Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 81 genes and 10 molecular subtypes across 395 patients, 64 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • RB1 mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • KDM6A mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • CDKN2A mutation correlated to 'METHLYATION_CNMF'.

  • STAG2 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • FGFR3 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ERCC2 mutation correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CREBBP mutation correlated to 'MIRSEQ_CNMF'.

  • HRAS mutation correlated to 'METHLYATION_CNMF'.

  • MLL mutation correlated to 'CN_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • KLF5 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • PSIP1 mutation correlated to 'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ZBTB7B mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RXRA mutation correlated to 'METHLYATION_CNMF'.

  • NFE2L2 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • NUDT11 mutation correlated to 'RPPA_CNMF'.

  • FAM47C mutation correlated to 'RPPA_CNMF'.

  • ATM mutation correlated to 'RPPA_CHIERARCHICAL'.

  • SF1 mutation correlated to 'RPPA_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • BCL2L1 mutation correlated to 'CN_CNMF'.

  • DNAH6 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TXNIP mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • ARID1B mutation correlated to 'CN_CNMF'.

  • RAI1 mutation correlated to 'MRNASEQ_CNMF'.

  • DAZAP1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • CNOT3 mutation correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • SSH3 mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 81 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 64 significant findings detected.

Clinical
Features 		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 Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
FGFR3 56 (14%) 339 1e-05
(0.000675) 		1e-05
(0.000675) 		3e-05
(0.00152) 		1e-05
(0.000675) 		5e-05
(0.00213) 		1e-05
(0.000675) 		1e-05
(0.000675) 		1e-05
(0.000675) 		1e-05
(0.000675) 		1e-05
(0.000675)
TP53 196 (50%) 199 1e-05
(0.000675) 		4e-05
(0.00191) 		0.00025
(0.0092) 		0.0242
(0.28) 		0.0166
(0.247) 		3e-05
(0.00152) 		0.291
(0.704) 		0.00504
(0.128) 		0.021
(0.25) 		3e-05
(0.00152)
RB1 70 (18%) 325 1e-05
(0.000675) 		0.0321
(0.316) 		5e-05
(0.00213) 		0.00017
(0.00656) 		3e-05
(0.00152) 		1e-05
(0.000675) 		0.265
(0.678) 		0.137
(0.553) 		0.00323
(0.0872) 		1e-05
(0.000675)
PSIP1 20 (5%) 375 0.426
(0.796) 		0.0225
(0.264) 		0.019
(0.247) 		0.166
(0.582) 		0.174
(0.582) 		0.0154
(0.243) 		0.052
(0.37) 		0.00953
(0.191) 		0.0345
(0.317) 		0.0174
(0.247)
KDM6A 103 (26%) 292 0.147
(0.565) 		0.00084
(0.0296) 		0.0519
(0.37) 		0.224
(0.63) 		0.00263
(0.0789) 		0.0114
(0.205) 		0.477
(0.838) 		0.145
(0.565) 		0.0504
(0.368) 		0.0285
(0.298)
MLL 44 (11%) 351 0.0137
(0.236) 		0.364
(0.756) 		0.0615
(0.395) 		0.171
(0.582) 		0.0853
(0.429) 		0.0757
(0.42) 		0.0279
(0.298) 		0.0192
(0.247) 		0.0188
(0.247) 		0.041
(0.342)
NFE2L2 24 (6%) 371 0.00012
(0.00486) 		0.0778
(0.42) 		0.12
(0.513) 		0.07
(0.412) 		0.00151
(0.0489) 		0.0086
(0.189) 		0.0751
(0.42) 		0.66
(0.898) 		0.392
(0.767) 		0.144
(0.562)
SF1 10 (3%) 385 0.05
(0.368) 		0.658
(0.898) 		0.304
(0.715) 		0.0179
(0.247) 		0.778
(0.938) 		1
(1.00) 		0.00826
(0.189) 		0.202
(0.616) 		0.169
(0.582) 		0.0142
(0.239)
DNAH6 16 (4%) 379 0.616
(0.893) 		0.104
(0.477) 		0.453
(0.824) 		0.191
(0.602) 		0.00959
(0.191) 		0.0123
(0.217) 		1
(1.00) 		0.0338
(0.316) 		0.0562
(0.382) 		0.0169
(0.247)
STAG2 56 (14%) 339 0.0304
(0.307) 		0.00365
(0.0954) 		0.108
(0.483) 		0.191
(0.602) 		0.417
(0.791) 		0.00692
(0.165) 		0.045
(0.357) 		0.18
(0.591) 		0.0208
(0.25) 		0.0465
(0.362)
ERCC2 38 (10%) 357 0.00309
(0.0872) 		0.082
(0.427) 		0.046
(0.362) 		0.255
(0.669) 		0.794
(0.939) 		0.707
(0.907) 		0.0968
(0.453) 		0.402
(0.774) 		0.285
(0.697) 		0.00991
(0.191)
CNOT3 10 (3%) 385 0.202
(0.616) 		0.391
(0.766) 		0.701
(0.904) 		0.172
(0.582) 		0.0205
(0.25) 		0.116
(0.512) 		0.919
(0.982) 		0.0515
(0.37) 		0.00133
(0.0449) 		0.0154
(0.243)
CDKN2A 26 (7%) 369 0.347
(0.746) 		0.0156
(0.243) 		0.686
(0.904) 		0.0281
(0.298) 		0.182
(0.591) 		0.449
(0.821) 		0.838
(0.955) 		0.0544
(0.376) 		0.0385
(0.336) 		0.151
(0.575)
CREBBP 48 (12%) 347 0.444
(0.819) 		0.425
(0.796) 		0.646
(0.895) 		0.817
(0.95) 		0.174
(0.582) 		0.543
(0.876) 		0.00244
(0.076) 		0.0328
(0.316) 		0.0849
(0.429) 		0.46
(0.824)
HRAS 17 (4%) 378 0.366
(0.756) 		0.0153
(0.243) 		0.507
(0.858) 		0.844
(0.959) 		0.7
(0.904) 		0.778
(0.938) 		1
(1.00) 		0.297
(0.71) 		0.317
(0.725) 		0.19
(0.602)
KLF5 23 (6%) 372 0.142
(0.558) 		0.98
(1.00) 		0.0487
(0.365) 		0.658
(0.898) 		0.629
(0.893) 		0.71
(0.908) 		0.49
(0.846) 		0.12
(0.513) 		0.0195
(0.247) 		0.236
(0.642)
ZBTB7B 11 (3%) 384 0.0896
(0.437) 		0.827
(0.955) 		0.785
(0.938) 		0.532
(0.876) 		0.54
(0.876) 		0.398
(0.773) 		0.355
(0.755) 		0.227
(0.633) 		0.47
(0.835) 		0.018
(0.247)
RXRA 24 (6%) 371 0.0421
(0.344) 		0.00865
(0.189) 		0.582
(0.884) 		0.275
(0.691) 		0.57
(0.876) 		0.255
(0.669) 		0.341
(0.741) 		0.061
(0.395) 		0.368
(0.756) 		0.0732
(0.42)
NUDT11 7 (2%) 388 0.491
(0.847) 		0.711
(0.908) 		0.00316
(0.0872) 		0.813
(0.948) 		0.632
(0.893) 		0.72
(0.909) 		1
(1.00) 		0.401
(0.774) 		0.275
(0.691) 		0.163
(0.582)
FAM47C 21 (5%) 374 0.555
(0.876) 		0.813
(0.948) 		0.00689
(0.165) 		0.743
(0.925) 		0.212
(0.621) 		0.715
(0.908) 		0.249
(0.664) 		0.165
(0.582) 		0.831
(0.955) 		0.744
(0.925)
ATM 53 (13%) 342 0.564
(0.876) 		0.688
(0.904) 		0.174
(0.582) 		0.0176
(0.247) 		0.616
(0.893) 		0.656
(0.898) 		0.0736
(0.42) 		0.211
(0.621) 		0.225
(0.63) 		0.18
(0.591)
BCL2L1 4 (1%) 391 0.0192
(0.247) 		0.0476
(0.365) 		0.0762
(0.42) 		0.524
(0.87) 		0.293
(0.705) 		0.693
(0.904) 		0.372
(0.76) 		0.397
(0.773) 		0.382
(0.764) 		0.905
(0.978)
TXNIP 17 (4%) 378 0.546
(0.876) 		0.698
(0.904) 		0.128
(0.52) 		0.746
(0.926) 		0.46
(0.824) 		0.00894
(0.191) 		0.434
(0.807) 		0.743
(0.925) 		0.805
(0.946) 		0.733
(0.919)
ARID1B 23 (6%) 372 0.00989
(0.191) 		0.215
(0.625) 		0.187
(0.598) 		0.588
(0.886) 		0.0866
(0.431) 		0.0579
(0.383) 		0.0829
(0.427) 		0.0582
(0.383) 		0.387
(0.765) 		0.2
(0.616)
RAI1 21 (5%) 374 0.971
(1.00) 		0.255
(0.669) 		0.118
(0.513) 		0.0769
(0.42) 		0.0114
(0.205) 		0.0332
(0.316) 		0.956
(0.998) 		0.0483
(0.365) 		0.48
(0.838) 		0.338
(0.74)
DAZAP1 6 (2%) 389 0.743
(0.925) 		0.0443
(0.355) 		0.554
(0.876) 		0.321
(0.73) 		0.179
(0.591) 		0.0109
(0.205) 		0.208
(0.621) 		0.0248
(0.282) 		0.345
(0.746) 		0.425
(0.796)
SSH3 15 (4%) 380 0.0174
(0.247) 		0.0946
(0.445) 		0.0352
(0.317) 		0.0434
(0.351) 		0.0499
(0.368) 		0.399
(0.774) 		0.0686
(0.412) 		0.106
(0.482) 		0.338
(0.74) 		0.255
(0.669)
ELF3 46 (12%) 349 0.379
(0.764) 		0.103
(0.476) 		0.627
(0.893) 		0.0631
(0.399) 		0.0258
(0.29) 		0.0415
(0.343) 		0.278
(0.692) 		0.331
(0.736) 		0.379
(0.764) 		0.608
(0.893)
TSC1 33 (8%) 362 0.335
(0.74) 		0.914
(0.982) 		0.313
(0.72) 		0.203
(0.616) 		0.125
(0.517) 		0.236
(0.642) 		0.147
(0.565) 		0.0657
(0.402) 		0.63
(0.893) 		0.71
(0.908)
PIK3CA 86 (22%) 309 0.327
(0.734) 		0.959
(0.998) 		0.839
(0.955) 		0.948
(0.995) 		0.631
(0.893) 		0.764
(0.935) 		0.937
(0.991) 		0.946
(0.995) 		0.946
(0.995) 		0.603
(0.893)
RHOB 26 (7%) 369 0.0373
(0.328) 		0.24
(0.647) 		0.918
(0.982) 		0.675
(0.904) 		0.375
(0.762) 		0.162
(0.582) 		0.838
(0.955) 		0.641
(0.893) 		0.888
(0.976) 		0.882
(0.976)
ARID1A 97 (25%) 298 0.624
(0.893) 		0.347
(0.746) 		0.766
(0.936) 		0.523
(0.87) 		0.572
(0.877) 		0.782
(0.938) 		0.0778
(0.42) 		0.167
(0.582) 		0.284
(0.697) 		0.0403
(0.342)
ZFP36L1 25 (6%) 370 0.583
(0.884) 		0.644
(0.893) 		0.308
(0.72) 		0.932
(0.99) 		0.896
(0.978) 		0.233
(0.642) 		0.624
(0.893) 		0.384
(0.764) 		0.883
(0.976) 		0.241
(0.647)
CDKN1A 35 (9%) 360 0.704
(0.905) 		0.202
(0.616) 		0.309
(0.72) 		0.0334
(0.316) 		0.382
(0.764) 		0.356
(0.755) 		0.0289
(0.298) 		0.169
(0.582) 		0.678
(0.904) 		0.599
(0.893)
EP300 61 (15%) 334 0.568
(0.876) 		0.876
(0.974) 		0.419
(0.793) 		0.664
(0.901) 		0.352
(0.752) 		0.309
(0.72) 		0.668
(0.901) 		0.644
(0.893) 		0.341
(0.741) 		0.152
(0.575)
MLL2 114 (29%) 281 0.735
(0.92) 		0.616
(0.893) 		0.908
(0.979) 		0.103
(0.476) 		0.835
(0.955) 		0.939
(0.992) 		0.141
(0.558) 		0.147
(0.565) 		0.26
(0.677) 		0.193
(0.606)
FOXA1 14 (4%) 381 0.44
(0.813) 		0.253
(0.669) 		0.814
(0.948) 		0.168
(0.582) 		0.317
(0.725) 		0.228
(0.634) 		0.283
(0.697) 		0.563
(0.876) 		0.0291
(0.298) 		0.123
(0.516)
KRAS 13 (3%) 382 0.0593
(0.387) 		0.922
(0.984) 		0.586
(0.884) 		0.153
(0.577) 		0.361
(0.756) 		0.173
(0.582) 		0.481
(0.838) 		0.448
(0.821) 		0.775
(0.938) 		0.56
(0.876)
RHOA 18 (5%) 377 0.211
(0.621) 		0.349
(0.749) 		0.407
(0.78) 		0.177
(0.589) 		0.412
(0.787) 		0.48
(0.838) 		0.0528
(0.372) 		0.089
(0.437) 		0.767
(0.936) 		0.628
(0.893)
KIAA1267 24 (6%) 371 0.0279
(0.298) 		0.0626
(0.399) 		0.955
(0.998) 		0.644
(0.893) 		0.509
(0.858) 		0.211
(0.621) 		0.275
(0.691) 		0.785
(0.938) 		0.0811
(0.427) 		0.16
(0.582)
FAT1 50 (13%) 345 0.0702
(0.412) 		0.0666
(0.402) 		0.23
(0.635) 		0.125
(0.517) 		0.557
(0.876) 		0.195
(0.609) 		0.107
(0.483) 		0.653
(0.898) 		0.191
(0.602) 		0.0878
(0.434)
PTEN 14 (4%) 381 0.886
(0.976) 		0.0933
(0.445) 		0.477
(0.838) 		0.369
(0.756) 		0.673
(0.904) 		0.161
(0.582) 		1
(1.00) 		0.96
(0.998) 		0.698
(0.904) 		0.758
(0.932)
C3ORF70 17 (4%) 378 0.681
(0.904) 		0.166
(0.582) 		1
(1.00) 		0.668
(0.901) 		0.95
(0.995) 		0.569
(0.876) 		0.776
(0.938) 		0.534
(0.876) 		0.789
(0.938) 		0.929
(0.989)
MLL3 74 (19%) 321 0.154
(0.577) 		0.919
(0.982) 		0.116
(0.512) 		0.224
(0.63) 		0.414
(0.789) 		0.483
(0.839) 		0.678
(0.904) 		0.0941
(0.445) 		0.0825
(0.427) 		0.559
(0.876)
ASXL2 36 (9%) 359 0.185
(0.597) 		0.545
(0.876) 		0.0939
(0.445) 		0.216
(0.625) 		0.623
(0.893) 		0.592
(0.888) 		0.364
(0.756) 		0.542
(0.876) 		0.387
(0.765) 		0.696
(0.904)
FBXW7 30 (8%) 365 0.511
(0.858) 		0.124
(0.516) 		0.714
(0.908) 		0.436
(0.808) 		0.597
(0.892) 		0.173
(0.582) 		0.211
(0.621) 		0.224
(0.63) 		0.0572
(0.383) 		0.202
(0.616)
RBM10 22 (6%) 373 0.815
(0.949) 		0.199
(0.616) 		0.484
(0.839) 		0.905
(0.978) 		0.566
(0.876) 		0.886
(0.976) 		0.423
(0.796) 		0.806
(0.946) 		0.299
(0.71) 		0.17
(0.582)
CUL1 19 (5%) 376 0.632
(0.893) 		0.919
(0.982) 		0.108
(0.483) 		0.297
(0.71) 		0.57
(0.876) 		0.457
(0.824) 		0.407
(0.78) 		0.905
(0.978) 		0.47
(0.835) 		0.579
(0.884)
HLA-A 5 (1%) 390 0.905
(0.978) 		0.305
(0.715) 		0.865
(0.972) 		1
(1.00) 		0.723
(0.909) 		0.721
(0.909) 		0.688
(0.904) 		0.496
(0.851)
GNA13 12 (3%) 383 0.736
(0.92) 		0.272
(0.691) 		0.366
(0.756) 		0.775
(0.938) 		0.0868
(0.431) 		0.365
(0.756) 		0.674
(0.904) 		0.356
(0.755) 		0.0699
(0.412) 		0.808
(0.946)
MBD1 12 (3%) 383 0.163
(0.582) 		0.914
(0.982) 		0.51
(0.858) 		0.292
(0.704) 		0.752
(0.928) 		0.658
(0.898) 		0.218
(0.625) 		0.751
(0.928) 		0.223
(0.63) 		0.559
(0.876)
SCARF2 8 (2%) 387 0.561
(0.876) 		0.0653
(0.402) 		0.328
(0.734) 		0.201
(0.616) 		0.0352
(0.317) 		0.162
(0.582) 		0.662
(0.9) 		0.218
(0.625) 		0.338
(0.74) 		0.568
(0.876)
FOXQ1 14 (4%) 381 0.536
(0.876) 		0.659
(0.898) 		0.62
(0.893) 		0.268
(0.682) 		0.303
(0.715) 		0.886
(0.976) 		0.933
(0.99) 		0.903
(0.978) 		0.934
(0.99) 		0.984
(1.00)
METTL3 17 (4%) 378 0.235
(0.642) 		0.644
(0.893) 		1
(1.00) 		0.691
(0.904) 		0.334
(0.74) 		0.22
(0.628) 		0.265
(0.678) 		0.0409
(0.342) 		0.635
(0.893) 		0.282
(0.697)
ZNF185 5 (1%) 390 0.0906
(0.437) 		0.564
(0.876) 		0.076
(0.42) 		0.358
(0.756) 		0.607
(0.893) 		0.865
(0.972) 		0.45
(0.821) 		0.181
(0.591) 		0.805
(0.946) 		0.786
(0.938)
ERBB2 48 (12%) 347 0.434
(0.807) 		0.427
(0.798) 		0.528
(0.872) 		0.68
(0.904) 		0.279
(0.692) 		0.205
(0.616) 		0.76
(0.932) 		0.186
(0.597) 		0.183
(0.592) 		0.287
(0.699)
UNC93B1 7 (2%) 388 0.278
(0.692) 		1
(1.00) 		0.51
(0.858) 		0.899
(0.978) 		0.559
(0.876) 		0.888
(0.976) 		0.791
(0.938) 		0.958
(0.998) 		0.716
(0.908) 		0.716
(0.908)
HES1 11 (3%) 384 0.847
(0.96) 		0.825
(0.955) 		0.582
(0.884) 		0.127
(0.52) 		0.629
(0.893) 		0.63
(0.893) 		0.676
(0.904) 		0.473
(0.838) 		0.325
(0.734) 		0.573
(0.877)
ERBB3 41 (10%) 354 0.311
(0.72) 		0.383
(0.764) 		0.901
(0.978) 		0.265
(0.678) 		0.378
(0.764) 		0.217
(0.625) 		0.787
(0.938) 		0.896
(0.978) 		0.874
(0.974) 		0.688
(0.904)
THRAP3 14 (4%) 381 0.56
(0.876) 		0.34
(0.741) 		1
(1.00) 		1
(1.00) 		0.833
(0.955) 		0.783
(0.938) 		1
(1.00) 		0.795
(0.939) 		1
(1.00) 		0.905
(0.978)
SPTAN1 45 (11%) 350 0.326
(0.734) 		0.218
(0.625) 		0.263
(0.678) 		0.121
(0.513) 		0.226
(0.632) 		0.205
(0.616) 		0.238
(0.646) 		0.0784
(0.421) 		0.0405
(0.342) 		0.0666
(0.402)
NRAS 7 (2%) 388 0.345
(0.746) 		0.469
(0.835) 		1
(1.00) 		0.636
(0.893) 		0.794
(0.939) 		0.637
(0.893) 		0.13
(0.525) 		0.463
(0.827) 		0.029
(0.298) 		0.0829
(0.427)
RPTN 15 (4%) 380 0.844
(0.959) 		0.892
(0.978) 		0.873
(0.974) 		0.764
(0.935) 		1
(1.00) 		1
(1.00) 		0.752
(0.928) 		0.11
(0.489) 		0.865
(0.972) 		0.65
(0.898)
TMCO4 12 (3%) 383 0.478
(0.838) 		0.0372
(0.328) 		0.552
(0.876) 		0.286
(0.698) 		0.416
(0.791) 		0.0759
(0.42) 		0.39
(0.766) 		0.298
(0.71) 		0.0762
(0.42) 		0.0842
(0.429)
CNOT1 21 (5%) 374 0.12
(0.513) 		0.524
(0.87) 		0.367
(0.756) 		0.387
(0.765) 		0.616
(0.893) 		0.454
(0.824) 		0.528
(0.872) 		0.714
(0.908) 		0.95
(0.995) 		0.966
(1.00)
PARD3 22 (6%) 373 0.78
(0.938) 		0.586
(0.884) 		0.422
(0.796) 		0.367
(0.756) 		0.695
(0.904) 		0.853
(0.965) 		0.159
(0.582) 		0.605
(0.893) 		0.534
(0.876) 		0.593
(0.888)
EZR 12 (3%) 383 0.3
(0.711) 		0.894
(0.978) 		1
(1.00) 		0.382
(0.764) 		0.568
(0.876) 		0.87
(0.974) 		0.701
(0.904) 		0.32
(0.729) 		0.949
(0.995) 		0.747
(0.926)
MOAP1 7 (2%) 388 0.626
(0.893) 		0.234
(0.642) 		0.523
(0.87) 		0.601
(0.893) 		0.0659
(0.402) 		0.641
(0.893) 		0.551
(0.876) 		0.604
(0.893) 		0.867
(0.972) 		0.693
(0.904)
SF3B1 24 (6%) 371 0.128
(0.52) 		0.79
(0.938) 		0.505
(0.858) 		0.458
(0.824) 		0.83
(0.955) 		0.614
(0.893) 		0.963
(1) 		0.936
(0.991) 		0.217
(0.625) 		0.329
(0.734)
RUNX1 13 (3%) 382 0.0562
(0.382) 		0.611
(0.893) 		0.26
(0.677) 		0.518
(0.866) 		0.0834
(0.427) 		0.0479
(0.365) 		0.754
(0.928) 		0.827
(0.955) 		0.928
(0.989) 		0.544
(0.876)
MEGF8 20 (5%) 375 0.119
(0.513) 		0.361
(0.756) 		0.688
(0.904) 		1
(1.00) 		0.123
(0.516) 		0.54
(0.876) 		0.915
(0.982) 		0.669
(0.901) 		1
(1.00) 		0.511
(0.858)
CASP8 14 (4%) 381 0.528
(0.872) 		0.374
(0.762) 		0.0816
(0.427) 		0.1
(0.466) 		0.541
(0.876) 		0.575
(0.879) 		0.323
(0.734) 		0.204
(0.616) 		0.66
(0.898) 		0.693
(0.904)
USP28 13 (3%) 382 0.855
(0.966) 		0.654
(0.898) 		0.584
(0.884) 		0.397
(0.773) 		0.718
(0.909) 		1
(1.00) 		0.62
(0.893) 		0.487
(0.843) 		0.95
(0.995) 		0.838
(0.955)
SETD2 27 (7%) 368 0.771
(0.938) 		0.458
(0.824) 		0.505
(0.858) 		0.827
(0.955) 		0.847
(0.96) 		0.82
(0.951) 		0.142
(0.558) 		0.786
(0.938) 		0.375
(0.762) 		0.506
(0.858)
EME1 5 (1%) 390 0.148
(0.565) 		0.326
(0.734) 		0.694
(0.904) 		0.284
(0.697) 		0.731
(0.918) 		0.336
(0.74) 		0.722
(0.909) 		0.481
(0.838) 		0.273
(0.691) 		0.288
(0.699)
ADC 5 (1%) 390 0.904
(0.978) 		0.871
(0.974) 		0.694
(0.904) 		0.703
(0.905) 		1
(1.00) 		1
(1.00) 		0.863
(0.972) 		0.456
(0.824) 		1
(1.00) 		0.796
(0.939)
AHR 22 (6%) 373 0.541
(0.876) 		0.0535
(0.373) 		0.155
(0.58) 		0.781
(0.938) 		0.0648
(0.402) 		0.0748
(0.42) 		0.666
(0.901) 		0.312
(0.72) 		0.535
(0.876) 		0.512
(0.858)
EIF4A2 11 (3%) 384 0.39
(0.766) 		0.808
(0.946) 		0.402
(0.774) 		0.612
(0.893) 		0.497
(0.851) 		0.262
(0.677) 		0.0903
(0.437) 		0.139
(0.558) 		0.882
(0.976) 		0.481
(0.838)
EPHA2 19 (5%) 376 0.838
(0.955) 		0.0203
(0.25) 		0.637
(0.893) 		0.493
(0.848) 		0.165
(0.582) 		1
(1.00) 		0.447
(0.821) 		0.159
(0.582) 		0.59
(0.886) 		0.369
(0.756)
OGDH 19 (5%) 376 0.0573
(0.383) 		0.244
(0.655) 		0.881
(0.976) 		0.564
(0.876) 		0.677
(0.904) 		0.867
(0.972) 		0.449
(0.821) 		0.313
(0.72) 		0.262
(0.677) 		0.636
(0.893)
POU3F1 3 (1%) 392 0.141
(0.558) 		0.164
(0.582) 		0.0307
(0.307) 		0.632
(0.893) 		0.175
(0.583) 		0.79
(0.938) 		0.247
(0.661) 		0.624
(0.893) 		0.034
(0.316) 		0.12
(0.513)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TP53 MUTATED 42 86 48 19
TP53 WILD-TYPE 120 51 11 15

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TP53 MUTATED 71 73 21 31
TP53 WILD-TYPE 64 39 48 48

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.0092

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
TP53 MUTATED 60 37 65
TP53 WILD-TYPE 60 69 38

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
TP53 MUTATED 42 46 60 14
TP53 WILD-TYPE 45 68 38 16

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TP53 MUTATED 59 73 62
TP53 WILD-TYPE 55 100 42

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TP53 MUTATED 60 33 101
TP53 WILD-TYPE 56 73 68

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TP53 MUTATED 62 41 92
TP53 WILD-TYPE 57 55 85
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00504 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
TP53 MUTATED 55 46 33 37 24
TP53 WILD-TYPE 31 53 56 28 29

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.25

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TP53 MUTATED 57 16 55 60
TP53 WILD-TYPE 36 27 72 59

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0015

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
TP53 MUTATED 33 18 49 33 3 52
TP53 WILD-TYPE 41 29 39 32 24 29

Figure S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S11.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RB1 MUTATED 5 32 29 4
RB1 WILD-TYPE 157 105 30 30

Figure S10.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0321 (Fisher's exact test), Q value = 0.32

Table S12.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RB1 MUTATED 31 14 7 18
RB1 WILD-TYPE 104 98 62 61

Figure S11.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0021

Table S13.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RB1 MUTATED 28 6 27
RB1 WILD-TYPE 92 100 76

Figure S12.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00017 (Fisher's exact test), Q value = 0.0066

Table S14.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RB1 MUTATED 18 9 30 4
RB1 WILD-TYPE 69 105 68 26

Figure S13.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0015

Table S15.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RB1 MUTATED 31 14 23
RB1 WILD-TYPE 83 159 81

Figure S14.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S16.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RB1 MUTATED 16 6 46
RB1 WILD-TYPE 100 100 123

Figure S15.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.68

Table S17.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RB1 MUTATED 21 12 36
RB1 WILD-TYPE 98 84 141
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.55

Table S18.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RB1 MUTATED 23 18 13 8 7
RB1 WILD-TYPE 63 81 76 57 46
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.087

Table S19.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RB1 MUTATED 29 5 17 17
RB1 WILD-TYPE 64 38 110 102

Figure S16.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S20.  Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RB1 MUTATED 10 4 16 7 0 31
RB1 WILD-TYPE 64 43 72 58 27 50

Figure S17.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.76

Table S21.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ELF3 MUTATED 19 15 5 7
ELF3 WILD-TYPE 143 122 54 27
'ELF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.48

Table S22.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ELF3 MUTATED 9 18 8 11
ELF3 WILD-TYPE 126 94 61 68
'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 0.89

Table S23.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ELF3 MUTATED 10 13 10
ELF3 WILD-TYPE 110 93 93
'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0631 (Fisher's exact test), Q value = 0.4

Table S24.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ELF3 MUTATED 10 17 5 1
ELF3 WILD-TYPE 77 97 93 29
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.29

Table S25.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ELF3 MUTATED 7 28 10
ELF3 WILD-TYPE 107 145 94

Figure S18.  Get High-res Image Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0415 (Fisher's exact test), Q value = 0.34

Table S26.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ELF3 MUTATED 16 17 12
ELF3 WILD-TYPE 100 89 157

Figure S19.  Get High-res Image Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.69

Table S27.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ELF3 MUTATED 10 15 21
ELF3 WILD-TYPE 109 81 156
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 0.74

Table S28.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ELF3 MUTATED 7 15 8 11 5
ELF3 WILD-TYPE 79 84 81 54 48
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 0.76

Table S29.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ELF3 MUTATED 8 8 16 13
ELF3 WILD-TYPE 85 35 111 106
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.608 (Fisher's exact test), Q value = 0.89

Table S30.  Gene #3: 'ELF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ELF3 MUTATED 7 7 12 10 3 6
ELF3 WILD-TYPE 67 40 76 55 24 75
'TSC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.74

Table S31.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TSC1 MUTATED 18 11 2 2
TSC1 WILD-TYPE 144 126 57 32
'TSC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 0.98

Table S32.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TSC1 MUTATED 10 9 7 7
TSC1 WILD-TYPE 125 103 62 72
'TSC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.72

Table S33.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
TSC1 MUTATED 11 11 5
TSC1 WILD-TYPE 109 95 98
'TSC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.62

Table S34.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
TSC1 MUTATED 5 14 5 3
TSC1 WILD-TYPE 82 100 93 27
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.52

Table S35.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TSC1 MUTATED 12 17 4
TSC1 WILD-TYPE 102 156 100
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 0.64

Table S36.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TSC1 MUTATED 11 12 10
TSC1 WILD-TYPE 105 94 159
'TSC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.56

Table S37.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TSC1 MUTATED 10 12 10
TSC1 WILD-TYPE 109 84 167
'TSC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0657 (Fisher's exact test), Q value = 0.4

Table S38.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
TSC1 MUTATED 4 13 6 2 7
TSC1 WILD-TYPE 82 86 83 63 46
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 0.89

Table S39.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TSC1 MUTATED 5 3 12 12
TSC1 WILD-TYPE 88 40 115 107
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.71 (Fisher's exact test), Q value = 0.91

Table S40.  Gene #4: 'TSC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
TSC1 MUTATED 7 3 8 8 2 4
TSC1 WILD-TYPE 67 44 80 57 25 77
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.73

Table S41.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
PIK3CA MUTATED 37 24 17 8
PIK3CA WILD-TYPE 125 113 42 26
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.959 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
PIK3CA MUTATED 30 26 14 16
PIK3CA WILD-TYPE 105 86 55 63
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 0.96

Table S43.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
PIK3CA MUTATED 26 22 25
PIK3CA WILD-TYPE 94 84 78
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.948 (Fisher's exact test), Q value = 0.99

Table S44.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
PIK3CA MUTATED 19 27 20 7
PIK3CA WILD-TYPE 68 87 78 23
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.89

Table S45.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
PIK3CA MUTATED 24 35 26
PIK3CA WILD-TYPE 90 138 78
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 0.93

Table S46.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PIK3CA MUTATED 28 22 35
PIK3CA WILD-TYPE 88 84 134
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 0.99

Table S47.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
PIK3CA MUTATED 25 20 40
PIK3CA WILD-TYPE 94 76 137
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.946 (Fisher's exact test), Q value = 0.99

Table S48.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
PIK3CA MUTATED 20 20 18 16 11
PIK3CA WILD-TYPE 66 79 71 49 42
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 0.99

Table S49.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
PIK3CA MUTATED 22 8 28 26
PIK3CA WILD-TYPE 71 35 99 93
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 0.89

Table S50.  Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
PIK3CA MUTATED 17 8 23 10 7 19
PIK3CA WILD-TYPE 57 39 65 55 20 62
'RHOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.33

Table S51.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RHOB MUTATED 5 15 3 3
RHOB WILD-TYPE 157 122 56 31

Figure S20.  Get High-res Image Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RHOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.65

Table S52.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RHOB MUTATED 8 12 3 3
RHOB WILD-TYPE 127 100 66 76
'RHOB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 0.98

Table S53.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RHOB MUTATED 7 6 7
RHOB WILD-TYPE 113 100 96
'RHOB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.675 (Fisher's exact test), Q value = 0.9

Table S54.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RHOB MUTATED 6 9 4 1
RHOB WILD-TYPE 81 105 94 29
'RHOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.76

Table S55.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RHOB MUTATED 5 15 6
RHOB WILD-TYPE 109 158 98
'RHOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.58

Table S56.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RHOB MUTATED 11 8 7
RHOB WILD-TYPE 105 98 162
'RHOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S57.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RHOB MUTATED 8 5 13
RHOB WILD-TYPE 111 91 164
'RHOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.89

Table S58.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RHOB MUTATED 5 5 9 3 4
RHOB WILD-TYPE 81 94 80 62 49
'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 0.98

Table S59.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RHOB MUTATED 5 2 10 8
RHOB WILD-TYPE 88 41 117 111
'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 0.98

Table S60.  Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RHOB MUTATED 5 3 5 5 3 4
RHOB WILD-TYPE 69 44 83 60 24 77
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.56

Table S61.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
KDM6A MUTATED 42 38 10 13
KDM6A WILD-TYPE 120 99 49 21
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.03

Table S62.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
KDM6A MUTATED 25 36 28 14
KDM6A WILD-TYPE 110 76 41 65

Figure S21.  Get High-res Image Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0519 (Fisher's exact test), Q value = 0.37

Table S63.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
KDM6A MUTATED 22 33 30
KDM6A WILD-TYPE 98 73 73
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.63

Table S64.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
KDM6A MUTATED 21 37 22 5
KDM6A WILD-TYPE 66 77 76 25
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00263 (Fisher's exact test), Q value = 0.079

Table S65.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
KDM6A MUTATED 18 58 26
KDM6A WILD-TYPE 96 115 78

Figure S22.  Get High-res Image Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.2

Table S66.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
KDM6A MUTATED 31 38 33
KDM6A WILD-TYPE 85 68 136

Figure S23.  Get High-res Image Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 0.84

Table S67.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
KDM6A MUTATED 26 25 50
KDM6A WILD-TYPE 93 71 127
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.56

Table S68.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
KDM6A MUTATED 19 23 30 20 9
KDM6A WILD-TYPE 67 76 59 45 44
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0504 (Fisher's exact test), Q value = 0.37

Table S69.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
KDM6A MUTATED 18 14 41 24
KDM6A WILD-TYPE 75 29 86 95
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0285 (Fisher's exact test), Q value = 0.3

Table S70.  Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
KDM6A MUTATED 17 15 27 10 12 16
KDM6A WILD-TYPE 57 32 61 55 15 65

Figure S24.  Get High-res Image Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 0.75

Table S71.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CDKN2A MUTATED 11 6 5 4
CDKN2A WILD-TYPE 151 131 54 30
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0156 (Fisher's exact test), Q value = 0.24

Table S72.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CDKN2A MUTATED 11 6 0 9
CDKN2A WILD-TYPE 124 106 69 70

Figure S25.  Get High-res Image Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.9

Table S73.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CDKN2A MUTATED 7 7 9
CDKN2A WILD-TYPE 113 99 94
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0281 (Fisher's exact test), Q value = 0.3

Table S74.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CDKN2A MUTATED 1 10 8 4
CDKN2A WILD-TYPE 86 104 90 26

Figure S26.  Get High-res Image Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.59

Table S75.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CDKN2A MUTATED 5 10 11
CDKN2A WILD-TYPE 109 163 93
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 0.82

Table S76.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CDKN2A MUTATED 5 7 14
CDKN2A WILD-TYPE 111 99 155
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S77.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CDKN2A MUTATED 8 5 13
CDKN2A WILD-TYPE 111 91 164
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0544 (Fisher's exact test), Q value = 0.38

Table S78.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
CDKN2A MUTATED 11 5 3 6 1
CDKN2A WILD-TYPE 75 94 86 59 52
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.34

Table S79.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CDKN2A MUTATED 11 0 8 5
CDKN2A WILD-TYPE 82 43 119 114

Figure S27.  Get High-res Image Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.57

Table S80.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
CDKN2A MUTATED 1 2 5 6 1 9
CDKN2A WILD-TYPE 73 45 83 59 26 72
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.89

Table S81.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ARID1A MUTATED 35 38 16 8
ARID1A WILD-TYPE 127 99 43 26
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 0.75

Table S82.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ARID1A MUTATED 28 34 15 20
ARID1A WILD-TYPE 107 78 54 59
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 0.94

Table S83.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ARID1A MUTATED 31 23 23
ARID1A WILD-TYPE 89 83 80
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.523 (Fisher's exact test), Q value = 0.87

Table S84.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ARID1A MUTATED 23 28 18 8
ARID1A WILD-TYPE 64 86 80 22
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 0.88

Table S85.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ARID1A MUTATED 31 44 22
ARID1A WILD-TYPE 83 129 82
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 0.94

Table S86.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ARID1A MUTATED 30 28 39
ARID1A WILD-TYPE 86 78 130
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0778 (Fisher's exact test), Q value = 0.42

Table S87.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ARID1A MUTATED 26 32 38
ARID1A WILD-TYPE 93 64 139
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.58

Table S88.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ARID1A MUTATED 16 28 17 17 18
ARID1A WILD-TYPE 70 71 72 48 35
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.7

Table S89.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ARID1A MUTATED 18 15 31 30
ARID1A WILD-TYPE 75 28 96 89
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.34

Table S90.  Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ARID1A MUTATED 22 15 27 14 2 14
ARID1A WILD-TYPE 52 32 61 51 25 67

Figure S28.  Get High-res Image Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0304 (Fisher's exact test), Q value = 0.31

Table S91.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
STAG2 MUTATED 30 13 5 8
STAG2 WILD-TYPE 132 124 54 26

Figure S29.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00365 (Fisher's exact test), Q value = 0.095

Table S92.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
STAG2 MUTATED 19 13 19 5
STAG2 WILD-TYPE 116 99 50 74

Figure S30.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.48

Table S93.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
STAG2 MUTATED 14 23 14
STAG2 WILD-TYPE 106 83 89
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.6

Table S94.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
STAG2 MUTATED 13 24 10 4
STAG2 WILD-TYPE 74 90 88 26
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.79

Table S95.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
STAG2 MUTATED 14 29 12
STAG2 WILD-TYPE 100 144 92
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00692 (Fisher's exact test), Q value = 0.16

Table S96.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
STAG2 MUTATED 12 25 18
STAG2 WILD-TYPE 104 81 151

Figure S31.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.36

Table S97.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
STAG2 MUTATED 16 7 32
STAG2 WILD-TYPE 103 89 145

Figure S32.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.59

Table S98.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
STAG2 MUTATED 10 9 19 10 7
STAG2 WILD-TYPE 76 90 70 55 46
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0208 (Fisher's exact test), Q value = 0.25

Table S99.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
STAG2 MUTATED 11 1 25 14
STAG2 WILD-TYPE 82 42 102 105

Figure S33.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.36

Table S100.  Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
STAG2 MUTATED 9 2 15 6 8 11
STAG2 WILD-TYPE 65 45 73 59 19 70

Figure S34.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 0.88

Table S101.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZFP36L1 MUTATED 10 8 3 4
ZFP36L1 WILD-TYPE 152 129 56 30
'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 0.89

Table S102.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZFP36L1 MUTATED 6 9 4 6
ZFP36L1 WILD-TYPE 129 103 65 73
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 0.72

Table S103.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ZFP36L1 MUTATED 6 4 9
ZFP36L1 WILD-TYPE 114 102 94
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 0.99

Table S104.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ZFP36L1 MUTATED 4 7 6 2
ZFP36L1 WILD-TYPE 83 107 92 28
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.896 (Fisher's exact test), Q value = 0.98

Table S105.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZFP36L1 MUTATED 8 10 7
ZFP36L1 WILD-TYPE 106 163 97
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.64

Table S106.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZFP36L1 MUTATED 10 8 7
ZFP36L1 WILD-TYPE 106 98 162
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.89

Table S107.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZFP36L1 MUTATED 9 7 9
ZFP36L1 WILD-TYPE 110 89 168
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.76

Table S108.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ZFP36L1 MUTATED 4 5 4 6 6
ZFP36L1 WILD-TYPE 82 94 85 59 47
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 0.98

Table S109.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZFP36L1 MUTATED 5 3 7 9
ZFP36L1 WILD-TYPE 88 40 120 110
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.241 (Fisher's exact test), Q value = 0.65

Table S110.  Gene #11: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ZFP36L1 MUTATED 6 4 9 2 0 3
ZFP36L1 WILD-TYPE 68 43 79 63 27 78
'CDKN1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.704 (Fisher's exact test), Q value = 0.9

Table S111.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CDKN1A MUTATED 18 10 5 2
CDKN1A WILD-TYPE 144 127 54 32
'CDKN1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.62

Table S112.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CDKN1A MUTATED 10 9 4 12
CDKN1A WILD-TYPE 125 103 65 67
'CDKN1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.72

Table S113.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CDKN1A MUTATED 7 12 10
CDKN1A WILD-TYPE 113 94 93
'CDKN1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0334 (Fisher's exact test), Q value = 0.32

Table S114.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CDKN1A MUTATED 3 17 7 2
CDKN1A WILD-TYPE 84 97 91 28

Figure S35.  Get High-res Image Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.76

Table S115.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CDKN1A MUTATED 8 19 7
CDKN1A WILD-TYPE 106 154 97
'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.75

Table S116.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CDKN1A MUTATED 11 12 11
CDKN1A WILD-TYPE 105 94 158
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0289 (Fisher's exact test), Q value = 0.3

Table S117.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CDKN1A MUTATED 5 14 16
CDKN1A WILD-TYPE 114 82 161

Figure S36.  Get High-res Image Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.58

Table S118.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
CDKN1A MUTATED 4 13 10 6 2
CDKN1A WILD-TYPE 82 86 79 59 51
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 0.9

Table S119.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CDKN1A MUTATED 6 5 13 10
CDKN1A WILD-TYPE 87 38 114 109
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 0.89

Table S120.  Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
CDKN1A MUTATED 4 6 8 6 4 6
CDKN1A WILD-TYPE 70 41 80 59 23 75
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.88

Table S121.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
EP300 MUTATED 22 23 12 4
EP300 WILD-TYPE 140 114 47 30
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 0.97

Table S122.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
EP300 MUTATED 23 16 9 13
EP300 WILD-TYPE 112 96 60 66
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 0.79

Table S123.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EP300 MUTATED 19 11 16
EP300 WILD-TYPE 101 95 87
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.664 (Fisher's exact test), Q value = 0.9

Table S124.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EP300 MUTATED 11 14 15 6
EP300 WILD-TYPE 76 100 83 24
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.75

Table S125.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
EP300 MUTATED 20 22 19
EP300 WILD-TYPE 94 151 85
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 0.72

Table S126.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EP300 MUTATED 18 12 31
EP300 WILD-TYPE 98 94 138
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 0.9

Table S127.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
EP300 MUTATED 17 13 31
EP300 WILD-TYPE 102 83 146
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.89

Table S128.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
EP300 MUTATED 9 16 15 12 9
EP300 WILD-TYPE 77 83 74 53 44
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.74

Table S129.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
EP300 MUTATED 19 5 20 14
EP300 WILD-TYPE 74 38 107 105
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.152 (Fisher's exact test), Q value = 0.57

Table S130.  Gene #13: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
EP300 MUTATED 9 4 16 8 2 19
EP300 WILD-TYPE 65 43 72 57 25 62
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.735 (Fisher's exact test), Q value = 0.92

Table S131.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
MLL2 MUTATED 42 43 18 9
MLL2 WILD-TYPE 120 94 41 25
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.89

Table S132.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
MLL2 MUTATED 43 34 18 19
MLL2 WILD-TYPE 92 78 51 60
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 0.98

Table S133.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MLL2 MUTATED 35 29 31
MLL2 WILD-TYPE 85 77 72
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.48

Table S134.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MLL2 MUTATED 20 29 33 13
MLL2 WILD-TYPE 67 85 65 17
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 0.96

Table S135.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
MLL2 MUTATED 31 49 32
MLL2 WILD-TYPE 83 124 72
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.939 (Fisher's exact test), Q value = 0.99

Table S136.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MLL2 MUTATED 32 30 50
MLL2 WILD-TYPE 84 76 119
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.56

Table S137.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
MLL2 MUTATED 29 24 60
MLL2 WILD-TYPE 90 72 117
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 0.56

Table S138.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
MLL2 MUTATED 24 27 24 27 11
MLL2 WILD-TYPE 62 72 65 38 42
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.68

Table S139.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
MLL2 MUTATED 31 9 39 28
MLL2 WILD-TYPE 62 34 88 91
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.61

Table S140.  Gene #14: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
MLL2 MUTATED 15 10 30 22 5 25
MLL2 WILD-TYPE 59 37 58 43 22 56
'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S141.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FGFR3 MUTATED 43 7 2 4
FGFR3 WILD-TYPE 119 130 57 30

Figure S37.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S142.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FGFR3 MUTATED 8 9 22 17
FGFR3 WILD-TYPE 127 103 47 62

Figure S38.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0015

Table S143.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FGFR3 MUTATED 7 29 12
FGFR3 WILD-TYPE 113 77 91

Figure S39.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S144.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FGFR3 MUTATED 5 34 6 3
FGFR3 WILD-TYPE 82 80 92 27

Figure S40.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0021

Table S145.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FGFR3 MUTATED 6 40 9
FGFR3 WILD-TYPE 108 133 95

Figure S41.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S146.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FGFR3 MUTATED 6 38 11
FGFR3 WILD-TYPE 110 68 158

Figure S42.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S147.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FGFR3 MUTATED 5 9 42
FGFR3 WILD-TYPE 114 87 135

Figure S43.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S148.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
FGFR3 MUTATED 7 7 32 9 1
FGFR3 WILD-TYPE 79 92 57 56 52

Figure S44.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S149.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FGFR3 MUTATED 3 2 36 11
FGFR3 WILD-TYPE 90 41 91 108

Figure S45.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00067

Table S150.  Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
FGFR3 MUTATED 4 2 15 8 20 3
FGFR3 WILD-TYPE 70 45 73 57 7 78

Figure S46.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ERCC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00309 (Fisher's exact test), Q value = 0.087

Table S151.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ERCC2 MUTATED 6 19 7 6
ERCC2 WILD-TYPE 156 118 52 28

Figure S47.  Get High-res Image Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ERCC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.082 (Fisher's exact test), Q value = 0.43

Table S152.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ERCC2 MUTATED 10 17 3 8
ERCC2 WILD-TYPE 125 95 66 71
'ERCC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.046 (Fisher's exact test), Q value = 0.36

Table S153.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ERCC2 MUTATED 7 8 16
ERCC2 WILD-TYPE 113 98 87

Figure S48.  Get High-res Image Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ERCC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.67

Table S154.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ERCC2 MUTATED 4 13 12 2
ERCC2 WILD-TYPE 83 101 86 28
'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 0.94

Table S155.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ERCC2 MUTATED 9 17 11
ERCC2 WILD-TYPE 105 156 93
'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.707 (Fisher's exact test), Q value = 0.91

Table S156.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ERCC2 MUTATED 11 8 18
ERCC2 WILD-TYPE 105 98 151
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0968 (Fisher's exact test), Q value = 0.45

Table S157.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ERCC2 MUTATED 7 14 16
ERCC2 WILD-TYPE 112 82 161
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.77

Table S158.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ERCC2 MUTATED 7 13 5 8 4
ERCC2 WILD-TYPE 79 86 84 57 49
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.7

Table S159.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ERCC2 MUTATED 11 6 13 7
ERCC2 WILD-TYPE 82 37 114 112
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00991 (Fisher's exact test), Q value = 0.19

Table S160.  Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ERCC2 MUTATED 4 8 10 2 0 13
ERCC2 WILD-TYPE 70 39 78 63 27 68

Figure S49.  Get High-res Image Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.82

Table S161.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CREBBP MUTATED 19 13 10 5
CREBBP WILD-TYPE 143 124 49 29
'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.8

Table S162.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CREBBP MUTATED 20 15 7 6
CREBBP WILD-TYPE 115 97 62 73
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 0.89

Table S163.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CREBBP MUTATED 14 10 14
CREBBP WILD-TYPE 106 96 89
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.817 (Fisher's exact test), Q value = 0.95

Table S164.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CREBBP MUTATED 9 14 13 2
CREBBP WILD-TYPE 78 100 85 28
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.58

Table S165.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CREBBP MUTATED 16 15 16
CREBBP WILD-TYPE 98 158 88
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.88

Table S166.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CREBBP MUTATED 12 11 24
CREBBP WILD-TYPE 104 95 145
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00244 (Fisher's exact test), Q value = 0.076

Table S167.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CREBBP MUTATED 15 3 29
CREBBP WILD-TYPE 104 93 148

Figure S50.  Get High-res Image Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0328 (Fisher's exact test), Q value = 0.32

Table S168.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
CREBBP MUTATED 17 5 9 9 7
CREBBP WILD-TYPE 69 94 80 56 46

Figure S51.  Get High-res Image Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0849 (Fisher's exact test), Q value = 0.43

Table S169.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CREBBP MUTATED 16 1 16 14
CREBBP WILD-TYPE 77 42 111 105
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 0.82

Table S170.  Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
CREBBP MUTATED 10 2 11 7 4 13
CREBBP WILD-TYPE 64 45 77 58 23 68
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.76

Table S171.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
HRAS MUTATED 10 4 1 2
HRAS WILD-TYPE 152 133 58 32
'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.24

Table S172.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
HRAS MUTATED 4 2 2 9
HRAS WILD-TYPE 131 110 67 70

Figure S52.  Get High-res Image Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.86

Table S173.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
HRAS MUTATED 4 7 4
HRAS WILD-TYPE 116 99 99
'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.844 (Fisher's exact test), Q value = 0.96

Table S174.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
HRAS MUTATED 3 5 5 2
HRAS WILD-TYPE 84 109 93 28
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 0.9

Table S175.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
HRAS MUTATED 4 7 6
HRAS WILD-TYPE 110 166 98
'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.778 (Fisher's exact test), Q value = 0.94

Table S176.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
HRAS MUTATED 4 4 9
HRAS WILD-TYPE 112 102 160
'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S177.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
HRAS MUTATED 5 4 8
HRAS WILD-TYPE 114 92 169
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.71

Table S178.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
HRAS MUTATED 5 3 7 1 1
HRAS WILD-TYPE 81 96 82 64 52
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.73

Table S179.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
HRAS MUTATED 6 2 6 2
HRAS WILD-TYPE 87 41 121 117
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.6

Table S180.  Gene #18: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
HRAS MUTATED 3 2 3 0 1 7
HRAS WILD-TYPE 71 45 85 65 26 74
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.81

Table S181.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FOXA1 MUTATED 4 7 1 2
FOXA1 WILD-TYPE 158 130 58 32
'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 0.67

Table S182.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FOXA1 MUTATED 2 7 2 3
FOXA1 WILD-TYPE 133 105 67 76
'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 0.95

Table S183.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FOXA1 MUTATED 4 5 3
FOXA1 WILD-TYPE 116 101 100
'FOXA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.58

Table S184.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FOXA1 MUTATED 4 7 1 0
FOXA1 WILD-TYPE 83 107 97 30
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.73

Table S185.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FOXA1 MUTATED 5 7 1
FOXA1 WILD-TYPE 109 166 103
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.63

Table S186.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FOXA1 MUTATED 4 6 3
FOXA1 WILD-TYPE 112 100 166
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.7

Table S187.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FOXA1 MUTATED 3 6 5
FOXA1 WILD-TYPE 116 90 172
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 0.88

Table S188.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
FOXA1 MUTATED 1 5 3 2 3
FOXA1 WILD-TYPE 85 94 86 63 50
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.3

Table S189.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FOXA1 MUTATED 0 4 4 5
FOXA1 WILD-TYPE 93 39 123 114

Figure S53.  Get High-res Image Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.52

Table S190.  Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
FOXA1 MUTATED 3 4 4 2 0 0
FOXA1 WILD-TYPE 71 43 84 63 27 81
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0593 (Fisher's exact test), Q value = 0.39

Table S191.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
KRAS MUTATED 10 2 0 1
KRAS WILD-TYPE 152 135 59 33
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.922 (Fisher's exact test), Q value = 0.98

Table S192.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
KRAS MUTATED 4 5 2 2
KRAS WILD-TYPE 131 107 67 77
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 0.88

Table S193.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
KRAS MUTATED 2 3 4
KRAS WILD-TYPE 118 103 99
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 0.58

Table S194.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
KRAS MUTATED 0 3 5 1
KRAS WILD-TYPE 87 111 93 29
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.76

Table S195.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
KRAS MUTATED 6 5 2
KRAS WILD-TYPE 108 168 102
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.58

Table S196.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
KRAS MUTATED 1 5 7
KRAS WILD-TYPE 115 101 162
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.84

Table S197.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
KRAS MUTATED 4 1 7
KRAS WILD-TYPE 115 95 170
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 0.82

Table S198.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
KRAS MUTATED 5 1 3 2 1
KRAS WILD-TYPE 81 98 86 63 52
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 0.94

Table S199.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
KRAS MUTATED 3 1 5 2
KRAS WILD-TYPE 90 42 122 117
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 0.88

Table S200.  Gene #20: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
KRAS MUTATED 2 1 3 0 1 4
KRAS WILD-TYPE 72 46 85 65 26 77
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.62

Table S201.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RHOA MUTATED 4 10 2 2
RHOA WILD-TYPE 158 127 57 32
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 0.75

Table S202.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RHOA MUTATED 3 7 3 5
RHOA WILD-TYPE 132 105 66 74
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.78

Table S203.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RHOA MUTATED 6 6 2
RHOA WILD-TYPE 114 100 101
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.59

Table S204.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RHOA MUTATED 6 6 1 1
RHOA WILD-TYPE 81 108 97 29
'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.79

Table S205.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RHOA MUTATED 4 11 3
RHOA WILD-TYPE 110 162 101
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.84

Table S206.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RHOA MUTATED 5 7 6
RHOA WILD-TYPE 111 99 163
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0528 (Fisher's exact test), Q value = 0.37

Table S207.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RHOA MUTATED 4 9 5
RHOA WILD-TYPE 115 87 172
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.089 (Fisher's exact test), Q value = 0.44

Table S208.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RHOA MUTATED 1 9 2 3 3
RHOA WILD-TYPE 85 90 87 62 50
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 0.94

Table S209.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RHOA MUTATED 3 3 6 6
RHOA WILD-TYPE 90 40 121 113
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 0.89

Table S210.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RHOA MUTATED 3 3 6 4 0 2
RHOA WILD-TYPE 71 44 82 61 27 79
'KIAA1267 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.3

Table S211.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
KIAA1267 MUTATED 13 11 0 0
KIAA1267 WILD-TYPE 149 126 59 34

Figure S54.  Get High-res Image Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KIAA1267 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0626 (Fisher's exact test), Q value = 0.4

Table S212.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
KIAA1267 MUTATED 5 9 8 2
KIAA1267 WILD-TYPE 130 103 61 77
'KIAA1267 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.955 (Fisher's exact test), Q value = 1

Table S213.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
KIAA1267 MUTATED 7 6 5
KIAA1267 WILD-TYPE 113 100 98
'KIAA1267 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 0.89

Table S214.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
KIAA1267 MUTATED 5 6 4 3
KIAA1267 WILD-TYPE 82 108 94 27
'KIAA1267 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.86

Table S215.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
KIAA1267 MUTATED 7 13 4
KIAA1267 WILD-TYPE 107 160 100
'KIAA1267 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.62

Table S216.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
KIAA1267 MUTATED 7 10 7
KIAA1267 WILD-TYPE 109 96 162
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.69

Table S217.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
KIAA1267 MUTATED 4 6 14
KIAA1267 WILD-TYPE 115 90 163
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.785 (Fisher's exact test), Q value = 0.94

Table S218.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
KIAA1267 MUTATED 5 5 8 4 2
KIAA1267 WILD-TYPE 81 94 81 61 51
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0811 (Fisher's exact test), Q value = 0.43

Table S219.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
KIAA1267 MUTATED 3 2 14 5
KIAA1267 WILD-TYPE 90 41 113 114
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.58

Table S220.  Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
KIAA1267 MUTATED 3 3 10 3 3 2
KIAA1267 WILD-TYPE 71 44 78 62 24 79
'MLL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0137 (Fisher's exact test), Q value = 0.24

Table S221.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
MLL MUTATED 11 20 11 1
MLL WILD-TYPE 151 117 48 33

Figure S55.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 0.76

Table S222.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
MLL MUTATED 18 15 5 6
MLL WILD-TYPE 117 97 64 73
'MLL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0615 (Fisher's exact test), Q value = 0.4

Table S223.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MLL MUTATED 7 11 16
MLL WILD-TYPE 113 95 87
'MLL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.58

Table S224.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MLL MUTATED 6 10 16 2
MLL WILD-TYPE 81 104 82 28
'MLL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0853 (Fisher's exact test), Q value = 0.43

Table S225.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
MLL MUTATED 15 13 16
MLL WILD-TYPE 99 160 88
'MLL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0757 (Fisher's exact test), Q value = 0.42

Table S226.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MLL MUTATED 17 6 21
MLL WILD-TYPE 99 100 148
'MLL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.3

Table S227.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
MLL MUTATED 16 16 12
MLL WILD-TYPE 103 80 165

Figure S56.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MLL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0192 (Fisher's exact test), Q value = 0.25

Table S228.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
MLL MUTATED 12 17 3 5 7
MLL WILD-TYPE 74 82 86 60 46

Figure S57.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.25

Table S229.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
MLL MUTATED 15 7 6 14
MLL WILD-TYPE 78 36 121 105

Figure S58.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.041 (Fisher's exact test), Q value = 0.34

Table S230.  Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
MLL MUTATED 9 8 3 10 1 11
MLL WILD-TYPE 65 39 85 55 26 70

Figure S59.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0702 (Fisher's exact test), Q value = 0.41

Table S231.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FAT1 MUTATED 29 15 4 2
FAT1 WILD-TYPE 133 122 55 32
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0666 (Fisher's exact test), Q value = 0.4

Table S232.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FAT1 MUTATED 23 14 3 10
FAT1 WILD-TYPE 112 98 66 69
'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.63

Table S233.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FAT1 MUTATED 19 9 14
FAT1 WILD-TYPE 101 97 89
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.52

Table S234.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FAT1 MUTATED 12 12 10 8
FAT1 WILD-TYPE 75 102 88 22
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 0.88

Table S235.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FAT1 MUTATED 15 18 15
FAT1 WILD-TYPE 99 155 89
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.61

Table S236.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FAT1 MUTATED 9 14 25
FAT1 WILD-TYPE 107 92 144
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.48

Table S237.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FAT1 MUTATED 20 7 23
FAT1 WILD-TYPE 99 89 154
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.9

Table S238.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
FAT1 MUTATED 15 10 10 8 7
FAT1 WILD-TYPE 71 89 79 57 46
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.6

Table S239.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FAT1 MUTATED 16 2 18 13
FAT1 WILD-TYPE 77 41 109 106
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0878 (Fisher's exact test), Q value = 0.43

Table S240.  Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
FAT1 MUTATED 8 1 16 7 4 13
FAT1 WILD-TYPE 66 46 72 58 23 68
'KLF5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.56

Table S241.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
KLF5 MUTATED 12 4 3 4
KLF5 WILD-TYPE 150 133 56 30
'KLF5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.98 (Fisher's exact test), Q value = 1

Table S242.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
KLF5 MUTATED 7 7 4 5
KLF5 WILD-TYPE 128 105 65 74
'KLF5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.37

Table S243.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
KLF5 MUTATED 3 11 7
KLF5 WILD-TYPE 117 95 96

Figure S60.  Get High-res Image Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KLF5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 0.9

Table S244.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
KLF5 MUTATED 4 10 6 1
KLF5 WILD-TYPE 83 104 92 29
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 0.89

Table S245.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
KLF5 MUTATED 7 12 4
KLF5 WILD-TYPE 107 161 100
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.71 (Fisher's exact test), Q value = 0.91

Table S246.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
KLF5 MUTATED 6 8 9
KLF5 WILD-TYPE 110 98 160
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.85

Table S247.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
KLF5 MUTATED 6 8 9
KLF5 WILD-TYPE 113 88 168
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.51

Table S248.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
KLF5 MUTATED 1 8 4 5 5
KLF5 WILD-TYPE 85 91 85 60 48
'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.25

Table S249.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
KLF5 MUTATED 1 6 7 8
KLF5 WILD-TYPE 92 37 120 111

Figure S61.  Get High-res Image Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 0.64

Table S250.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
KLF5 MUTATED 5 5 5 5 1 1
KLF5 WILD-TYPE 69 42 83 60 26 80
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 0.98

Table S251.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
PTEN MUTATED 5 5 3 1
PTEN WILD-TYPE 157 132 56 33
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0933 (Fisher's exact test), Q value = 0.45

Table S252.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
PTEN MUTATED 7 6 1 0
PTEN WILD-TYPE 128 106 68 79
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 0.84

Table S253.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
PTEN MUTATED 4 4 1
PTEN WILD-TYPE 116 102 102
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.76

Table S254.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
PTEN MUTATED 1 3 3 2
PTEN WILD-TYPE 86 111 95 28
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 0.9

Table S255.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
PTEN MUTATED 3 5 5
PTEN WILD-TYPE 111 168 99
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.58

Table S256.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PTEN MUTATED 1 4 8
PTEN WILD-TYPE 115 102 161
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S257.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
PTEN MUTATED 4 3 6
PTEN WILD-TYPE 115 93 171
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S258.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
PTEN MUTATED 4 3 3 2 1
PTEN WILD-TYPE 82 96 86 63 52
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.698 (Fisher's exact test), Q value = 0.9

Table S259.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
PTEN MUTATED 3 0 5 5
PTEN WILD-TYPE 90 43 122 114
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 0.93

Table S260.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
PTEN MUTATED 3 1 2 2 0 5
PTEN WILD-TYPE 71 46 86 63 27 76
'C3ORF70 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.9

Table S261.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
C3ORF70 MUTATED 8 4 3 2
C3ORF70 WILD-TYPE 154 133 56 32
'C3ORF70 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.58

Table S262.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
C3ORF70 MUTATED 7 7 0 3
C3ORF70 WILD-TYPE 128 105 69 76
'C3ORF70 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S263.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
C3ORF70 MUTATED 4 4 4
C3ORF70 WILD-TYPE 116 102 99
'C3ORF70 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.9

Table S264.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
C3ORF70 MUTATED 3 3 4 2
C3ORF70 WILD-TYPE 84 111 94 28
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.95 (Fisher's exact test), Q value = 0.99

Table S265.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
C3ORF70 MUTATED 5 7 5
C3ORF70 WILD-TYPE 109 166 99
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 0.88

Table S266.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
C3ORF70 MUTATED 3 5 9
C3ORF70 WILD-TYPE 113 101 160
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 0.94

Table S267.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
C3ORF70 MUTATED 5 3 9
C3ORF70 WILD-TYPE 114 93 168
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 0.88

Table S268.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
C3ORF70 MUTATED 5 4 3 1 4
C3ORF70 WILD-TYPE 81 95 86 64 49
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 0.94

Table S269.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
C3ORF70 MUTATED 5 1 4 6
C3ORF70 WILD-TYPE 88 42 123 113
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.929 (Fisher's exact test), Q value = 0.99

Table S270.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
C3ORF70 MUTATED 3 2 4 4 0 3
C3ORF70 WILD-TYPE 71 45 84 61 27 78
'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 0.8

Table S271.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
PSIP1 MUTATED 8 10 1 1
PSIP1 WILD-TYPE 154 127 58 33
'PSIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0225 (Fisher's exact test), Q value = 0.26

Table S272.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
PSIP1 MUTATED 3 12 2 3
PSIP1 WILD-TYPE 132 100 67 76

Figure S62.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.25

Table S273.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
PSIP1 MUTATED 4 11 2
PSIP1 WILD-TYPE 116 95 101

Figure S63.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PSIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.58

Table S274.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
PSIP1 MUTATED 4 10 2 1
PSIP1 WILD-TYPE 83 104 96 29
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.58

Table S275.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
PSIP1 MUTATED 3 13 4
PSIP1 WILD-TYPE 111 160 100
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.24

Table S276.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PSIP1 MUTATED 5 11 4
PSIP1 WILD-TYPE 111 95 165

Figure S64.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.052 (Fisher's exact test), Q value = 0.37

Table S277.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
PSIP1 MUTATED 2 4 14
PSIP1 WILD-TYPE 117 92 163
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00953 (Fisher's exact test), Q value = 0.19

Table S278.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
PSIP1 MUTATED 0 5 7 7 1
PSIP1 WILD-TYPE 86 94 82 58 52

Figure S65.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.32

Table S279.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
PSIP1 MUTATED 1 1 12 6
PSIP1 WILD-TYPE 92 42 115 113

Figure S66.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0174 (Fisher's exact test), Q value = 0.25

Table S280.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
PSIP1 MUTATED 1 1 8 6 3 1
PSIP1 WILD-TYPE 73 46 80 59 24 80

Figure S67.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.58

Table S281.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
MLL3 MUTATED 34 27 5 7
MLL3 WILD-TYPE 128 110 54 27
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 0.98

Table S282.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
MLL3 MUTATED 23 23 13 15
MLL3 WILD-TYPE 112 89 56 64
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.51

Table S283.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MLL3 MUTATED 19 28 18
MLL3 WILD-TYPE 101 78 85
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.63

Table S284.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MLL3 MUTATED 12 29 18 6
MLL3 WILD-TYPE 75 85 80 24
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.79

Table S285.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
MLL3 MUTATED 17 35 22
MLL3 WILD-TYPE 97 138 82
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 0.84

Table S286.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MLL3 MUTATED 19 24 31
MLL3 WILD-TYPE 97 82 138
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 0.9

Table S287.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
MLL3 MUTATED 20 17 37
MLL3 WILD-TYPE 99 79 140
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0941 (Fisher's exact test), Q value = 0.45

Table S288.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
MLL3 MUTATED 22 17 17 14 4
MLL3 WILD-TYPE 64 82 72 51 49
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0825 (Fisher's exact test), Q value = 0.43

Table S289.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
MLL3 MUTATED 23 6 28 15
MLL3 WILD-TYPE 70 37 99 104
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.88

Table S290.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
MLL3 MUTATED 10 7 22 12 5 16
MLL3 WILD-TYPE 64 40 66 53 22 65
'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.6

Table S291.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ASXL2 MUTATED 14 18 3 1
ASXL2 WILD-TYPE 148 119 56 33
'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 0.88

Table S292.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ASXL2 MUTATED 10 14 6 6
ASXL2 WILD-TYPE 125 98 63 73
'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0939 (Fisher's exact test), Q value = 0.45

Table S293.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ASXL2 MUTATED 5 10 12
ASXL2 WILD-TYPE 115 96 91
'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test), Q value = 0.62

Table S294.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ASXL2 MUTATED 6 13 8 0
ASXL2 WILD-TYPE 81 101 90 30
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 0.89

Table S295.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ASXL2 MUTATED 11 13 11
ASXL2 WILD-TYPE 103 160 93
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.89

Table S296.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ASXL2 MUTATED 13 8 14
ASXL2 WILD-TYPE 103 98 155
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 0.76

Table S297.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ASXL2 MUTATED 11 12 13
ASXL2 WILD-TYPE 108 84 164
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.542 (Fisher's exact test), Q value = 0.88

Table S298.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ASXL2 MUTATED 7 12 8 3 6
ASXL2 WILD-TYPE 79 87 81 62 47
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.77

Table S299.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ASXL2 MUTATED 7 7 10 11
ASXL2 WILD-TYPE 86 36 117 108
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 0.9

Table S300.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ASXL2 MUTATED 6 6 7 8 3 5
ASXL2 WILD-TYPE 68 41 81 57 24 76
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0896 (Fisher's exact test), Q value = 0.44

Table S301.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZBTB7B MUTATED 5 1 4 1
ZBTB7B WILD-TYPE 157 136 55 33
'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 0.95

Table S302.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZBTB7B MUTATED 4 4 2 1
ZBTB7B WILD-TYPE 131 108 67 78
'ZBTB7B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 0.94

Table S303.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ZBTB7B MUTATED 4 4 2
ZBTB7B WILD-TYPE 116 102 101
'ZBTB7B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 0.88

Table S304.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ZBTB7B MUTATED 2 4 2 2
ZBTB7B WILD-TYPE 85 110 96 28
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.88

Table S305.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZBTB7B MUTATED 2 7 2
ZBTB7B WILD-TYPE 112 166 102
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.77

Table S306.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZBTB7B MUTATED 2 5 4
ZBTB7B WILD-TYPE 114 101 165
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.75

Table S307.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZBTB7B MUTATED 5 3 3
ZBTB7B WILD-TYPE 114 93 174
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.227 (Fisher's exact test), Q value = 0.63

Table S308.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ZBTB7B MUTATED 0 4 2 2 3
ZBTB7B WILD-TYPE 86 95 87 63 50
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.84

Table S309.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZBTB7B MUTATED 2 2 2 5
ZBTB7B WILD-TYPE 91 41 125 114
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.018 (Fisher's exact test), Q value = 0.25

Table S310.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ZBTB7B MUTATED 5 2 0 0 2 2
ZBTB7B WILD-TYPE 69 45 88 65 25 79

Figure S68.  Get High-res Image Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RXRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0421 (Fisher's exact test), Q value = 0.34

Table S311.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RXRA MUTATED 7 15 1 1
RXRA WILD-TYPE 155 122 58 33

Figure S69.  Get High-res Image Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RXRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00865 (Fisher's exact test), Q value = 0.19

Table S312.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RXRA MUTATED 7 13 0 4
RXRA WILD-TYPE 128 99 69 75

Figure S70.  Get High-res Image Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RXRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 0.88

Table S313.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RXRA MUTATED 6 9 6
RXRA WILD-TYPE 114 97 97
'RXRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.69

Table S314.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RXRA MUTATED 3 8 6 4
RXRA WILD-TYPE 84 106 92 26
'RXRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.88

Table S315.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RXRA MUTATED 5 13 6
RXRA WILD-TYPE 109 160 98
'RXRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.67

Table S316.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RXRA MUTATED 5 10 9
RXRA WILD-TYPE 111 96 160
'RXRA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.74

Table S317.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RXRA MUTATED 6 9 9
RXRA WILD-TYPE 113 87 168
'RXRA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.061 (Fisher's exact test), Q value = 0.4

Table S318.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RXRA MUTATED 4 10 1 6 3
RXRA WILD-TYPE 82 89 88 59 50
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.76

Table S319.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RXRA MUTATED 4 5 9 6
RXRA WILD-TYPE 89 38 118 113
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0732 (Fisher's exact test), Q value = 0.42

Table S320.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RXRA MUTATED 4 6 9 1 0 4
RXRA WILD-TYPE 70 41 79 64 27 77
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.86

Table S321.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FBXW7 MUTATED 14 8 6 1
FBXW7 WILD-TYPE 148 129 53 33
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.52

Table S322.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FBXW7 MUTATED 16 7 2 5
FBXW7 WILD-TYPE 119 105 67 74
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.91

Table S323.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FBXW7 MUTATED 7 9 7
FBXW7 WILD-TYPE 113 97 96
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 0.81

Table S324.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FBXW7 MUTATED 6 5 10 2
FBXW7 WILD-TYPE 81 109 88 28
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 0.89

Table S325.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FBXW7 MUTATED 9 11 10
FBXW7 WILD-TYPE 105 162 94
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.58

Table S326.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FBXW7 MUTATED 6 6 18
FBXW7 WILD-TYPE 110 100 151
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.62

Table S327.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FBXW7 MUTATED 5 8 17
FBXW7 WILD-TYPE 114 88 160
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.63

Table S328.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
FBXW7 MUTATED 11 7 6 5 1
FBXW7 WILD-TYPE 75 92 83 60 52
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0572 (Fisher's exact test), Q value = 0.38

Table S329.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FBXW7 MUTATED 13 4 8 5
FBXW7 WILD-TYPE 80 39 119 114
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.62

Table S330.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
FBXW7 MUTATED 2 6 6 4 2 10
FBXW7 WILD-TYPE 72 41 82 61 25 71
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 0.95

Table S331.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RBM10 MUTATED 7 9 3 2
RBM10 WILD-TYPE 155 128 56 32
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.62

Table S332.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RBM10 MUTATED 10 8 3 1
RBM10 WILD-TYPE 125 104 66 78
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.84

Table S333.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RBM10 MUTATED 5 6 8
RBM10 WILD-TYPE 115 100 95
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.905 (Fisher's exact test), Q value = 0.98

Table S334.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RBM10 MUTATED 5 6 7 1
RBM10 WILD-TYPE 82 108 91 29
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.88

Table S335.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RBM10 MUTATED 5 9 8
RBM10 WILD-TYPE 109 164 96
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 0.98

Table S336.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RBM10 MUTATED 6 7 9
RBM10 WILD-TYPE 110 99 160
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.8

Table S337.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RBM10 MUTATED 5 8 9
RBM10 WILD-TYPE 114 88 168
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.806 (Fisher's exact test), Q value = 0.95

Table S338.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RBM10 MUTATED 4 8 4 4 2
RBM10 WILD-TYPE 82 91 85 61 51
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.71

Table S339.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RBM10 MUTATED 5 4 4 9
RBM10 WILD-TYPE 88 39 123 110
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.58

Table S340.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RBM10 MUTATED 3 6 4 6 0 3
RBM10 WILD-TYPE 71 41 84 59 27 78
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0049

Table S341.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
NFE2L2 MUTATED 18 1 1 4
NFE2L2 WILD-TYPE 144 136 58 30

Figure S71.  Get High-res Image Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0778 (Fisher's exact test), Q value = 0.42

Table S342.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
NFE2L2 MUTATED 11 3 2 8
NFE2L2 WILD-TYPE 124 109 67 71
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.51

Table S343.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
NFE2L2 MUTATED 11 3 7
NFE2L2 WILD-TYPE 109 103 96
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.07 (Fisher's exact test), Q value = 0.41

Table S344.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
NFE2L2 MUTATED 5 3 9 4
NFE2L2 WILD-TYPE 82 111 89 26
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.049

Table S345.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
NFE2L2 MUTATED 8 3 12
NFE2L2 WILD-TYPE 106 170 92

Figure S72.  Get High-res Image Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0086 (Fisher's exact test), Q value = 0.19

Table S346.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NFE2L2 MUTATED 6 1 16
NFE2L2 WILD-TYPE 110 105 153

Figure S73.  Get High-res Image Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0751 (Fisher's exact test), Q value = 0.42

Table S347.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
NFE2L2 MUTATED 12 4 7
NFE2L2 WILD-TYPE 107 92 170
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.66 (Fisher's exact test), Q value = 0.9

Table S348.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
NFE2L2 MUTATED 7 5 3 5 3
NFE2L2 WILD-TYPE 79 94 86 60 50
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.77

Table S349.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
NFE2L2 MUTATED 8 1 5 8
NFE2L2 WILD-TYPE 85 42 122 111
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.56

Table S350.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
NFE2L2 MUTATED 4 1 2 8 1 6
NFE2L2 WILD-TYPE 70 46 86 57 26 75
'CUL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.89

Table S351.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CUL1 MUTATED 6 5 4 2
CUL1 WILD-TYPE 156 132 55 32
'CUL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 0.98

Table S352.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CUL1 MUTATED 6 5 3 5
CUL1 WILD-TYPE 129 107 66 74
'CUL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.48

Table S353.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CUL1 MUTATED 9 2 3
CUL1 WILD-TYPE 111 104 100
'CUL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.71

Table S354.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CUL1 MUTATED 5 2 5 2
CUL1 WILD-TYPE 82 112 93 28
'CUL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.88

Table S355.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CUL1 MUTATED 4 8 7
CUL1 WILD-TYPE 110 165 97
'CUL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 0.82

Table S356.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CUL1 MUTATED 4 4 11
CUL1 WILD-TYPE 112 102 158
'CUL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.78

Table S357.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CUL1 MUTATED 8 5 6
CUL1 WILD-TYPE 111 91 171
'CUL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.905 (Fisher's exact test), Q value = 0.98

Table S358.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
CUL1 MUTATED 3 5 6 3 2
CUL1 WILD-TYPE 83 94 83 62 51
'CUL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.84

Table S359.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CUL1 MUTATED 7 1 4 6
CUL1 WILD-TYPE 86 42 123 113
'CUL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.579 (Fisher's exact test), Q value = 0.88

Table S360.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
CUL1 MUTATED 6 2 2 2 1 5
CUL1 WILD-TYPE 68 45 86 63 26 76
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 0.98

Table S361.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
HLA-A MUTATED 3 2 0 0
HLA-A WILD-TYPE 159 135 59 34
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.72

Table S362.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
HLA-A MUTATED 2 0 2 1
HLA-A WILD-TYPE 133 112 67 78
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 0.97

Table S363.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
HLA-A MUTATED 2 2 1
HLA-A WILD-TYPE 112 171 103
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S364.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
HLA-A MUTATED 2 1 2
HLA-A WILD-TYPE 114 105 167
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 0.91

Table S365.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
HLA-A MUTATED 1 2 2
HLA-A WILD-TYPE 118 94 175
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 0.91

Table S366.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
HLA-A MUTATED 1 2 0 1 1
HLA-A WILD-TYPE 85 97 89 64 52
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.9

Table S367.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
HLA-A MUTATED 1 1 1 2
HLA-A WILD-TYPE 92 42 126 117
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 0.85

Table S368.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
HLA-A MUTATED 1 1 0 1 1 1
HLA-A WILD-TYPE 73 46 88 64 26 80
'GNA13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 0.92

Table S369.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
GNA13 MUTATED 5 6 1 0
GNA13 WILD-TYPE 157 131 58 34
'GNA13 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.69

Table S370.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
GNA13 MUTATED 2 3 2 5
GNA13 WILD-TYPE 133 109 67 74
'GNA13 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.76

Table S371.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
GNA13 MUTATED 6 2 2
GNA13 WILD-TYPE 114 104 101
'GNA13 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 0.94

Table S372.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
GNA13 MUTATED 4 3 3 0
GNA13 WILD-TYPE 83 111 95 30
'GNA13 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0868 (Fisher's exact test), Q value = 0.43

Table S373.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
GNA13 MUTATED 7 4 1
GNA13 WILD-TYPE 107 169 103
'GNA13 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.76

Table S374.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
GNA13 MUTATED 6 2 4
GNA13 WILD-TYPE 110 104 165
'GNA13 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 0.9

Table S375.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
GNA13 MUTATED 3 4 4
GNA13 WILD-TYPE 116 92 173
'GNA13 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.75

Table S376.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
GNA13 MUTATED 2 4 2 0 3
GNA13 WILD-TYPE 84 95 87 65 50
'GNA13 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0699 (Fisher's exact test), Q value = 0.41

Table S377.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
GNA13 MUTATED 0 1 3 7
GNA13 WILD-TYPE 93 42 124 112
'GNA13 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.808 (Fisher's exact test), Q value = 0.95

Table S378.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
GNA13 MUTATED 3 1 3 3 0 1
GNA13 WILD-TYPE 71 46 85 62 27 80
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.85

Table S379.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
NUDT11 MUTATED 4 1 1 1
NUDT11 WILD-TYPE 158 136 58 33
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.711 (Fisher's exact test), Q value = 0.91

Table S380.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
NUDT11 MUTATED 2 1 2 2
NUDT11 WILD-TYPE 133 111 67 77
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00316 (Fisher's exact test), Q value = 0.087

Table S381.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
NUDT11 MUTATED 0 1 6
NUDT11 WILD-TYPE 120 105 97

Figure S74.  Get High-res Image Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.813 (Fisher's exact test), Q value = 0.95

Table S382.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
NUDT11 MUTATED 1 3 3 0
NUDT11 WILD-TYPE 86 111 95 30
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 0.89

Table S383.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
NUDT11 MUTATED 3 2 2
NUDT11 WILD-TYPE 111 171 102
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.72 (Fisher's exact test), Q value = 0.91

Table S384.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NUDT11 MUTATED 1 2 4
NUDT11 WILD-TYPE 115 104 165
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S385.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
NUDT11 MUTATED 2 2 3
NUDT11 WILD-TYPE 117 94 174
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.77

Table S386.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
NUDT11 MUTATED 1 4 2 0 0
NUDT11 WILD-TYPE 85 95 87 65 53
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.69

Table S387.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
NUDT11 MUTATED 2 2 1 1
NUDT11 WILD-TYPE 91 41 126 118
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.58

Table S388.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
NUDT11 MUTATED 1 2 0 0 1 2
NUDT11 WILD-TYPE 73 45 88 65 26 79
'MBD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.58

Table S389.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
MBD1 MUTATED 2 5 3 2
MBD1 WILD-TYPE 160 132 56 32
'MBD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 0.98

Table S390.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
MBD1 MUTATED 3 4 2 3
MBD1 WILD-TYPE 132 108 67 76
'MBD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 0.86

Table S391.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MBD1 MUTATED 4 2 5
MBD1 WILD-TYPE 116 104 98
'MBD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.7

Table S392.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MBD1 MUTATED 2 2 5 2
MBD1 WILD-TYPE 85 112 93 28
'MBD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 0.93

Table S393.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
MBD1 MUTATED 4 4 4
MBD1 WILD-TYPE 110 169 100
'MBD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 0.9

Table S394.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MBD1 MUTATED 2 4 6
MBD1 WILD-TYPE 114 102 163
'MBD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.62

Table S395.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
MBD1 MUTATED 2 1 8
MBD1 WILD-TYPE 117 95 169
'MBD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.751 (Fisher's exact test), Q value = 0.93

Table S396.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
MBD1 MUTATED 3 1 3 2 2
MBD1 WILD-TYPE 83 98 86 63 51
'MBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.63

Table S397.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
MBD1 MUTATED 5 1 3 1
MBD1 WILD-TYPE 88 42 124 118
'MBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.88

Table S398.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
MBD1 MUTATED 2 1 3 0 0 4
MBD1 WILD-TYPE 72 46 85 65 27 77
'SCARF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 0.88

Table S399.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SCARF2 MUTATED 3 4 0 1
SCARF2 WILD-TYPE 159 133 59 33
'SCARF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0653 (Fisher's exact test), Q value = 0.4

Table S400.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SCARF2 MUTATED 0 3 3 2
SCARF2 WILD-TYPE 135 109 66 77
'SCARF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.73

Table S401.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SCARF2 MUTATED 1 4 1
SCARF2 WILD-TYPE 119 102 102
'SCARF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.62

Table S402.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SCARF2 MUTATED 0 4 1 1
SCARF2 WILD-TYPE 87 110 97 29
'SCARF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.32

Table S403.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SCARF2 MUTATED 0 7 1
SCARF2 WILD-TYPE 114 166 103

Figure S75.  Get High-res Image Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SCARF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.58

Table S404.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SCARF2 MUTATED 3 4 1
SCARF2 WILD-TYPE 113 102 168
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 0.9

Table S405.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SCARF2 MUTATED 2 3 3
SCARF2 WILD-TYPE 117 93 174
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.62

Table S406.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
SCARF2 MUTATED 0 2 1 3 2
SCARF2 WILD-TYPE 86 97 88 62 51
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.74

Table S407.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SCARF2 MUTATED 0 1 4 2
SCARF2 WILD-TYPE 93 42 123 117
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.88

Table S408.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
SCARF2 MUTATED 1 1 3 2 0 0
SCARF2 WILD-TYPE 73 46 85 63 27 81
'FOXQ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.536 (Fisher's exact test), Q value = 0.88

Table S409.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FOXQ1 MUTATED 6 7 1 0
FOXQ1 WILD-TYPE 156 130 58 34
'FOXQ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.659 (Fisher's exact test), Q value = 0.9

Table S410.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FOXQ1 MUTATED 5 5 3 1
FOXQ1 WILD-TYPE 130 107 66 78
'FOXQ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 0.89

Table S411.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FOXQ1 MUTATED 3 4 5
FOXQ1 WILD-TYPE 117 102 98
'FOXQ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.68

Table S412.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FOXQ1 MUTATED 1 6 3 2
FOXQ1 WILD-TYPE 86 108 95 28
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.71

Table S413.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FOXQ1 MUTATED 2 9 3
FOXQ1 WILD-TYPE 112 164 101
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 0.98

Table S414.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FOXQ1 MUTATED 5 3 6
FOXQ1 WILD-TYPE 111 103 163
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 0.99

Table S415.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FOXQ1 MUTATED 3 3 7
FOXQ1 WILD-TYPE 116 93 170
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.903 (Fisher's exact test), Q value = 0.98

Table S416.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
FOXQ1 MUTATED 3 2 4 2 2
FOXQ1 WILD-TYPE 83 97 85 63 51
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 0.99

Table S417.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FOXQ1 MUTATED 3 2 4 4
FOXQ1 WILD-TYPE 90 41 123 115
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.984 (Fisher's exact test), Q value = 1

Table S418.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
FOXQ1 MUTATED 3 2 3 2 0 3
FOXQ1 WILD-TYPE 71 45 85 63 27 78
'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.88

Table S419.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FAM47C MUTATED 7 9 2 3
FAM47C WILD-TYPE 155 128 57 31
'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 0.95

Table S420.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FAM47C MUTATED 8 6 2 5
FAM47C WILD-TYPE 127 106 67 74
'FAM47C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00689 (Fisher's exact test), Q value = 0.16

Table S421.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FAM47C MUTATED 3 3 12
FAM47C WILD-TYPE 117 103 91

Figure S76.  Get High-res Image Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 0.92

Table S422.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FAM47C MUTATED 3 7 7 1
FAM47C WILD-TYPE 84 107 91 29
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.62

Table S423.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FAM47C MUTATED 4 8 9
FAM47C WILD-TYPE 110 165 95
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.715 (Fisher's exact test), Q value = 0.91

Table S424.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FAM47C MUTATED 7 4 10
FAM47C WILD-TYPE 109 102 159
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.66

Table S425.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FAM47C MUTATED 7 2 12
FAM47C WILD-TYPE 112 94 165
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 0.58

Table S426.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
FAM47C MUTATED 8 2 3 5 3
FAM47C WILD-TYPE 78 97 86 60 50
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 0.96

Table S427.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FAM47C MUTATED 6 1 6 7
FAM47C WILD-TYPE 87 42 121 112
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 0.92

Table S428.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
FAM47C MUTATED 4 1 5 4 0 6
FAM47C WILD-TYPE 70 46 83 61 27 75
'METTL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.64

Table S429.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
METTL3 MUTATED 5 8 1 3
METTL3 WILD-TYPE 157 129 58 31
'METTL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 0.89

Table S430.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
METTL3 MUTATED 4 7 3 3
METTL3 WILD-TYPE 131 105 66 76
'METTL3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S431.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
METTL3 MUTATED 6 6 5
METTL3 WILD-TYPE 114 100 98
'METTL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 0.9

Table S432.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
METTL3 MUTATED 5 7 3 2
METTL3 WILD-TYPE 82 107 95 28
'METTL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.74

Table S433.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
METTL3 MUTATED 5 10 2
METTL3 WILD-TYPE 109 163 102
'METTL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.63

Table S434.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
METTL3 MUTATED 7 6 4
METTL3 WILD-TYPE 109 100 165
'METTL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.68

Table S435.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
METTL3 MUTATED 4 2 11
METTL3 WILD-TYPE 115 94 166
'METTL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0409 (Fisher's exact test), Q value = 0.34

Table S436.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
METTL3 MUTATED 2 1 4 7 3
METTL3 WILD-TYPE 84 98 85 58 50

Figure S77.  Get High-res Image Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'METTL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.635 (Fisher's exact test), Q value = 0.89

Table S437.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
METTL3 MUTATED 2 1 7 6
METTL3 WILD-TYPE 91 42 120 113
'METTL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.7

Table S438.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
METTL3 MUTATED 2 1 7 4 1 1
METTL3 WILD-TYPE 72 46 81 61 26 80
'ZNF185 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0906 (Fisher's exact test), Q value = 0.44

Table S439.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZNF185 MUTATED 1 1 1 2
ZNF185 WILD-TYPE 161 136 58 32
'ZNF185 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.88

Table S440.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZNF185 MUTATED 1 2 0 2
ZNF185 WILD-TYPE 134 110 69 77
'ZNF185 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.076 (Fisher's exact test), Q value = 0.42

Table S441.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ZNF185 MUTATED 0 1 3
ZNF185 WILD-TYPE 120 105 100
'ZNF185 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 0.76

Table S442.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ZNF185 MUTATED 0 1 3 0
ZNF185 WILD-TYPE 87 113 95 30
'ZNF185 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 0.89

Table S443.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZNF185 MUTATED 2 1 2
ZNF185 WILD-TYPE 112 172 102
'ZNF185 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 0.97

Table S444.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZNF185 MUTATED 1 1 3
ZNF185 WILD-TYPE 115 105 166
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.82

Table S445.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZNF185 MUTATED 1 0 4
ZNF185 WILD-TYPE 118 96 173
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 0.59

Table S446.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ZNF185 MUTATED 3 0 1 0 1
ZNF185 WILD-TYPE 83 99 88 65 52
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 0.95

Table S447.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZNF185 MUTATED 2 0 1 1
ZNF185 WILD-TYPE 91 43 126 118
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 0.94

Table S448.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ZNF185 MUTATED 0 0 1 1 0 2
ZNF185 WILD-TYPE 74 47 87 64 27 79
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.81

Table S449.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ERBB2 MUTATED 17 16 11 4
ERBB2 WILD-TYPE 145 121 48 30
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.8

Table S450.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ERBB2 MUTATED 18 9 10 11
ERBB2 WILD-TYPE 117 103 59 68
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.87

Table S451.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ERBB2 MUTATED 16 9 11
ERBB2 WILD-TYPE 104 97 92
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 0.9

Table S452.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ERBB2 MUTATED 8 11 14 3
ERBB2 WILD-TYPE 79 103 84 27
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.69

Table S453.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ERBB2 MUTATED 15 16 16
ERBB2 WILD-TYPE 99 157 88
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 0.62

Table S454.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ERBB2 MUTATED 10 11 26
ERBB2 WILD-TYPE 106 95 143
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.76 (Fisher's exact test), Q value = 0.93

Table S455.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ERBB2 MUTATED 16 11 19
ERBB2 WILD-TYPE 103 85 158
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 0.6

Table S456.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ERBB2 MUTATED 11 12 10 3 10
ERBB2 WILD-TYPE 75 87 79 62 43
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.59

Table S457.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ERBB2 MUTATED 14 4 9 17
ERBB2 WILD-TYPE 79 39 118 102
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.7

Table S458.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ERBB2 MUTATED 7 5 7 11 1 13
ERBB2 WILD-TYPE 67 42 81 54 26 68
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.88

Table S459.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ATM MUTATED 25 15 7 6
ATM WILD-TYPE 137 122 52 28
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.9

Table S460.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ATM MUTATED 21 16 8 8
ATM WILD-TYPE 114 96 61 71
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.58

Table S461.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ATM MUTATED 13 19 10
ATM WILD-TYPE 107 87 93
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0176 (Fisher's exact test), Q value = 0.25

Table S462.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ATM MUTATED 4 20 12 6
ATM WILD-TYPE 83 94 86 24

Figure S78.  Get High-res Image Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.89

Table S463.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ATM MUTATED 14 27 12
ATM WILD-TYPE 100 146 92
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 0.9

Table S464.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ATM MUTATED 17 16 20
ATM WILD-TYPE 99 90 149
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0736 (Fisher's exact test), Q value = 0.42

Table S465.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ATM MUTATED 9 16 27
ATM WILD-TYPE 110 80 150
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.62

Table S466.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ATM MUTATED 8 16 11 13 4
ATM WILD-TYPE 78 83 78 52 49
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.63

Table S467.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ATM MUTATED 15 7 20 10
ATM WILD-TYPE 78 36 107 109
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.59

Table S468.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ATM MUTATED 6 8 17 5 5 11
ATM WILD-TYPE 68 39 71 60 22 70
'UNC93B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.69

Table S469.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
UNC93B1 MUTATED 1 3 2 1
UNC93B1 WILD-TYPE 161 134 57 33
'UNC93B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S470.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
UNC93B1 MUTATED 3 2 1 1
UNC93B1 WILD-TYPE 132 110 68 78
'UNC93B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 0.86

Table S471.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
UNC93B1 MUTATED 4 1 2
UNC93B1 WILD-TYPE 116 105 101
'UNC93B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.899 (Fisher's exact test), Q value = 0.98

Table S472.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
UNC93B1 MUTATED 2 2 2 1
UNC93B1 WILD-TYPE 85 112 96 29
'UNC93B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 0.88

Table S473.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
UNC93B1 MUTATED 1 3 3
UNC93B1 WILD-TYPE 113 170 101
'UNC93B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.888 (Fisher's exact test), Q value = 0.98

Table S474.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
UNC93B1 MUTATED 2 1 4
UNC93B1 WILD-TYPE 114 105 165
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 0.94

Table S475.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
UNC93B1 MUTATED 3 1 3
UNC93B1 WILD-TYPE 116 95 174
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S476.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
UNC93B1 MUTATED 2 1 2 1 1
UNC93B1 WILD-TYPE 84 98 87 64 52
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.716 (Fisher's exact test), Q value = 0.91

Table S477.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
UNC93B1 MUTATED 3 0 2 2
UNC93B1 WILD-TYPE 90 43 125 117
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 0.91

Table S478.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
UNC93B1 MUTATED 1 1 2 0 0 3
UNC93B1 WILD-TYPE 73 46 86 65 27 78
'SF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.05 (Fisher's exact test), Q value = 0.37

Table S479.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SF1 MUTATED 2 8 0 0
SF1 WILD-TYPE 160 129 59 34
'SF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 0.9

Table S480.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SF1 MUTATED 3 3 3 1
SF1 WILD-TYPE 132 109 66 78
'SF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.72

Table S481.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SF1 MUTATED 2 2 5
SF1 WILD-TYPE 118 104 98
'SF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.25

Table S482.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SF1 MUTATED 0 2 7 0
SF1 WILD-TYPE 87 112 91 30

Figure S79.  Get High-res Image Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 0.94

Table S483.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SF1 MUTATED 4 4 2
SF1 WILD-TYPE 110 169 102
'SF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S484.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SF1 MUTATED 3 3 4
SF1 WILD-TYPE 113 103 165
'SF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00826 (Fisher's exact test), Q value = 0.19

Table S485.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SF1 MUTATED 0 6 4
SF1 WILD-TYPE 119 90 173

Figure S80.  Get High-res Image Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.62

Table S486.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
SF1 MUTATED 1 6 2 1 0
SF1 WILD-TYPE 85 93 87 64 53
'SF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.58

Table S487.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SF1 MUTATED 2 3 4 1
SF1 WILD-TYPE 91 40 123 118
'SF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.24

Table S488.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
SF1 MUTATED 0 4 1 0 1 4
SF1 WILD-TYPE 74 43 87 65 26 77

Figure S81.  Get High-res Image Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BCL2L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0192 (Fisher's exact test), Q value = 0.25

Table S489.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
BCL2L1 MUTATED 0 2 0 2
BCL2L1 WILD-TYPE 162 135 59 32

Figure S82.  Get High-res Image Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BCL2L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0476 (Fisher's exact test), Q value = 0.37

Table S490.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
BCL2L1 MUTATED 0 1 0 3
BCL2L1 WILD-TYPE 135 111 69 76

Figure S83.  Get High-res Image Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BCL2L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0762 (Fisher's exact test), Q value = 0.42

Table S491.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
BCL2L1 MUTATED 0 1 3
BCL2L1 WILD-TYPE 120 105 100
'BCL2L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 0.87

Table S492.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
BCL2L1 MUTATED 0 3 1 0
BCL2L1 WILD-TYPE 87 111 97 30
'BCL2L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.71

Table S493.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
BCL2L1 MUTATED 0 2 2
BCL2L1 WILD-TYPE 114 171 102
'BCL2L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 0.9

Table S494.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
BCL2L1 MUTATED 1 2 1
BCL2L1 WILD-TYPE 115 104 168
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.76

Table S495.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
BCL2L1 MUTATED 0 1 3
BCL2L1 WILD-TYPE 119 95 174
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.77

Table S496.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
BCL2L1 MUTATED 1 1 0 2 0
BCL2L1 WILD-TYPE 85 98 89 63 53
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.76

Table S497.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
BCL2L1 MUTATED 1 1 2 0
BCL2L1 WILD-TYPE 92 42 125 119
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.905 (Fisher's exact test), Q value = 0.98

Table S498.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
BCL2L1 MUTATED 0 1 1 1 0 1
BCL2L1 WILD-TYPE 74 46 87 64 27 80
'DNAH6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.89

Table S499.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
DNAH6 MUTATED 6 8 1 1
DNAH6 WILD-TYPE 156 129 58 33
'DNAH6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.48

Table S500.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
DNAH6 MUTATED 3 7 5 1
DNAH6 WILD-TYPE 132 105 64 78
'DNAH6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.82

Table S501.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
DNAH6 MUTATED 6 7 3
DNAH6 WILD-TYPE 114 99 100
'DNAH6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.6

Table S502.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
DNAH6 MUTATED 3 9 2 2
DNAH6 WILD-TYPE 84 105 96 28
'DNAH6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00959 (Fisher's exact test), Q value = 0.19

Table S503.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
DNAH6 MUTATED 4 12 0
DNAH6 WILD-TYPE 110 161 104

Figure S84.  Get High-res Image Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'DNAH6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.22

Table S504.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
DNAH6 MUTATED 5 9 2
DNAH6 WILD-TYPE 111 97 167

Figure S85.  Get High-res Image Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DNAH6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S505.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
DNAH6 MUTATED 5 4 7
DNAH6 WILD-TYPE 114 92 170
'DNAH6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.32

Table S506.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
DNAH6 MUTATED 0 5 2 5 4
DNAH6 WILD-TYPE 86 94 87 60 49

Figure S86.  Get High-res Image Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'DNAH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 0.38

Table S507.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
DNAH6 MUTATED 0 2 8 5
DNAH6 WILD-TYPE 93 41 119 114
'DNAH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0169 (Fisher's exact test), Q value = 0.25

Table S508.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
DNAH6 MUTATED 5 2 6 0 2 0
DNAH6 WILD-TYPE 69 45 82 65 25 81

Figure S87.  Get High-res Image Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HES1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 0.96

Table S509.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
HES1 MUTATED 5 5 1 0
HES1 WILD-TYPE 157 132 58 34
'HES1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 0.95

Table S510.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
HES1 MUTATED 4 4 2 1
HES1 WILD-TYPE 131 108 67 78
'HES1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 0.88

Table S511.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
HES1 MUTATED 2 3 4
HES1 WILD-TYPE 118 103 99
'HES1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.52

Table S512.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
HES1 MUTATED 0 4 3 2
HES1 WILD-TYPE 87 110 95 28
'HES1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 0.89

Table S513.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
HES1 MUTATED 2 5 4
HES1 WILD-TYPE 112 168 100
'HES1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 0.89

Table S514.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
HES1 MUTATED 2 4 5
HES1 WILD-TYPE 114 102 164
'HES1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.9

Table S515.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
HES1 MUTATED 3 4 4
HES1 WILD-TYPE 116 92 173
'HES1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.84

Table S516.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
HES1 MUTATED 1 4 1 3 2
HES1 WILD-TYPE 85 95 88 62 51
'HES1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.73

Table S517.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
HES1 MUTATED 3 3 3 2
HES1 WILD-TYPE 90 40 124 117
'HES1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.88

Table S518.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
HES1 MUTATED 1 3 2 3 0 2
HES1 WILD-TYPE 73 44 86 62 27 79
'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.72

Table S519.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ERBB3 MUTATED 12 19 6 4
ERBB3 WILD-TYPE 150 118 53 30
'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.76

Table S520.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ERBB3 MUTATED 10 15 6 10
ERBB3 WILD-TYPE 125 97 63 69
'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 0.98

Table S521.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ERBB3 MUTATED 14 11 10
ERBB3 WILD-TYPE 106 95 93
'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.68

Table S522.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ERBB3 MUTATED 13 13 6 3
ERBB3 WILD-TYPE 74 101 92 27
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.76

Table S523.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ERBB3 MUTATED 8 21 11
ERBB3 WILD-TYPE 106 152 93
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.62

Table S524.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ERBB3 MUTATED 8 15 17
ERBB3 WILD-TYPE 108 91 152
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.787 (Fisher's exact test), Q value = 0.94

Table S525.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ERBB3 MUTATED 13 8 20
ERBB3 WILD-TYPE 106 88 157
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.896 (Fisher's exact test), Q value = 0.98

Table S526.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ERBB3 MUTATED 11 10 9 5 6
ERBB3 WILD-TYPE 75 89 80 60 47
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 0.97

Table S527.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ERBB3 MUTATED 9 3 14 14
ERBB3 WILD-TYPE 84 40 113 105
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 0.9

Table S528.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ERBB3 MUTATED 9 3 11 4 3 10
ERBB3 WILD-TYPE 65 44 77 61 24 71
'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.546 (Fisher's exact test), Q value = 0.88

Table S529.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TXNIP MUTATED 6 5 2 3
TXNIP WILD-TYPE 156 132 57 31
'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.698 (Fisher's exact test), Q value = 0.9

Table S530.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TXNIP MUTATED 4 6 4 3
TXNIP WILD-TYPE 131 106 65 76
'TXNIP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.52

Table S531.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
TXNIP MUTATED 4 2 8
TXNIP WILD-TYPE 116 104 95
'TXNIP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.746 (Fisher's exact test), Q value = 0.93

Table S532.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
TXNIP MUTATED 3 7 3 1
TXNIP WILD-TYPE 84 107 95 29
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.82

Table S533.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TXNIP MUTATED 3 10 4
TXNIP WILD-TYPE 111 163 100
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00894 (Fisher's exact test), Q value = 0.19

Table S534.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TXNIP MUTATED 11 3 3
TXNIP WILD-TYPE 105 103 166

Figure S88.  Get High-res Image Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.81

Table S535.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TXNIP MUTATED 5 2 10
TXNIP WILD-TYPE 114 94 167
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 0.92

Table S536.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
TXNIP MUTATED 4 3 5 4 1
TXNIP WILD-TYPE 82 96 84 61 52
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 0.95

Table S537.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TXNIP MUTATED 3 2 5 7
TXNIP WILD-TYPE 90 41 122 112
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 0.92

Table S538.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
TXNIP MUTATED 4 2 6 3 0 2
TXNIP WILD-TYPE 70 45 82 62 27 79
'THRAP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.88

Table S539.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
THRAP3 MUTATED 4 6 2 2
THRAP3 WILD-TYPE 158 131 57 32
'THRAP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.74

Table S540.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
THRAP3 MUTATED 3 5 1 5
THRAP3 WILD-TYPE 132 107 68 74
'THRAP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S541.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
THRAP3 MUTATED 3 3 3
THRAP3 WILD-TYPE 117 103 100
'THRAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S542.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
THRAP3 MUTATED 2 3 3 1
THRAP3 WILD-TYPE 85 111 95 29
'THRAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 0.96

Table S543.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
THRAP3 MUTATED 3 7 4
THRAP3 WILD-TYPE 111 166 100
'THRAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.783 (Fisher's exact test), Q value = 0.94

Table S544.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
THRAP3 MUTATED 5 4 5
THRAP3 WILD-TYPE 111 102 164
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S545.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
THRAP3 MUTATED 4 3 7
THRAP3 WILD-TYPE 115 93 170
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 0.94

Table S546.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
THRAP3 MUTATED 2 5 2 3 2
THRAP3 WILD-TYPE 84 94 87 62 51
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S547.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
THRAP3 MUTATED 3 1 5 5
THRAP3 WILD-TYPE 90 42 122 114
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.905 (Fisher's exact test), Q value = 0.98

Table S548.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
THRAP3 MUTATED 3 1 4 1 1 4
THRAP3 WILD-TYPE 71 46 84 64 26 77
'SPTAN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.73

Table S549.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SPTAN1 MUTATED 24 13 5 2
SPTAN1 WILD-TYPE 138 124 54 32
'SPTAN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.62

Table S550.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SPTAN1 MUTATED 10 17 7 11
SPTAN1 WILD-TYPE 125 95 62 68
'SPTAN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 0.68

Table S551.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SPTAN1 MUTATED 13 17 9
SPTAN1 WILD-TYPE 107 89 94
'SPTAN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.51

Table S552.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SPTAN1 MUTATED 11 19 6 3
SPTAN1 WILD-TYPE 76 95 92 27
'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.63

Table S553.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SPTAN1 MUTATED 12 25 8
SPTAN1 WILD-TYPE 102 148 96
'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 0.62

Table S554.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SPTAN1 MUTATED 16 15 14
SPTAN1 WILD-TYPE 100 91 155
'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.65

Table S555.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SPTAN1 MUTATED 9 14 22
SPTAN1 WILD-TYPE 110 82 155
'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0784 (Fisher's exact test), Q value = 0.42

Table S556.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
SPTAN1 MUTATED 4 13 16 7 5
SPTAN1 WILD-TYPE 82 86 73 58 48
'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.34

Table S557.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SPTAN1 MUTATED 6 2 22 15
SPTAN1 WILD-TYPE 87 41 105 104

Figure S89.  Get High-res Image Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0666 (Fisher's exact test), Q value = 0.4

Table S558.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
SPTAN1 MUTATED 8 4 12 8 8 5
SPTAN1 WILD-TYPE 66 43 76 57 19 76
'ARID1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00989 (Fisher's exact test), Q value = 0.19

Table S559.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ARID1B MUTATED 7 15 0 1
ARID1B WILD-TYPE 155 122 59 33

Figure S90.  Get High-res Image Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.62

Table S560.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ARID1B MUTATED 5 10 2 6
ARID1B WILD-TYPE 130 102 67 73
'ARID1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.6

Table S561.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ARID1B MUTATED 4 4 9
ARID1B WILD-TYPE 116 102 94
'ARID1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 0.89

Table S562.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ARID1B MUTATED 4 8 5 0
ARID1B WILD-TYPE 83 106 93 30
'ARID1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0866 (Fisher's exact test), Q value = 0.43

Table S563.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ARID1B MUTATED 7 14 2
ARID1B WILD-TYPE 107 159 102
'ARID1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0579 (Fisher's exact test), Q value = 0.38

Table S564.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ARID1B MUTATED 12 5 6
ARID1B WILD-TYPE 104 101 163
'ARID1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0829 (Fisher's exact test), Q value = 0.43

Table S565.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ARID1B MUTATED 4 10 9
ARID1B WILD-TYPE 115 86 168
'ARID1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0582 (Fisher's exact test), Q value = 0.38

Table S566.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ARID1B MUTATED 1 9 6 6 1
ARID1B WILD-TYPE 85 90 83 59 52
'ARID1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.77

Table S567.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ARID1B MUTATED 4 5 7 6
ARID1B WILD-TYPE 89 38 120 113
'ARID1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.62

Table S568.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ARID1B MUTATED 3 5 8 4 0 2
ARID1B WILD-TYPE 71 42 80 61 27 79
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.75

Table S569.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
NRAS MUTATED 2 5 0 0
NRAS WILD-TYPE 160 132 59 34
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.84

Table S570.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
NRAS MUTATED 2 3 2 0
NRAS WILD-TYPE 133 109 67 79
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S571.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
NRAS MUTATED 2 1 1
NRAS WILD-TYPE 118 105 102
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.636 (Fisher's exact test), Q value = 0.89

Table S572.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
NRAS MUTATED 1 1 1 1
NRAS WILD-TYPE 86 113 97 29
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 0.94

Table S573.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
NRAS MUTATED 1 4 2
NRAS WILD-TYPE 113 169 102
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.89

Table S574.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NRAS MUTATED 3 2 2
NRAS WILD-TYPE 113 104 167
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.53

Table S575.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
NRAS MUTATED 0 3 4
NRAS WILD-TYPE 119 93 173
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 0.83

Table S576.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
NRAS MUTATED 1 3 3 0 0
NRAS WILD-TYPE 85 96 86 65 53
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.3

Table S577.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
NRAS MUTATED 2 3 2 0
NRAS WILD-TYPE 91 40 125 119

Figure S91.  Get High-res Image Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0829 (Fisher's exact test), Q value = 0.43

Table S578.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
NRAS MUTATED 0 3 2 0 1 1
NRAS WILD-TYPE 74 44 86 65 26 80
'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 0.96

Table S579.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RPTN MUTATED 5 7 2 1
RPTN WILD-TYPE 157 130 57 33
'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.892 (Fisher's exact test), Q value = 0.98

Table S580.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RPTN MUTATED 6 5 2 2
RPTN WILD-TYPE 129 107 67 77
'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.873 (Fisher's exact test), Q value = 0.97

Table S581.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RPTN MUTATED 5 3 4
RPTN WILD-TYPE 115 103 99
'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 0.93

Table S582.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RPTN MUTATED 3 4 3 2
RPTN WILD-TYPE 84 110 95 28
'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S583.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RPTN MUTATED 4 7 4
RPTN WILD-TYPE 110 166 100
'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S584.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RPTN MUTATED 4 4 7
RPTN WILD-TYPE 112 102 162
'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 0.93

Table S585.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RPTN MUTATED 4 5 6
RPTN WILD-TYPE 115 91 171
'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.49

Table S586.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RPTN MUTATED 3 8 3 0 1
RPTN WILD-TYPE 83 91 86 65 52
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 0.97

Table S587.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RPTN MUTATED 5 1 5 4
RPTN WILD-TYPE 88 42 122 115
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.65 (Fisher's exact test), Q value = 0.9

Table S588.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RPTN MUTATED 4 1 4 1 0 5
RPTN WILD-TYPE 70 46 84 64 27 76
'RAI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.971 (Fisher's exact test), Q value = 1

Table S589.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RAI1 MUTATED 8 8 3 2
RAI1 WILD-TYPE 154 129 56 32
'RAI1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.67

Table S590.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RAI1 MUTATED 4 9 5 3
RAI1 WILD-TYPE 131 103 64 76
'RAI1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.51

Table S591.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RAI1 MUTATED 3 9 7
RAI1 WILD-TYPE 117 97 96
'RAI1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0769 (Fisher's exact test), Q value = 0.42

Table S592.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RAI1 MUTATED 2 12 4 1
RAI1 WILD-TYPE 85 102 94 29
'RAI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0114 (Fisher's exact test), Q value = 0.2

Table S593.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RAI1 MUTATED 2 16 3
RAI1 WILD-TYPE 112 157 101

Figure S92.  Get High-res Image Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0332 (Fisher's exact test), Q value = 0.32

Table S594.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RAI1 MUTATED 5 11 5
RAI1 WILD-TYPE 111 95 164

Figure S93.  Get High-res Image Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RAI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S595.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RAI1 MUTATED 6 4 10
RAI1 WILD-TYPE 113 92 167
'RAI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0483 (Fisher's exact test), Q value = 0.37

Table S596.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RAI1 MUTATED 1 3 7 7 2
RAI1 WILD-TYPE 85 96 82 58 51

Figure S94.  Get High-res Image Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.84

Table S597.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RAI1 MUTATED 3 2 10 5
RAI1 WILD-TYPE 90 41 117 114
'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.74

Table S598.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RAI1 MUTATED 4 2 9 2 1 2
RAI1 WILD-TYPE 70 45 79 63 26 79
'TMCO4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.84

Table S599.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TMCO4 MUTATED 4 7 1 0
TMCO4 WILD-TYPE 158 130 58 34
'TMCO4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0372 (Fisher's exact test), Q value = 0.33

Table S600.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TMCO4 MUTATED 1 5 5 1
TMCO4 WILD-TYPE 134 107 64 78

Figure S95.  Get High-res Image Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TMCO4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 0.88

Table S601.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
TMCO4 MUTATED 4 5 2
TMCO4 WILD-TYPE 116 101 101
'TMCO4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.7

Table S602.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
TMCO4 MUTATED 3 5 1 2
TMCO4 WILD-TYPE 84 109 97 28
'TMCO4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 0.79

Table S603.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TMCO4 MUTATED 2 8 2
TMCO4 WILD-TYPE 112 165 102
'TMCO4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0759 (Fisher's exact test), Q value = 0.42

Table S604.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TMCO4 MUTATED 2 7 3
TMCO4 WILD-TYPE 114 99 166
'TMCO4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.77

Table S605.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TMCO4 MUTATED 2 2 8
TMCO4 WILD-TYPE 117 94 169
'TMCO4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.71

Table S606.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
TMCO4 MUTATED 1 2 6 2 1
TMCO4 WILD-TYPE 85 97 83 63 52
'TMCO4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0762 (Fisher's exact test), Q value = 0.42

Table S607.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TMCO4 MUTATED 1 0 8 2
TMCO4 WILD-TYPE 92 43 119 117
'TMCO4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0842 (Fisher's exact test), Q value = 0.43

Table S608.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
TMCO4 MUTATED 1 0 6 1 2 1
TMCO4 WILD-TYPE 73 47 82 64 25 80
'CNOT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.51

Table S609.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CNOT1 MUTATED 9 9 0 3
CNOT1 WILD-TYPE 153 128 59 31
'CNOT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.524 (Fisher's exact test), Q value = 0.87

Table S610.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CNOT1 MUTATED 5 9 3 4
CNOT1 WILD-TYPE 130 103 66 75
'CNOT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.76

Table S611.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CNOT1 MUTATED 4 6 8
CNOT1 WILD-TYPE 116 100 95
'CNOT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.77

Table S612.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CNOT1 MUTATED 2 8 7 1
CNOT1 WILD-TYPE 85 106 91 29
'CNOT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.89

Table S613.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CNOT1 MUTATED 4 11 5
CNOT1 WILD-TYPE 110 162 99
'CNOT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.82

Table S614.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CNOT1 MUTATED 5 8 7
CNOT1 WILD-TYPE 111 98 162
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.87

Table S615.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CNOT1 MUTATED 4 6 11
CNOT1 WILD-TYPE 115 90 166
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 0.91

Table S616.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
CNOT1 MUTATED 4 5 4 6 2
CNOT1 WILD-TYPE 82 94 85 59 51
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.95 (Fisher's exact test), Q value = 0.99

Table S617.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CNOT1 MUTATED 4 2 8 6
CNOT1 WILD-TYPE 89 41 119 113
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S618.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
CNOT1 MUTATED 3 3 5 3 2 4
CNOT1 WILD-TYPE 71 44 83 62 25 77
'PARD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 0.94

Table S619.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
PARD3 MUTATED 8 8 3 3
PARD3 WILD-TYPE 154 129 56 31
'PARD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 0.88

Table S620.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
PARD3 MUTATED 8 8 4 2
PARD3 WILD-TYPE 127 104 65 77
'PARD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.8

Table S621.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
PARD3 MUTATED 4 7 7
PARD3 WILD-TYPE 116 99 96
'PARD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.76

Table S622.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
PARD3 MUTATED 3 8 7 0
PARD3 WILD-TYPE 84 106 91 30
'PARD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 0.9

Table S623.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
PARD3 MUTATED 7 11 4
PARD3 WILD-TYPE 107 162 100
'PARD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 0.96

Table S624.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PARD3 MUTATED 6 5 11
PARD3 WILD-TYPE 110 101 158
'PARD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.58

Table S625.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
PARD3 MUTATED 3 8 9
PARD3 WILD-TYPE 116 88 168
'PARD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.605 (Fisher's exact test), Q value = 0.89

Table S626.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
PARD3 MUTATED 4 7 2 4 3
PARD3 WILD-TYPE 82 92 87 61 50
'PARD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 0.88

Table S627.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
PARD3 MUTATED 4 4 5 5
PARD3 WILD-TYPE 89 39 122 114
'PARD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.89

Table S628.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
PARD3 MUTATED 4 4 5 3 0 2
PARD3 WILD-TYPE 70 43 83 62 27 79
'EZR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.71

Table S629.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
EZR MUTATED 5 3 4 0
EZR WILD-TYPE 157 134 55 34
'EZR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 0.98

Table S630.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
EZR MUTATED 5 4 1 2
EZR WILD-TYPE 130 108 68 77
'EZR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S631.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EZR MUTATED 4 3 3
EZR WILD-TYPE 116 103 100
'EZR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.76

Table S632.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EZR MUTATED 2 2 4 2
EZR WILD-TYPE 85 112 94 28
'EZR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.88

Table S633.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
EZR MUTATED 5 5 2
EZR WILD-TYPE 109 168 102
'EZR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.87 (Fisher's exact test), Q value = 0.97

Table S634.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EZR MUTATED 3 4 5
EZR WILD-TYPE 113 102 164
'EZR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 0.9

Table S635.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
EZR MUTATED 5 2 5
EZR WILD-TYPE 114 94 172
'EZR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.73

Table S636.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
EZR MUTATED 1 3 3 1 4
EZR WILD-TYPE 85 96 86 64 49
'EZR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.949 (Fisher's exact test), Q value = 0.99

Table S637.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
EZR MUTATED 2 1 5 4
EZR WILD-TYPE 91 42 122 115
'EZR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.747 (Fisher's exact test), Q value = 0.93

Table S638.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
EZR MUTATED 3 1 5 1 0 2
EZR WILD-TYPE 71 46 83 64 27 79
'MOAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 0.89

Table S639.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
MOAP1 MUTATED 3 4 0 0
MOAP1 WILD-TYPE 159 133 59 34
'MOAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 0.64

Table S640.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
MOAP1 MUTATED 1 4 0 2
MOAP1 WILD-TYPE 134 108 69 77
'MOAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.87

Table S641.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MOAP1 MUTATED 1 3 2
MOAP1 WILD-TYPE 119 103 101
'MOAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 0.89

Table S642.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MOAP1 MUTATED 1 3 1 1
MOAP1 WILD-TYPE 86 111 97 29
'MOAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0659 (Fisher's exact test), Q value = 0.4

Table S643.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
MOAP1 MUTATED 0 6 1
MOAP1 WILD-TYPE 114 167 103
'MOAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.89

Table S644.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MOAP1 MUTATED 3 2 2
MOAP1 WILD-TYPE 113 104 167
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 0.88

Table S645.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
MOAP1 MUTATED 2 3 2
MOAP1 WILD-TYPE 117 93 175
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.604 (Fisher's exact test), Q value = 0.89

Table S646.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
MOAP1 MUTATED 0 3 2 1 1
MOAP1 WILD-TYPE 86 96 87 64 52
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 0.97

Table S647.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
MOAP1 MUTATED 1 1 3 2
MOAP1 WILD-TYPE 92 42 124 117
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 0.9

Table S648.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
MOAP1 MUTATED 2 1 2 0 1 1
MOAP1 WILD-TYPE 72 46 86 65 26 80
'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.52

Table S649.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SF3B1 MUTATED 7 13 4 0
SF3B1 WILD-TYPE 155 124 55 34
'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 0.94

Table S650.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SF3B1 MUTATED 8 9 3 4
SF3B1 WILD-TYPE 127 103 66 75
'SF3B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.86

Table S651.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SF3B1 MUTATED 4 5 7
SF3B1 WILD-TYPE 116 101 96
'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.82

Table S652.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SF3B1 MUTATED 3 8 3 2
SF3B1 WILD-TYPE 84 106 95 28
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 0.96

Table S653.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SF3B1 MUTATED 7 12 5
SF3B1 WILD-TYPE 107 161 99
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 0.89

Table S654.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SF3B1 MUTATED 5 8 11
SF3B1 WILD-TYPE 111 98 158
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S655.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SF3B1 MUTATED 7 6 10
SF3B1 WILD-TYPE 112 90 167
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.936 (Fisher's exact test), Q value = 0.99

Table S656.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
SF3B1 MUTATED 4 6 6 3 4
SF3B1 WILD-TYPE 82 93 83 62 49
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.62

Table S657.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SF3B1 MUTATED 2 4 7 9
SF3B1 WILD-TYPE 91 39 120 110
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 0.73

Table S658.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
SF3B1 MUTATED 3 4 5 7 1 2
SF3B1 WILD-TYPE 71 43 83 58 26 79
'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 0.38

Table S659.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RUNX1 MUTATED 2 9 2 0
RUNX1 WILD-TYPE 160 128 57 34
'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 0.89

Table S660.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RUNX1 MUTATED 4 5 3 1
RUNX1 WILD-TYPE 131 107 66 78
'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.68

Table S661.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RUNX1 MUTATED 4 1 5
RUNX1 WILD-TYPE 116 105 98
'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.87

Table S662.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RUNX1 MUTATED 2 2 5 1
RUNX1 WILD-TYPE 85 112 93 29
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0834 (Fisher's exact test), Q value = 0.43

Table S663.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RUNX1 MUTATED 6 2 5
RUNX1 WILD-TYPE 108 171 99
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0479 (Fisher's exact test), Q value = 0.37

Table S664.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RUNX1 MUTATED 5 0 8
RUNX1 WILD-TYPE 111 106 161

Figure S96.  Get High-res Image Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.754 (Fisher's exact test), Q value = 0.93

Table S665.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RUNX1 MUTATED 3 2 7
RUNX1 WILD-TYPE 116 94 170
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 0.95

Table S666.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
RUNX1 MUTATED 4 2 2 2 2
RUNX1 WILD-TYPE 82 97 87 63 51
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 0.99

Table S667.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RUNX1 MUTATED 4 1 4 3
RUNX1 WILD-TYPE 89 42 123 116
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.544 (Fisher's exact test), Q value = 0.88

Table S668.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
RUNX1 MUTATED 1 1 2 4 0 4
RUNX1 WILD-TYPE 73 46 86 61 27 77
'MEGF8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.51

Table S669.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
MEGF8 MUTATED 6 12 2 0
MEGF8 WILD-TYPE 156 125 57 34
'MEGF8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.76

Table S670.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
MEGF8 MUTATED 4 9 3 4
MEGF8 WILD-TYPE 131 103 66 75
'MEGF8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.9

Table S671.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MEGF8 MUTATED 5 7 4
MEGF8 WILD-TYPE 115 99 99
'MEGF8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S672.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MEGF8 MUTATED 4 6 5 1
MEGF8 WILD-TYPE 83 108 93 29
'MEGF8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.52

Table S673.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
MEGF8 MUTATED 2 11 7
MEGF8 WILD-TYPE 112 162 97
'MEGF8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 0.88

Table S674.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MEGF8 MUTATED 4 7 9
MEGF8 WILD-TYPE 112 99 160
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.915 (Fisher's exact test), Q value = 0.98

Table S675.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
MEGF8 MUTATED 5 5 10
MEGF8 WILD-TYPE 114 91 167
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.669 (Fisher's exact test), Q value = 0.9

Table S676.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
MEGF8 MUTATED 3 7 5 4 1
MEGF8 WILD-TYPE 83 92 84 61 52
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S677.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
MEGF8 MUTATED 5 2 7 6
MEGF8 WILD-TYPE 88 41 120 113
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 0.86

Table S678.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
MEGF8 MUTATED 3 2 8 2 0 5
MEGF8 WILD-TYPE 71 45 80 63 27 76
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.87

Table S679.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CASP8 MUTATED 7 3 2 2
CASP8 WILD-TYPE 155 134 57 32
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.76

Table S680.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CASP8 MUTATED 6 6 1 1
CASP8 WILD-TYPE 129 106 68 78
'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0816 (Fisher's exact test), Q value = 0.43

Table S681.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CASP8 MUTATED 1 5 6
CASP8 WILD-TYPE 119 101 97
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.47

Table S682.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CASP8 MUTATED 0 6 5 1
CASP8 WILD-TYPE 87 108 93 29
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.88

Table S683.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CASP8 MUTATED 6 5 3
CASP8 WILD-TYPE 108 168 101
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.575 (Fisher's exact test), Q value = 0.88

Table S684.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CASP8 MUTATED 5 2 7
CASP8 WILD-TYPE 111 104 162
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.73

Table S685.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CASP8 MUTATED 5 1 8
CASP8 WILD-TYPE 114 95 169
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.62

Table S686.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
CASP8 MUTATED 6 2 1 2 3
CASP8 WILD-TYPE 80 97 88 63 50
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 0.9

Table S687.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CASP8 MUTATED 4 0 4 5
CASP8 WILD-TYPE 89 43 123 114
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 0.9

Table S688.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
CASP8 MUTATED 3 0 3 3 0 4
CASP8 WILD-TYPE 71 47 85 62 27 77
'DAZAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 0.92

Table S689.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
DAZAP1 MUTATED 2 2 1 1
DAZAP1 WILD-TYPE 160 135 58 33
'DAZAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.36

Table S690.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
DAZAP1 MUTATED 1 5 0 0
DAZAP1 WILD-TYPE 134 107 69 79

Figure S97.  Get High-res Image Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DAZAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.88

Table S691.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
DAZAP1 MUTATED 2 2 0
DAZAP1 WILD-TYPE 118 104 103
'DAZAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.73

Table S692.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
DAZAP1 MUTATED 1 2 0 1
DAZAP1 WILD-TYPE 86 112 98 29
'DAZAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.59

Table S693.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
DAZAP1 MUTATED 1 5 0
DAZAP1 WILD-TYPE 113 168 104
'DAZAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.2

Table S694.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
DAZAP1 MUTATED 0 5 1
DAZAP1 WILD-TYPE 116 101 168

Figure S98.  Get High-res Image Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.62

Table S695.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
DAZAP1 MUTATED 1 0 5
DAZAP1 WILD-TYPE 118 96 172
'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0248 (Fisher's exact test), Q value = 0.28

Table S696.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
DAZAP1 MUTATED 0 0 3 3 0
DAZAP1 WILD-TYPE 86 99 86 62 53

Figure S99.  Get High-res Image Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.75

Table S697.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
DAZAP1 MUTATED 1 0 3 0
DAZAP1 WILD-TYPE 92 43 124 119
'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.8

Table S698.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
DAZAP1 MUTATED 0 0 3 0 0 1
DAZAP1 WILD-TYPE 74 47 85 65 27 80
'USP28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.855 (Fisher's exact test), Q value = 0.97

Table S699.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
USP28 MUTATED 5 4 3 1
USP28 WILD-TYPE 157 133 56 33
'USP28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 0.9

Table S700.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
USP28 MUTATED 5 3 1 4
USP28 WILD-TYPE 130 109 68 75
'USP28 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 0.88

Table S701.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
USP28 MUTATED 2 3 4
USP28 WILD-TYPE 118 103 99
'USP28 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.77

Table S702.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
USP28 MUTATED 1 3 5 0
USP28 WILD-TYPE 86 111 93 30
'USP28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 0.91

Table S703.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
USP28 MUTATED 4 7 2
USP28 WILD-TYPE 110 166 102
'USP28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S704.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
USP28 MUTATED 4 3 6
USP28 WILD-TYPE 112 103 163
'USP28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 0.89

Table S705.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
USP28 MUTATED 3 2 8
USP28 WILD-TYPE 116 94 169
'USP28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.84

Table S706.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
USP28 MUTATED 1 3 4 4 1
USP28 WILD-TYPE 85 96 85 61 52
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.95 (Fisher's exact test), Q value = 0.99

Table S707.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
USP28 MUTATED 2 1 5 4
USP28 WILD-TYPE 91 42 122 115
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S708.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
USP28 MUTATED 3 1 4 2 1 1
USP28 WILD-TYPE 71 46 84 63 26 80
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 0.94

Table S709.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SETD2 MUTATED 9 11 5 2
SETD2 WILD-TYPE 153 126 54 32
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.82

Table S710.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SETD2 MUTATED 9 11 4 3
SETD2 WILD-TYPE 126 101 65 76
'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.86

Table S711.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SETD2 MUTATED 6 9 5
SETD2 WILD-TYPE 114 97 98
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 0.95

Table S712.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SETD2 MUTATED 5 9 5 1
SETD2 WILD-TYPE 82 105 93 29
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 0.96

Table S713.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SETD2 MUTATED 9 11 7
SETD2 WILD-TYPE 105 162 97
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 0.95

Table S714.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SETD2 MUTATED 9 6 12
SETD2 WILD-TYPE 107 100 157
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.56

Table S715.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SETD2 MUTATED 11 8 7
SETD2 WILD-TYPE 108 88 170
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 0.94

Table S716.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
SETD2 MUTATED 5 7 4 5 5
SETD2 WILD-TYPE 81 92 85 60 48
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.76

Table S717.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SETD2 MUTATED 8 1 6 10
SETD2 WILD-TYPE 85 42 121 109
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 0.86

Table S718.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
SETD2 MUTATED 5 1 7 6 0 6
SETD2 WILD-TYPE 69 46 81 59 27 75
'EME1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.56

Table S719.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
EME1 MUTATED 5 0 0 0
EME1 WILD-TYPE 157 137 59 34
'EME1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.73

Table S720.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
EME1 MUTATED 2 0 1 2
EME1 WILD-TYPE 133 112 68 77
'EME1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 0.9

Table S721.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EME1 MUTATED 1 1 2
EME1 WILD-TYPE 119 105 101
'EME1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.7

Table S722.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EME1 MUTATED 0 1 2 1
EME1 WILD-TYPE 87 113 96 29
'EME1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 0.92

Table S723.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
EME1 MUTATED 1 2 2
EME1 WILD-TYPE 113 171 102
'EME1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.336 (Fisher's exact test), Q value = 0.74

Table S724.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EME1 MUTATED 1 0 4
EME1 WILD-TYPE 115 106 165
'EME1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.91

Table S725.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
EME1 MUTATED 1 2 2
EME1 WILD-TYPE 118 94 175
'EME1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.84

Table S726.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
EME1 MUTATED 0 3 1 1 0
EME1 WILD-TYPE 86 96 88 64 53
'EME1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.69

Table S727.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
EME1 MUTATED 1 1 0 2
EME1 WILD-TYPE 92 42 127 117
'EME1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.7

Table S728.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
EME1 MUTATED 1 1 0 2 0 0
EME1 WILD-TYPE 73 46 88 63 27 81
'ADC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.904 (Fisher's exact test), Q value = 0.98

Table S729.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ADC MUTATED 3 2 0 0
ADC WILD-TYPE 159 135 59 34
'ADC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 0.97

Table S730.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ADC MUTATED 2 2 0 1
ADC WILD-TYPE 133 110 69 78
'ADC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 0.9

Table S731.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ADC MUTATED 1 1 2
ADC WILD-TYPE 119 105 101
'ADC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 0.9

Table S732.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ADC MUTATED 0 2 2 0
ADC WILD-TYPE 87 112 96 30
'ADC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S733.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ADC MUTATED 1 3 1
ADC WILD-TYPE 113 170 103
'ADC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S734.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ADC MUTATED 2 1 2
ADC WILD-TYPE 114 105 167
'ADC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 0.97

Table S735.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ADC MUTATED 1 1 3
ADC WILD-TYPE 118 95 174
'ADC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.82

Table S736.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
ADC MUTATED 0 2 1 2 0
ADC WILD-TYPE 86 97 88 63 53
'ADC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S737.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ADC MUTATED 1 0 2 2
ADC WILD-TYPE 92 43 125 117
'ADC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 0.94

Table S738.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
ADC MUTATED 1 1 2 1 0 0
ADC WILD-TYPE 73 46 86 64 27 81
'CNOT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.62

Table S739.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CNOT3 MUTATED 5 1 3 1
CNOT3 WILD-TYPE 157 136 56 33
'CNOT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.77

Table S740.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CNOT3 MUTATED 6 1 1 2
CNOT3 WILD-TYPE 129 111 68 77
'CNOT3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 0.9

Table S741.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CNOT3 MUTATED 3 2 4
CNOT3 WILD-TYPE 117 104 99
'CNOT3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.58

Table S742.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CNOT3 MUTATED 1 2 6 0
CNOT3 WILD-TYPE 86 112 92 30
'CNOT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.25

Table S743.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CNOT3 MUTATED 3 1 6
CNOT3 WILD-TYPE 111 172 98

Figure S100.  Get High-res Image Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CNOT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.51

Table S744.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CNOT3 MUTATED 3 0 7
CNOT3 WILD-TYPE 113 106 162
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 0.98

Table S745.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CNOT3 MUTATED 3 3 4
CNOT3 WILD-TYPE 116 93 173
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0515 (Fisher's exact test), Q value = 0.37

Table S746.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
CNOT3 MUTATED 3 6 0 1 0
CNOT3 WILD-TYPE 83 93 89 64 53
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00133 (Fisher's exact test), Q value = 0.045

Table S747.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CNOT3 MUTATED 6 3 0 1
CNOT3 WILD-TYPE 87 40 127 118

Figure S101.  Get High-res Image Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CNOT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.24

Table S748.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
CNOT3 MUTATED 0 2 0 2 0 6
CNOT3 WILD-TYPE 74 45 88 63 27 75

Figure S102.  Get High-res Image Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SSH3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.25

Table S749.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SSH3 MUTATED 10 2 0 3
SSH3 WILD-TYPE 152 135 59 31

Figure S103.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SSH3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0946 (Fisher's exact test), Q value = 0.45

Table S750.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SSH3 MUTATED 2 3 5 5
SSH3 WILD-TYPE 133 109 64 74
'SSH3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.32

Table S751.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SSH3 MUTATED 1 8 3
SSH3 WILD-TYPE 119 98 100

Figure S104.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'SSH3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.35

Table S752.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SSH3 MUTATED 2 9 1 0
SSH3 WILD-TYPE 85 105 97 30

Figure S105.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SSH3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.37

Table S753.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SSH3 MUTATED 1 11 3
SSH3 WILD-TYPE 113 162 101

Figure S106.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SSH3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 0.77

Table S754.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SSH3 MUTATED 6 5 4
SSH3 WILD-TYPE 110 101 165
'SSH3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0686 (Fisher's exact test), Q value = 0.41

Table S755.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SSH3 MUTATED 1 6 8
SSH3 WILD-TYPE 118 90 169
'SSH3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 0.48

Table S756.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
SSH3 MUTATED 0 6 4 4 1
SSH3 WILD-TYPE 86 93 85 61 52
'SSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.74

Table S757.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SSH3 MUTATED 2 3 7 3
SSH3 WILD-TYPE 91 40 120 116
'SSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.67

Table S758.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
SSH3 MUTATED 1 3 4 4 2 1
SSH3 WILD-TYPE 73 44 84 61 25 80
'AHR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.88

Table S759.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
AHR MUTATED 9 9 4 0
AHR WILD-TYPE 153 128 55 34
'AHR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0535 (Fisher's exact test), Q value = 0.37

Table S760.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
AHR MUTATED 3 7 8 4
AHR WILD-TYPE 132 105 61 75
'AHR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.58

Table S761.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
AHR MUTATED 4 10 6
AHR WILD-TYPE 116 96 97
'AHR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 0.94

Table S762.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
AHR MUTATED 6 8 4 2
AHR WILD-TYPE 81 106 94 28
'AHR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0648 (Fisher's exact test), Q value = 0.4

Table S763.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
AHR MUTATED 3 15 4
AHR WILD-TYPE 111 158 100
'AHR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0748 (Fisher's exact test), Q value = 0.42

Table S764.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
AHR MUTATED 7 10 5
AHR WILD-TYPE 109 96 164
'AHR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 0.9

Table S765.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
AHR MUTATED 5 5 12
AHR WILD-TYPE 114 91 165
'AHR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.72

Table S766.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
AHR MUTATED 2 4 8 5 3
AHR WILD-TYPE 84 95 81 60 50
'AHR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 0.88

Table S767.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
AHR MUTATED 3 2 10 6
AHR WILD-TYPE 90 41 117 113
'AHR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.86

Table S768.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
AHR MUTATED 3 4 7 3 2 2
AHR WILD-TYPE 71 43 81 62 25 79
'EIF4A2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.77

Table S769.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
EIF4A2 MUTATED 3 3 2 2
EIF4A2 WILD-TYPE 159 134 57 32
'EIF4A2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 0.95

Table S770.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
EIF4A2 MUTATED 3 3 3 2
EIF4A2 WILD-TYPE 132 109 66 77
'EIF4A2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 0.77

Table S771.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EIF4A2 MUTATED 2 3 5
EIF4A2 WILD-TYPE 118 103 98
'EIF4A2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.612 (Fisher's exact test), Q value = 0.89

Table S772.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EIF4A2 MUTATED 2 3 5 0
EIF4A2 WILD-TYPE 85 111 93 30
'EIF4A2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.85

Table S773.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
EIF4A2 MUTATED 4 3 4
EIF4A2 WILD-TYPE 110 170 100
'EIF4A2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.68

Table S774.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EIF4A2 MUTATED 1 3 7
EIF4A2 WILD-TYPE 115 103 162
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0903 (Fisher's exact test), Q value = 0.44

Table S775.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
EIF4A2 MUTATED 3 0 8
EIF4A2 WILD-TYPE 116 96 169
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.56

Table S776.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
EIF4A2 MUTATED 4 0 4 1 2
EIF4A2 WILD-TYPE 82 99 85 64 51
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 0.98

Table S777.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
EIF4A2 MUTATED 3 0 4 3
EIF4A2 WILD-TYPE 90 43 123 116
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.84

Table S778.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
EIF4A2 MUTATED 1 0 4 1 0 4
EIF4A2 WILD-TYPE 73 47 84 64 27 77
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S779.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
EPHA2 MUTATED 7 8 2 2
EPHA2 WILD-TYPE 155 129 57 32
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.25

Table S780.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
EPHA2 MUTATED 4 10 0 5
EPHA2 WILD-TYPE 131 102 69 74

Figure S107.  Get High-res Image Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.637 (Fisher's exact test), Q value = 0.89

Table S781.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EPHA2 MUTATED 6 6 3
EPHA2 WILD-TYPE 114 100 100
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 0.85

Table S782.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EPHA2 MUTATED 3 5 4 3
EPHA2 WILD-TYPE 84 109 94 27
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.58

Table S783.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
EPHA2 MUTATED 2 9 7
EPHA2 WILD-TYPE 112 164 97
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S784.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EPHA2 MUTATED 5 5 8
EPHA2 WILD-TYPE 111 101 161
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.82

Table S785.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
EPHA2 MUTATED 7 6 6
EPHA2 WILD-TYPE 112 90 171
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.58

Table S786.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
EPHA2 MUTATED 5 7 1 5 1
EPHA2 WILD-TYPE 81 92 88 60 52
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.89

Table S787.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
EPHA2 MUTATED 7 2 6 4
EPHA2 WILD-TYPE 86 41 121 115
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.76

Table S788.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
EPHA2 MUTATED 1 3 5 2 1 7
EPHA2 WILD-TYPE 73 44 83 63 26 74
'OGDH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.38

Table S789.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
OGDH MUTATED 4 10 5 0
OGDH WILD-TYPE 158 127 54 34
'OGDH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.66

Table S790.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
OGDH MUTATED 10 5 3 1
OGDH WILD-TYPE 125 107 66 78
'OGDH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.881 (Fisher's exact test), Q value = 0.98

Table S791.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
OGDH MUTATED 4 4 5
OGDH WILD-TYPE 116 102 98
'OGDH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.88

Table S792.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
OGDH MUTATED 2 4 5 2
OGDH WILD-TYPE 85 110 93 28
'OGDH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.9

Table S793.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
OGDH MUTATED 7 7 4
OGDH WILD-TYPE 107 166 100
'OGDH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 0.97

Table S794.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
OGDH MUTATED 5 4 9
OGDH WILD-TYPE 111 102 160
'OGDH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.82

Table S795.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
OGDH MUTATED 7 6 6
OGDH WILD-TYPE 112 90 171
'OGDH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.72

Table S796.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
OGDH MUTATED 5 6 1 3 4
OGDH WILD-TYPE 81 93 88 62 49
'OGDH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.68

Table S797.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
OGDH MUTATED 7 3 3 6
OGDH WILD-TYPE 86 40 124 113
'OGDH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.636 (Fisher's exact test), Q value = 0.89

Table S798.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
OGDH MUTATED 2 3 4 5 0 5
OGDH WILD-TYPE 72 44 84 60 27 76
'POU3F1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.56

Table S799.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
POU3F1 MUTATED 0 2 0 1
POU3F1 WILD-TYPE 162 135 59 33
'POU3F1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.58

Table S800.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
POU3F1 MUTATED 0 1 0 2
POU3F1 WILD-TYPE 135 111 69 77
'POU3F1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0307 (Fisher's exact test), Q value = 0.31

Table S801.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
POU3F1 MUTATED 0 0 3
POU3F1 WILD-TYPE 120 106 100

Figure S108.  Get High-res Image Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'POU3F1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 0.89

Table S802.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
POU3F1 MUTATED 0 1 2 0
POU3F1 WILD-TYPE 87 113 96 30
'POU3F1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.58

Table S803.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
POU3F1 MUTATED 2 0 1
POU3F1 WILD-TYPE 112 173 103
'POU3F1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.79 (Fisher's exact test), Q value = 0.94

Table S804.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
POU3F1 MUTATED 1 0 2
POU3F1 WILD-TYPE 115 106 167
'POU3F1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.66

Table S805.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
POU3F1 MUTATED 0 2 1
POU3F1 WILD-TYPE 119 94 176
'POU3F1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.624 (Fisher's exact test), Q value = 0.89

Table S806.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 86 99 89 65 53
POU3F1 MUTATED 1 2 0 0 0
POU3F1 WILD-TYPE 85 97 89 65 53
'POU3F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.32

Table S807.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
POU3F1 MUTATED 0 2 1 0
POU3F1 WILD-TYPE 93 41 126 119

Figure S109.  Get High-res Image Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'POU3F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.51

Table S808.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 47 88 65 27 81
POU3F1 MUTATED 0 2 1 0 0 0
POU3F1 WILD-TYPE 74 45 87 65 27 81
Methods & Data
Input

  • Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline

  • Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/BLCA-TP/19921883/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/20125359/BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 395

  • Number of significantly mutated genes = 81

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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