FBXW7 MUTATED 0 12 6
FBXW7 WILD-TYPE 6 34 58

Figure S53.  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 = 0.000349 (Chi-square test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
CTCF MUTATED 38 1 0 2 0
CTCF WILD-TYPE 118 22 54 5 2

Figure S54.  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 S55.  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 S56.  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 = 0.000847 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
CTCF MUTATED 5 16 23
CTCF WILD-TYPE 74 69 58

Figure S57.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.000449 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 82 83
CTCF MUTATED 23 16 5
CTCF WILD-TYPE 57 66 78

Figure S58.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
CTCF MUTATED 5 23 16
CTCF WILD-TYPE 62 73 61

Figure S59.  Get High-res Image Gene #10: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00699 (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 2 131 107
CTCF MUTATED 0 33 11
CTCF WILD-TYPE 2 98 96

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

'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.01 (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 35 55 26
CTCF MUTATED 1 12 1
CTCF WILD-TYPE 34 43 25

Figure S61.  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 = 0.0582 (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
ALL 6 46 64
CTCF MUTATED 0 2 12
CTCF WILD-TYPE 6 44 52
'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 S62.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 3.93e-07 (Chi-square test), Q value = 0.00014

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
ARID1A MUTATED 68 3 3 5 1
ARID1A WILD-TYPE 88 20 51 2 1

Figure S63.  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 S64.  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 = 0.0215 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
ARID1A MUTATED 17 33 32
ARID1A WILD-TYPE 62 52 49

Figure S65.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0164 (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 80 82 83
ARID1A MUTATED 33 31 18
ARID1A WILD-TYPE 47 51 65

Figure S66.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
ARID1A MUTATED 15 40 25
ARID1A WILD-TYPE 52 56 52

Figure S67.  Get High-res Image Gene #11: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0577 (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 2 131 107
ARID1A MUTATED 1 51 28
ARID1A WILD-TYPE 1 80 79
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0281 (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 35 55 26
ARID1A MUTATED 6 24 10
ARID1A WILD-TYPE 29 31 16

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

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0622 (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
ALL 6 46 64
ARID1A MUTATED 1 11 28
ARID1A WILD-TYPE 5 35 36
'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 = 0.86 (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
ALL 156 23 54 7 2
SPOP MUTATED 15 2 3 1 0
SPOP WILD-TYPE 141 21 51 6 2
'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 = 0.229 (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
ALL 79 85 81
SPOP MUTATED 5 11 5
SPOP WILD-TYPE 74 74 76
'SPOP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.927 (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 80 82 83
SPOP MUTATED 6 7 8
SPOP WILD-TYPE 74 75 75
'SPOP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
SPOP MUTATED 7 8 6
SPOP WILD-TYPE 60 88 71
'SPOP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.367 (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 2 131 107
SPOP MUTATED 0 9 12
SPOP WILD-TYPE 2 122 95
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.55 (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 35 55 26
SPOP MUTATED 4 3 2
SPOP WILD-TYPE 31 52 24
'SPOP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.688 (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
ALL 6 46 64
SPOP MUTATED 0 5 4
SPOP WILD-TYPE 6 41 60
'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 = 0.0316 (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
ALL 156 23 54 7 2
ARID5B MUTATED 25 2 0 1 0
ARID5B WILD-TYPE 131 21 54 6 2

Figure S69.  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 = 0.159 (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
ALL 79 85 81
ARID5B MUTATED 5 13 11
ARID5B WILD-TYPE 74 72 70
'ARID5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.111 (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 80 82 83
ARID5B MUTATED 12 12 5
ARID5B WILD-TYPE 68 70 78
'ARID5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
ARID5B MUTATED 4 14 9
ARID5B WILD-TYPE 63 82 68
'ARID5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.762 (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 2 131 107
ARID5B MUTATED 0 14 13
ARID5B WILD-TYPE 2 117 94
'ARID5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.304 (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 35 55 26
ARID5B MUTATED 1 5 0
ARID5B WILD-TYPE 34 50 26
'ARID5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.565 (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
ALL 6 46 64
ARID5B MUTATED 0 1 5
ARID5B WILD-TYPE 6 45 59
'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 = 0.317 (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
ALL 156 23 54 7 2
FGFR2 MUTATED 22 3 3 2 0
FGFR2 WILD-TYPE 134 20 51 5 2
'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 = 1 (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
ALL 79 85 81
FGFR2 MUTATED 10 10 10
FGFR2 WILD-TYPE 69 75 71
'FGFR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.836 (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 80 82 83
FGFR2 MUTATED 11 10 9
FGFR2 WILD-TYPE 69 72 74
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
FGFR2 MUTATED 6 12 12
FGFR2 WILD-TYPE 61 84 65
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.648 (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 2 131 107
FGFR2 MUTATED 0 15 15
FGFR2 WILD-TYPE 2 116 92
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.587 (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 35 55 26
FGFR2 MUTATED 6 8 2
FGFR2 WILD-TYPE 29 47 24
'FGFR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.879 (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
ALL 6 46 64
FGFR2 MUTATED 0 7 9
FGFR2 WILD-TYPE 6 39 55
'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 = 0.0207 (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
ALL 156 23 54 7 2
NFE2L2 MUTATED 10 3 0 2 0
NFE2L2 WILD-TYPE 146 20 54 5 2

Figure S70.  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 = 0.014 (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
ALL 79 85 81
NFE2L2 MUTATED 2 2 10
NFE2L2 WILD-TYPE 77 83 71

Figure S71.  Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0456 (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 80 82 83
NFE2L2 MUTATED 9 2 3
NFE2L2 WILD-TYPE 71 80 80

Figure S72.  Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
NFE2L2 MUTATED 3 9 3
NFE2L2 WILD-TYPE 64 87 74
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.722 (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 2 131 107
NFE2L2 MUTATED 0 9 6
NFE2L2 WILD-TYPE 2 122 101
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.304 (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 35 55 26
NFE2L2 MUTATED 1 5 0
NFE2L2 WILD-TYPE 34 50 26
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.565 (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
ALL 6 46 64
NFE2L2 MUTATED 0 1 5
NFE2L2 WILD-TYPE 6 45 59
'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 = 0.0848 (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
ALL 156 23 54 7 2
CCND1 MUTATED 14 0 0 0 0
CCND1 WILD-TYPE 142 23 54 7 2
'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 = 0.458 (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
ALL 79 85 81
CCND1 MUTATED 3 7 4
CCND1 WILD-TYPE 76 78 77
'CCND1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.591 (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 80 82 83
CCND1 MUTATED 5 6 3
CCND1 WILD-TYPE 75 76 80
'CCND1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
CCND1 MUTATED 1 5 8
CCND1 WILD-TYPE 66 91 69
'CCND1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.542 (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 2 131 107
CCND1 MUTATED 0 9 5
CCND1 WILD-TYPE 2 122 102
'CCND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.441 (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 35 55 26
CCND1 MUTATED 0 3 1
CCND1 WILD-TYPE 35 52 25
'CCND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.709 (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
ALL 6 46 64
CCND1 MUTATED 0 1 3
CCND1 WILD-TYPE 6 45 61
'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 = 0.438 (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
ALL 156 23 54 7 2
CHD4 MUTATED 25 1 7 2 0
CHD4 WILD-TYPE 131 22 47 5 2
'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 = 0.37 (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
ALL 79 85 81
CHD4 MUTATED 15 10 10
CHD4 WILD-TYPE 64 75 71
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.442 (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 80 82 83
CHD4 MUTATED 11 9 15
CHD4 WILD-TYPE 69 73 68
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.609 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
CHD4 MUTATED 8 10 12
CHD4 WILD-TYPE 59 86 65
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.648 (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 2 131 107
CHD4 MUTATED 0 15 15
CHD4 WILD-TYPE 2 116 92
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.415 (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 35 55 26
CHD4 MUTATED 4 10 2
CHD4 WILD-TYPE 31 45 24
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.733 (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
ALL 6 46 64
CHD4 MUTATED 0 6 10
CHD4 WILD-TYPE 6 40 54
'FAM9A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.63 (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
ALL 156 23 54 7 2
FAM9A MUTATED 10 0 3 1 0
FAM9A WILD-TYPE 146 23 51 6 2
'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 S73.  Get High-res Image Gene #18: 'FAM9A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'FAM9A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0733 (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
ALL 79 85 81
FAM9A MUTATED 7 6 1
FAM9A WILD-TYPE 72 79 80
'FAM9A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.147 (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 80 82 83
FAM9A MUTATED 2 4 8
FAM9A WILD-TYPE 78 78 75
'FAM9A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
FAM9A MUTATED 5 4 5
FAM9A WILD-TYPE 62 92 72
'FAM9A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.151 (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 2 131 107
FAM9A MUTATED 0 4 10
FAM9A WILD-TYPE 2 127 97
'FAM9A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.022 (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 35 55 26
FAM9A MUTATED 6 2 0
FAM9A WILD-TYPE 29 53 26

Figure S74.  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 = 0.135 (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
ALL 6 46 64
FAM9A MUTATED 0 6 2
FAM9A WILD-TYPE 6 40 62
'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 = 0.371 (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
ALL 156 23 54 7 2
MORC4 MUTATED 16 2 1 1 0
MORC4 WILD-TYPE 140 21 53 6 2
'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 S75.  Get High-res Image Gene #19: 'MORC4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MORC4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.144 (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
ALL 79 85 81
MORC4 MUTATED 7 10 3
MORC4 WILD-TYPE 72 75 78
'MORC4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.179 (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 80 82 83
MORC4 MUTATED 3 9 8
MORC4 WILD-TYPE 77 73 75
'MORC4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0606 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
MORC4 MUTATED 3 5 11
MORC4 WILD-TYPE 64 91 66
'MORC4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (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 2 131 107
MORC4 MUTATED 0 7 12
MORC4 WILD-TYPE 2 124 95
'MORC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.348 (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 35 55 26
MORC4 MUTATED 2 3 4
MORC4 WILD-TYPE 33 52 22
'MORC4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL 6 46 64
MORC4 MUTATED 0 4 5
MORC4 WILD-TYPE 6 42 59
'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 = 0.0407 (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
ALL 156 23 54 7 2
CASP8 MUTATED 14 0 1 2 0
CASP8 WILD-TYPE 142 23 53 5 2

Figure S76.  Get High-res Image Gene #20: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'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 = 0.626 (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
ALL 79 85 81
CASP8 MUTATED 7 6 4
CASP8 WILD-TYPE 72 79 77
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.239 (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 80 82 83
CASP8 MUTATED 4 4 9
CASP8 WILD-TYPE 76 78 74
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
CASP8 MUTATED 7 5 4
CASP8 WILD-TYPE 60 91 73
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.257 (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 2 131 107
CASP8 MUTATED 0 6 10
CASP8 WILD-TYPE 2 125 97
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.363 (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 35 55 26
CASP8 MUTATED 3 4 0
CASP8 WILD-TYPE 32 51 26
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL 6 46 64
CASP8 MUTATED 0 3 4
CASP8 WILD-TYPE 6 43 60
'FOXA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.867 (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
ALL 156 23 54 7 2
FOXA2 MUTATED 7 2 3 0 0
FOXA2 WILD-TYPE 149 21 51 7 2
'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 = 0.817 (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
ALL 79 85 81
FOXA2 MUTATED 3 4 5
FOXA2 WILD-TYPE 76 81 76
'FOXA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.712 (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 80 82 83
FOXA2 MUTATED 5 3 4
FOXA2 WILD-TYPE 75 79 79
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 1

Table S243.  Gene #21: 'FOXA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
FOXA2 MUTATED 1 6 4
FOXA2 WILD-TYPE 66 90 73
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.411 (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 2 131 107
FOXA2 MUTATED 0 8 3
FOXA2 WILD-TYPE 2 123 104
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (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 35 55 26
FOXA2 MUTATED 1 4 2
FOXA2 WILD-TYPE 34 51 24
'FOXA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.179 (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
ALL 6 46 64
FOXA2 MUTATED 1 1 5
FOXA2 WILD-TYPE 5 45 59
'ABI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.691 (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
ALL 156 23 54 7 2
ABI1 MUTATED 4 0 0 0 0
ABI1 WILD-TYPE 152 23 54 7 2
'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 = 0.551 (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
ALL 79 85 81
ABI1 MUTATED 0 2 2
ABI1 WILD-TYPE 79 83 79
'ABI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.697 (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 80 82 83
ABI1 MUTATED 2 1 1
ABI1 WILD-TYPE 78 81 82
'ABI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S252.  Gene #22: 'ABI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
ABI1 MUTATED 0 2 2
ABI1 WILD-TYPE 67 94 75
'ABI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.642 (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 2 131 107
ABI1 MUTATED 0 3 1
ABI1 WILD-TYPE 2 128 106
'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 = 0.000461 (Chi-square test), Q value = 0.16

Table S256.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
DNER MUTATED 15 0 0 3 0
DNER WILD-TYPE 141 23 54 4 2

Figure S77.  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 S78.  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 = 0.864 (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
ALL 79 85 81
DNER MUTATED 6 7 5
DNER WILD-TYPE 73 78 76
'DNER MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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 80 82 83
DNER MUTATED 6 6 6
DNER WILD-TYPE 74 76 77
'DNER MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S262.  Gene #23: 'DNER MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
DNER MUTATED 5 5 7
DNER WILD-TYPE 62 91 70
'DNER MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.217 (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 2 131 107
DNER MUTATED 0 6 11
DNER WILD-TYPE 2 125 96
'DNER MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (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 35 55 26
DNER MUTATED 1 4 2
DNER WILD-TYPE 34 51 24
'DNER MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL 6 46 64
DNER MUTATED 0 3 4
DNER WILD-TYPE 6 43 60
'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 = 0.00145 (Chi-square test), Q value = 0.49

Table S268.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 156 23 54 7 2
BCOR MUTATED 25 1 0 3 0
BCOR WILD-TYPE 131 22 54 4 2

Figure S79.  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 S80.  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 = 0.0328 (Fisher's exact test), Q value = 1

Table S272.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
BCOR MUTATED 6 17 7
BCOR WILD-TYPE 73 68 74

Figure S81.  Get High-res Image Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'BCOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.143 (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 80 82 83
BCOR MUTATED 7 15 8
BCOR WILD-TYPE 73 67 75
'BCOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S274.  Gene #24: 'BCOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
BCOR MUTATED 9 10 10
BCOR WILD-TYPE 58 86 67
'BCOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.558 (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 2 131 107
BCOR MUTATED 0 14 15
BCOR WILD-TYPE 2 117 92
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.928 (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 35 55 26
BCOR MUTATED 3 7 3
BCOR WILD-TYPE 32 48 23
'BCOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0902 (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
ALL 6 46 64
BCOR MUTATED 1 2 10
BCOR WILD-TYPE 5 44 54
'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 = 0.211 (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
ALL 156 23 54 7 2
BRS3 MUTATED 13 1 0 1 0
BRS3 WILD-TYPE 143 22 54 6 2
'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 = 0.0818 (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
ALL 79 85 81
BRS3 MUTATED 6 7 1
BRS3 WILD-TYPE 73 78 80
'BRS3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S285.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 82 83
BRS3 MUTATED 2 6 6
BRS3 WILD-TYPE 78 76 77
'BRS3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 1

Table S286.  Gene #25: 'BRS3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
BRS3 MUTATED 4 3 7
BRS3 WILD-TYPE 63 93 70
'BRS3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (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 2 131 107
BRS3 MUTATED 0 5 9
BRS3 WILD-TYPE 2 126 98
'BRS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.56 (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 35 55 26
BRS3 MUTATED 2 1 1
BRS3 WILD-TYPE 33 54 25
'BRS3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.441 (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
ALL 6 46 64
BRS3 MUTATED 0 3 1
BRS3 WILD-TYPE 6 43 63
'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 = 0.338 (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
ALL 156 23 54 7 2
SGK1 MUTATED 10 3 1 1 0
SGK1 WILD-TYPE 146 20 53 6 2
'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 = 0.302 (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
ALL 79 85 81
SGK1 MUTATED 4 8 3
SGK1 WILD-TYPE 75 77 78
'SGK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.944 (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 80 82 83
SGK1 MUTATED 4 5 6
SGK1 WILD-TYPE 76 77 77
'SGK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 1

Table S298.  Gene #26: 'SGK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
SGK1 MUTATED 2 5 7
SGK1 WILD-TYPE 65 91 70
'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 2 131 107
SGK1 MUTATED 0 8 6
SGK1 WILD-TYPE 2 123 101
'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.811 (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 35 55 26
SGK1 MUTATED 1 3 0
SGK1 WILD-TYPE 34 52 26
'SGK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.709 (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
ALL 6 46 64
SGK1 MUTATED 0 1 3
SGK1 WILD-TYPE 6 45 61
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.415 (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
ALL 156 23 54 7 2
NRAS MUTATED 7 0 1 1 0
NRAS WILD-TYPE 149 23 53 6 2
'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 = 0.706 (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
ALL 79 85 81
NRAS MUTATED 4 3 2
NRAS WILD-TYPE 75 82 79
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.645 (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 80 82 83
NRAS MUTATED 4 2 3
NRAS WILD-TYPE 76 80 80
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S307.  Gene #27: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
NRAS MUTATED 3 2 4
NRAS WILD-TYPE 64 94 73
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.754 (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 2 131 107
NRAS MUTATED 0 4 5
NRAS WILD-TYPE 2 127 102
'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 = 0.162 (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
ALL 156 23 54 7 2
TIAL1 MUTATED 10 0 0 1 0
TIAL1 WILD-TYPE 146 23 54 6 2
'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 = 0.0444 (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
ALL 79 85 81
TIAL1 MUTATED 2 8 1
TIAL1 WILD-TYPE 77 77 80

Figure S82.  Get High-res Image Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TIAL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (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 80 82 83
TIAL1 MUTATED 2 5 4
TIAL1 WILD-TYPE 78 77 79
'TIAL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S317.  Gene #28: 'TIAL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
TIAL1 MUTATED 2 5 4
TIAL1 WILD-TYPE 65 91 73
'TIAL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.298 (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 2 131 107
TIAL1 MUTATED 0 4 7
TIAL1 WILD-TYPE 2 127 100
'TIAL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.304 (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 35 55 26
TIAL1 MUTATED 1 5 0
TIAL1 WILD-TYPE 34 50 26
'TIAL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.187 (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
ALL 6 46 64
TIAL1 MUTATED 1 1 4
TIAL1 WILD-TYPE 5 45 60
'SIN3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0463 (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
ALL 156 23 54 7 2
SIN3A MUTATED 16 2 0 2 0
SIN3A WILD-TYPE 140 21 54 5 2

Figure S83.  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 S84.  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 = 0.0216 (Fisher's exact test), Q value = 1

Table S325.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 79 85 81
SIN3A MUTATED 7 12 2
SIN3A WILD-TYPE 72 73 79

Figure S85.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SIN3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0421 (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 80 82 83
SIN3A MUTATED 2 10 9
SIN3A WILD-TYPE 78 72 74

Figure S86.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SIN3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0226 (Fisher's exact test), Q value = 1

Table S327.  Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
SIN3A MUTATED 7 3 11
SIN3A WILD-TYPE 60 93 66

Figure S87.  Get High-res Image Gene #29: 'SIN3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SIN3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0876 (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 2 131 107
SIN3A MUTATED 0 7 14
SIN3A WILD-TYPE 2 124 93
'SIN3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.514 (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 35 55 26
SIN3A MUTATED 4 3 3
SIN3A WILD-TYPE 31 52 23
'SIN3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.358 (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
ALL 6 46 64
SIN3A MUTATED 1 5 4
SIN3A WILD-TYPE 5 41 60
'SLC48A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.589 (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
ALL 156 23 54 7 2
SLC48A1 MUTATED 5 0 0 0 0
SLC48A1 WILD-TYPE 151 23 54 7 2
'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 = 0.624 (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
ALL 79 85 81
SLC48A1 MUTATED 1 3 1
SLC48A1 WILD-TYPE 78 82 80
'SLC48A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.747 (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 80 82 83
SLC48A1 MUTATED 2 2 1
SLC48A1 WILD-TYPE 78 80 82
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0697 (Fisher's exact test), Q value = 1

Table S337.  Gene #30: 'SLC48A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
SLC48A1 MUTATED 0 1 4
SLC48A1 WILD-TYPE 67 95 73
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.674 (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 2 131 107
SLC48A1 MUTATED 0 2 3
SLC48A1 WILD-TYPE 2 129 104
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.795 (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 35 55 26
SLC48A1 MUTATED 1 1 1
SLC48A1 WILD-TYPE 34 54 25
'SLC48A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.634 (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
ALL 6 46 64
SLC48A1 MUTATED 0 2 1
SLC48A1 WILD-TYPE 6 44 63
'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 = 0.295 (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
ALL 156 23 54 7 2
RNF43 MUTATED 10 1 0 1 0
RNF43 WILD-TYPE 146 22 54 6 2
'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 = 0.0478 (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
ALL 79 85 81
RNF43 MUTATED 3 8 1
RNF43 WILD-TYPE 76 77 80

Figure S88.  Get High-res Image Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RNF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 1

Table S348.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 80 82 83
RNF43 MUTATED 1 9 2
RNF43 WILD-TYPE 79 73 81

Figure S89.  Get High-res Image Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RNF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 1

Table S349.  Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
RNF43 MUTATED 2 2 8
RNF43 WILD-TYPE 65 94 69

Figure S90.  Get High-res Image Gene #31: 'RNF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'RNF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.211 (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 2 131 107
RNF43 MUTATED 0 4 8
RNF43 WILD-TYPE 2 127 99
'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.346 (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 35 55 26
RNF43 MUTATED 1 1 2
RNF43 WILD-TYPE 34 54 24
'RNF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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
ALL 6 46 64
RNF43 MUTATED 0 2 2
RNF43 WILD-TYPE 6 44 62
'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 S91.  Get High-res Image Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'ZFHX3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0686 (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
ALL 156 23 54 7 2
ZFHX3 MUTATED 34 3 3 2 0
ZFHX3 WILD-TYPE 122 20 51 5 2
'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 = 0.924 (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
ALL 79 85 81
ZFHX3 MUTATED 13 16 14
ZFHX3 WILD-TYPE 66 69 67
'ZFHX3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.959 (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 80 82 83
ZFHX3 MUTATED 15 14 14
ZFHX3 WILD-TYPE 65 68 69
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 1

Table S361.  Gene #32: 'ZFHX3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
ZFHX3 MUTATED 7 16 18
ZFHX3 WILD-TYPE 60 80 59
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.568 (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 2 131 107
ZFHX3 MUTATED 0 20 21
ZFHX3 WILD-TYPE 2 111 86
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.575 (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 35 55 26
ZFHX3 MUTATED 3 9 4
ZFHX3 WILD-TYPE 32 46 22
'ZFHX3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.258 (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
ALL 6 46 64
ZFHX3 MUTATED 2 5 9
ZFHX3 WILD-TYPE 4 41 55
'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 = 0.177 (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
ALL 156 23 54 7 2
RB1 MUTATED 15 1 2 2 0
RB1 WILD-TYPE 141 22 52 5 2
'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 = 0.478 (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
ALL 79 85 81
RB1 MUTATED 9 6 5
RB1 WILD-TYPE 70 79 76
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.383 (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 80 82 83
RB1 MUTATED 8 4 8
RB1 WILD-TYPE 72 78 75
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 1

Table S373.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 96 77
RB1 MUTATED 3 6 10
RB1 WILD-TYPE 64 90 67
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0872 (Fisher's exact test), Q value = 1

Table S374.  Gene #33: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 2 131 107
RB1 MUTATED 1 8 10
RB1 WILD-TYPE 1 123 97
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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 35 55 26
RB1 MUTATED 1 3 1
RB1 WILD-TYPE 34 52 25
'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
ALL 6 46 64
RB1 MUTATED 0 2 3
RB1 WILD-TYPE 6 44 61
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.

Download Results

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

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] 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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