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 118 genes and 10 molecular subtypes across 395 patients, 34 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

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

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

  • ERCC2 mutation correlated to 'CN_CNMF'.

  • CREBBP mutation correlated to 'MIRSEQ_CNMF'.

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

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

  • TFG mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NFE2L3 mutation correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 118 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, 34 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
(0.000983) 		1e-05
(0.000983) 		0.0677
(0.559) 		0.0112
(0.276) 		2e-05
(0.00169) 		1e-05
(0.000983) 		1e-05
(0.000983) 		1e-05
(0.000983) 		1e-05
(0.000983) 		1e-05
(0.000983)
TP53 196 (50%) 199 1e-05
(0.000983) 		1e-05
(0.000983) 		0.03
(0.437) 		0.00619
(0.22) 		0.0172
(0.337) 		2e-05
(0.00169) 		0.293
(0.837) 		0.00501
(0.219) 		0.0202
(0.346) 		4e-05
(0.00295)
RB1 70 (18%) 325 1e-05
(0.000983) 		0.031
(0.441) 		0.72
(1.00) 		0.0748
(0.566) 		3e-05
(0.00236) 		1e-05
(0.000983) 		0.264
(0.808) 		0.14
(0.704) 		0.00325
(0.153) 		1e-05
(0.000983)
BAP1 14 (4%) 381 0.0792
(0.574) 		0.00593
(0.22) 		0.74
(1.00) 		0.469
(0.945) 		0.0969
(0.591) 		0.00568
(0.22) 		0.0119
(0.282) 		0.409
(0.899) 		0.00556
(0.22) 		0.00607
(0.22)
KDM6A 103 (26%) 292 0.148
(0.712) 		0.00117
(0.0767) 		0.594
(0.992) 		0.283
(0.829) 		0.00292
(0.145) 		0.0115
(0.276) 		0.479
(0.946) 		0.149
(0.713) 		0.0505
(0.509) 		0.0295
(0.437)
STAG2 56 (14%) 339 0.0297
(0.437) 		0.00354
(0.161) 		0.137
(0.704) 		0.462
(0.945) 		0.412
(0.903) 		0.00635
(0.22) 		0.0448
(0.491) 		0.18
(0.735) 		0.02
(0.346) 		0.047
(0.508)
NFE2L2 24 (6%) 371 0.00018
(0.0125) 		0.0793
(0.574) 		0.257
(0.805) 		0.683
(1.00) 		0.00196
(0.11) 		0.00806
(0.264) 		0.0768
(0.566) 		0.656
(1.00) 		0.39
(0.894) 		0.142
(0.707)
TFG 11 (3%) 384 0.543
(0.981) 		0.086
(0.574) 		0.372
(0.892) 		0.0915
(0.577) 		0.00546
(0.22) 		0.0976
(0.591) 		0.178
(0.735) 		0.21
(0.771) 		0.0754
(0.566) 		0.00176
(0.104)
ERCC2 38 (10%) 357 0.00294
(0.145) 		0.0826
(0.574) 		0.0954
(0.591) 		0.0589
(0.53) 		0.798
(1.00) 		0.706
(1.00) 		0.0966
(0.591) 		0.403
(0.896) 		0.284
(0.829) 		0.00936
(0.268)
CREBBP 48 (12%) 347 0.444
(0.934) 		0.425
(0.917) 		0.985
(1.00) 		0.159
(0.714) 		0.175
(0.73) 		0.544
(0.981) 		0.00247
(0.132) 		0.0339
(0.442) 		0.0848
(0.574) 		0.463
(0.945)
NFE2L3 14 (4%) 381 0.315
(0.843) 		0.00136
(0.0845) 		0.109
(0.622) 		0.869
(1.00) 		0.65
(1.00) 		0.106
(0.618) 		1
(1.00) 		0.568
(0.981) 		0.879
(1.00) 		0.768
(1.00)
PIK3CA 86 (22%) 309 0.329
(0.853) 		0.959
(1.00) 		0.322
(0.853) 		0.729
(1.00) 		0.63
(0.998) 		0.766
(1.00) 		0.939
(1.00) 		0.949
(1.00) 		0.946
(1.00) 		0.602
(0.994)
CDKN2A 26 (7%) 369 0.346
(0.864) 		0.0166
(0.333) 		0.416
(0.91) 		0.207
(0.769) 		0.184
(0.743) 		0.45
(0.938) 		0.839
(1.00) 		0.0542
(0.521) 		0.0381
(0.45) 		0.151
(0.714)
RHOB 26 (7%) 369 0.0385
(0.45) 		0.241
(0.789) 		0.576
(0.984) 		0.525
(0.981) 		0.376
(0.893) 		0.162
(0.714) 		0.839
(1.00) 		0.639
(1.00) 		0.89
(1.00) 		0.88
(1.00)
ELF3 46 (12%) 349 0.377
(0.893) 		0.104
(0.609) 		0.654
(1.00) 		0.522
(0.981) 		0.0259
(0.419) 		0.0421
(0.469) 		0.28
(0.827) 		0.33
(0.853) 		0.376
(0.893) 		0.608
(0.998)
TSC1 33 (8%) 362 0.333
(0.855) 		0.914
(1.00) 		0.612
(0.998) 		0.567
(0.981) 		0.126
(0.668) 		0.234
(0.785) 		0.144
(0.707) 		0.0658
(0.552) 		0.629
(0.998) 		0.708
(1.00)
CDKN1A 35 (9%) 360 0.702
(1.00) 		0.203
(0.76) 		0.731
(1.00) 		0.876
(1.00) 		0.385
(0.893) 		0.356
(0.875) 		0.0292
(0.437) 		0.168
(0.714) 		0.677
(1.00) 		0.598
(0.993)
EP300 61 (15%) 334 0.568
(0.981) 		0.877
(1.00) 		0.384
(0.893) 		0.385
(0.893) 		0.349
(0.866) 		0.31
(0.842) 		0.668
(1.00) 		0.645
(1.00) 		0.335
(0.857) 		0.155
(0.714)
ARID1A 97 (25%) 298 0.621
(0.998) 		0.347
(0.865) 		0.456
(0.939) 		0.154
(0.714) 		0.571
(0.981) 		0.782
(1.00) 		0.0752
(0.566) 		0.169
(0.714) 		0.285
(0.831) 		0.0404
(0.46)
ZFP36L1 29 (7%) 366 0.615
(0.998) 		0.469
(0.945) 		0.93
(1.00) 		0.233
(0.785) 		1
(1.00) 		0.331
(0.854) 		1
(1.00) 		0.479
(0.946) 		0.982
(1.00) 		0.0974
(0.591)
FBXW7 32 (8%) 363 0.395
(0.895) 		0.273
(0.814) 		0.276
(0.82) 		0.666
(1.00) 		0.819
(1.00) 		0.25
(0.794) 		0.129
(0.683) 		0.225
(0.783) 		0.0796
(0.574) 		0.157
(0.714)
HRAS 17 (4%) 378 0.37
(0.891) 		0.015
(0.322) 		0.0113
(0.276) 		0.233
(0.785) 		0.7
(1.00) 		0.776
(1.00) 		1
(1.00) 		0.297
(0.837) 		0.316
(0.843) 		0.19
(0.743)
KRAS 14 (4%) 381 0.0317
(0.442) 		0.773
(1.00) 		0.478
(0.946) 		0.0982
(0.591) 		0.315
(0.843) 		0.404
(0.896) 		0.625
(0.998) 		0.496
(0.964)
RHOA 18 (5%) 377 0.214
(0.772) 		0.35
(0.868) 		0.18
(0.735) 		0.403
(0.896) 		0.408
(0.899) 		0.483
(0.951) 		0.0515
(0.509) 		0.0896
(0.577) 		0.769
(1.00) 		0.628
(0.998)
PTEN 14 (4%) 381 0.887
(1.00) 		0.094
(0.59) 		0.424
(0.917) 		0.432
(0.922) 		0.673
(1.00) 		0.159
(0.714) 		1
(1.00) 		0.96
(1.00) 		0.697
(1.00) 		0.756
(1.00)
C3ORF70 17 (4%) 378 0.682
(1.00) 		0.169
(0.714) 		0.188
(0.743) 		1
(1.00) 		0.95
(1.00) 		0.568
(0.981) 		0.774
(1.00) 		0.534
(0.981) 		0.788
(1.00) 		0.927
(1.00)
RBM10 22 (6%) 373 0.817
(1.00) 		0.199
(0.76) 		0.471
(0.945) 		0.891
(1.00) 		0.562
(0.981) 		0.886
(1.00) 		0.424
(0.917) 		0.805
(1.00) 		0.3
(0.837) 		0.17
(0.717)
PSIP1 20 (5%) 375 0.425
(0.917) 		0.0229
(0.386) 		0.0956
(0.591) 		0.313
(0.843) 		0.171
(0.717) 		0.0165
(0.333) 		0.0505
(0.509) 		0.00971
(0.268) 		0.0353
(0.444) 		0.0179
(0.341)
ASXL2 36 (9%) 359 0.188
(0.743) 		0.544
(0.981) 		0.313
(0.843) 		0.553
(0.981) 		0.619
(0.998) 		0.59
(0.992) 		0.364
(0.886) 		0.542
(0.981) 		0.389
(0.894) 		0.696
(1.00)
FAT1 50 (13%) 345 0.0711
(0.566) 		0.0657
(0.552) 		0.307
(0.84) 		0.714
(1.00) 		0.558
(0.981) 		0.196
(0.754) 		0.106
(0.618) 		0.654
(1.00) 		0.187
(0.743) 		0.0895
(0.577)
SPTAN1 45 (11%) 350 0.327
(0.853) 		0.218
(0.776) 		0.936
(1.00) 		0.168
(0.714) 		0.226
(0.785) 		0.204
(0.761) 		0.239
(0.785) 		0.0767
(0.566) 		0.041
(0.461) 		0.0659
(0.552)
ZBTB7B 11 (3%) 384 0.0885
(0.577) 		0.826
(1.00) 		0.396
(0.896) 		0.39
(0.894) 		0.54
(0.981) 		0.399
(0.896) 		0.359
(0.878) 		0.227
(0.785) 		0.474
(0.946) 		0.0181
(0.341)
CUL1 19 (5%) 376 0.631
(0.998) 		0.92
(1.00) 		0.683
(1.00) 		0.156
(0.714) 		0.572
(0.982) 		0.454
(0.939) 		0.409
(0.899) 		0.904
(1.00) 		0.467
(0.945) 		0.581
(0.987)
KLF5 23 (6%) 372 0.139
(0.704) 		0.98
(1.00) 		0.271
(0.814) 		0.306
(0.84) 		0.63
(0.998) 		0.706
(1.00) 		0.49
(0.959) 		0.122
(0.66) 		0.0196
(0.346) 		0.236
(0.785)
RXRA 24 (6%) 371 0.0405
(0.46) 		0.00859
(0.268) 		0.141
(0.704) 		0.721
(1.00) 		0.571
(0.981) 		0.26
(0.808) 		0.346
(0.864) 		0.0616
(0.547) 		0.37
(0.891) 		0.0727
(0.566)
GNA13 12 (3%) 383 0.738
(1.00) 		0.267
(0.811) 		0.726
(1.00) 		0.931
(1.00) 		0.0856
(0.574) 		0.368
(0.891) 		0.675
(1.00) 		0.354
(0.873) 		0.0725
(0.566) 		0.809
(1.00)
METTL3 17 (4%) 378 0.236
(0.785) 		0.641
(1.00) 		0.333
(0.855) 		0.222
(0.776) 		0.264
(0.808) 		0.0402
(0.46) 		0.636
(1.00) 		0.283
(0.829)
ERBB3 41 (10%) 354 0.312
(0.843) 		0.385
(0.893) 		0.59
(0.992) 		0.398
(0.896) 		0.381
(0.893) 		0.219
(0.776) 		0.791
(1.00) 		0.898
(1.00) 		0.877
(1.00) 		0.688
(1.00)
RUNX1 14 (4%) 381 0.0284
(0.437) 		0.473
(0.946) 		1
(1.00) 		0.19
(0.743) 		0.193
(0.744) 		0.222
(0.776) 		0.621
(0.998) 		0.775
(1.00) 		0.912
(1.00) 		0.62
(0.998)
MBD1 13 (3%) 382 0.0867
(0.574) 		0.979
(1.00) 		0.812
(1.00) 		0.715
(1.00) 		0.593
(0.992) 		0.518
(0.981) 		0.287
(0.832) 		0.553
(0.981) 		0.462
(0.945) 		0.508
(0.979)
FOXQ1 14 (4%) 381 0.541
(0.981) 		0.66
(1.00) 		0.53
(0.981) 		0.264
(0.808) 		0.303
(0.837) 		0.886
(1.00) 		0.935
(1.00) 		0.904
(1.00) 		0.933
(1.00) 		0.985
(1.00)
RPTN 15 (4%) 380 0.845
(1.00) 		0.89
(1.00) 		0.0902
(0.577) 		0.329
(0.853) 		1
(1.00) 		1
(1.00) 		0.75
(1.00) 		0.11
(0.622) 		0.865
(1.00) 		0.653
(1.00)
SF1 10 (3%) 385 0.0487
(0.509) 		0.655
(1.00) 		1
(1.00) 		0.189
(0.743) 		0.778
(1.00) 		1
(1.00) 		0.00793
(0.264) 		0.202
(0.76) 		0.167
(0.714) 		0.0148
(0.322)
DNAH6 16 (4%) 379 0.617
(0.998) 		0.103
(0.609) 		0.534
(0.981) 		0.625
(0.998) 		0.00883
(0.268) 		0.0114
(0.276) 		1
(1.00) 		0.0337
(0.442) 		0.056
(0.521) 		0.0167
(0.333)
ZNF185 5 (1%) 390 0.0914
(0.577) 		0.561
(0.981) 		0.612
(0.998) 		0.865
(1.00) 		0.45
(0.938) 		0.181
(0.736) 		0.805
(1.00) 		0.788
(1.00)
ATM 53 (13%) 342 0.564
(0.981) 		0.687
(1.00) 		0.18
(0.735) 		0.821
(1.00) 		0.618
(0.998) 		0.654
(1.00) 		0.0748
(0.566) 		0.212
(0.771) 		0.223
(0.777) 		0.18
(0.735)
UNC93B1 7 (2%) 388 0.278
(0.824) 		1
(1.00) 		0.556
(0.981) 		0.889
(1.00) 		0.791
(1.00) 		0.959
(1.00) 		0.716
(1.00) 		0.718
(1.00)
UBA52 7 (2%) 388 0.49
(0.959) 		0.66
(1.00) 		0.715
(1.00) 		0.213
(0.772) 		0.288
(0.832) 		0.88
(1.00) 		0.835
(1.00) 		0.901
(1.00)
CNOT1 21 (5%) 374 0.121
(0.659) 		0.524
(0.981) 		0.415
(0.908) 		0.86
(1.00) 		0.616
(0.998) 		0.451
(0.938) 		0.53
(0.981) 		0.715
(1.00) 		0.95
(1.00) 		0.965
(1.00)
ERBB2 48 (12%) 347 0.432
(0.922) 		0.43
(0.922) 		0.156
(0.714) 		0.408
(0.899) 		0.279
(0.826) 		0.205
(0.763) 		0.759
(1.00) 		0.185
(0.743) 		0.186
(0.743) 		0.288
(0.832)
FAM47C 21 (5%) 374 0.556
(0.981) 		0.811
(1.00) 		0.0574
(0.525) 		0.182
(0.738) 		0.212
(0.771) 		0.718
(1.00) 		0.252
(0.797) 		0.165
(0.714) 		0.831
(1.00) 		0.742
(1.00)
SF3B1 24 (6%) 371 0.13
(0.683) 		0.79
(1.00) 		0.267
(0.811) 		0.429
(0.922) 		0.832
(1.00) 		0.615
(0.998) 		0.962
(1.00) 		0.936
(1.00) 		0.22
(0.776) 		0.33
(0.853)
EPS8 14 (4%) 381 0.111
(0.622) 		0.515
(0.981) 		0.782
(1.00) 		0.941
(1.00) 		0.0634
(0.552) 		0.676
(1.00) 		0.192
(0.744) 		0.273
(0.814)
EPHA2 19 (5%) 376 0.841
(1.00) 		0.0196
(0.346) 		0.448
(0.938) 		0.938
(1.00) 		0.165
(0.714) 		1
(1.00) 		0.447
(0.936) 		0.16
(0.714) 		0.586
(0.99) 		0.37
(0.891)
OGDH 19 (5%) 376 0.0559
(0.521) 		0.247
(0.793) 		0.144
(0.707) 		0.326
(0.853) 		0.677
(1.00) 		0.866
(1.00) 		0.446
(0.936) 		0.315
(0.843) 		0.262
(0.808) 		0.636
(1.00)
SCARF2 8 (2%) 387 0.56
(0.981) 		0.0652
(0.552) 		0.0348
(0.442) 		0.162
(0.714) 		0.661
(1.00) 		0.22
(0.776) 		0.336
(0.857) 		0.569
(0.981)
SSH3 15 (4%) 380 0.0182
(0.341) 		0.0955
(0.591) 		0.533
(0.981) 		0.868
(1.00) 		0.0496
(0.509) 		0.398
(0.896) 		0.0699
(0.566) 		0.103
(0.609) 		0.338
(0.858) 		0.256
(0.805)
HLA-A 5 (1%) 390 0.906
(1.00) 		0.303
(0.837) 		0.864
(1.00) 		1
(1.00) 		0.722
(1.00) 		0.722
(1.00) 		0.69
(1.00) 		0.495
(0.964)
PARD3 23 (6%) 372 0.715
(1.00) 		0.544
(0.981) 		0.824
(1.00) 		0.263
(0.808) 		0.892
(1.00) 		0.762
(1.00) 		0.157
(0.714) 		0.606
(0.998) 		0.534
(0.981) 		0.754
(1.00)
RIPK4 17 (4%) 378 0.531
(0.981) 		0.0747
(0.566) 		1
(1.00) 		1
(1.00) 		0.0505
(0.509) 		0.015
(0.322) 		0.733
(1.00) 		0.779
(1.00) 		0.271
(0.814) 		0.117
(0.648)
TMCO4 12 (3%) 383 0.477
(0.946) 		0.0367
(0.45) 		0.418
(0.912) 		0.073
(0.566) 		0.393
(0.895) 		0.301
(0.837) 		0.0763
(0.566) 		0.0856
(0.574)
CDH1 14 (4%) 381 0.574
(0.982) 		0.731
(1.00) 		1
(1.00) 		0.753
(1.00) 		0.94
(1.00) 		0.401
(0.896) 		0.264
(0.808) 		0.0595
(0.532) 		0.603
(0.994) 		0.326
(0.853)
NRAS 7 (2%) 388 0.34
(0.86) 		0.47
(0.945) 		0.797
(1.00) 		0.64
(1.00) 		0.13
(0.683) 		0.464
(0.945) 		0.0288
(0.437) 		0.085
(0.574)
ARID1B 23 (6%) 372 0.00998
(0.268) 		0.214
(0.772) 		0.925
(1.00) 		0.514
(0.981) 		0.0856
(0.574) 		0.0569
(0.525) 		0.0838
(0.574) 		0.0585
(0.53) 		0.391
(0.894) 		0.2
(0.76)
ZNF511 10 (3%) 385 0.554
(0.981) 		0.342
(0.863) 		1
(1.00) 		1
(1.00) 		0.759
(1.00) 		0.148
(0.712) 		0.561
(0.981) 		0.467
(0.945)
FUS 9 (2%) 386 0.296
(0.837) 		0.799
(1.00) 		0.148
(0.712) 		1
(1.00) 		0.755
(1.00) 		0.359
(0.878) 		0.692
(1.00) 		0.345
(0.864) 		0.959
(1.00) 		0.991
(1.00)
ASXL1 22 (6%) 373 0.135
(0.701) 		0.0376
(0.45) 		0.79
(1.00) 		0.289
(0.832) 		0.642
(1.00) 		0.379
(0.893) 		0.0503
(0.509) 		0.302
(0.837) 		0.453
(0.939) 		0.161
(0.714)
CNOT3 11 (3%) 384 0.1
(0.597) 		0.625
(0.998) 		0.118
(0.648) 		0.803
(1.00) 		0.0911
(0.577) 		0.0895
(0.577) 		1
(1.00) 		0.0674
(0.559) 		0.00969
(0.268) 		0.0135
(0.307)
ARID2 29 (7%) 366 0.378
(0.893) 		0.399
(0.896) 		0.494
(0.963) 		0.263
(0.808) 		0.248
(0.793) 		0.189
(0.743) 		0.0126
(0.292) 		0.308
(0.841) 		0.0195
(0.346) 		0.161
(0.714)
ZNF773 7 (2%) 388 0.59
(0.992) 		0.592
(0.992) 		0.435
(0.923) 		0.501
(0.967) 		0.702
(1.00) 		0.634
(1.00) 		0.189
(0.743) 		0.324
(0.853)
DAZAP1 6 (2%) 389 0.741
(1.00) 		0.045
(0.491) 		0.18
(0.735) 		0.0104
(0.274) 		0.209
(0.771) 		0.024
(0.4) 		0.344
(0.864) 		0.428
(0.921)
ADC 6 (2%) 389 0.855
(1.00) 		0.638
(1.00) 		1
(1.00) 		0.582
(0.987) 		0.773
(1.00) 		0.309
(0.842) 		0.941
(1.00) 		0.707
(1.00)
FUT5 3 (1%) 392 1
(1.00) 		0.394
(0.895) 		0.791
(1.00) 		0.111
(0.622) 		0.797
(1.00) 		0.337
(0.857) 		0.847
(1.00) 		0.273
(0.814)
AHR 22 (6%) 373 0.545
(0.981) 		0.0533
(0.52) 		0.543
(0.981) 		0.211
(0.771) 		0.0644
(0.552) 		0.0755
(0.566) 		0.666
(1.00) 		0.313
(0.843) 		0.531
(0.981) 		0.511
(0.981)
THRAP3 14 (4%) 381 0.564
(0.981) 		0.336
(0.857) 		0.0723
(0.566) 		0.931
(1.00) 		0.836
(1.00) 		0.785
(1.00) 		1
(1.00) 		0.794
(1.00) 		1
(1.00) 		0.902
(1.00)
TFPI2 6 (2%) 389 0.742
(1.00) 		0.85
(1.00) 		0.773
(1.00) 		0.775
(1.00) 		0.67
(1.00) 		0.232
(0.785) 		0.202
(0.76) 		0.546
(0.981)
NPAS4 13 (3%) 382 0.249
(0.794) 		0.824
(1.00) 		0.803
(1.00) 		0.865
(1.00) 		0.823
(1.00) 		0.594
(0.992) 		0.549
(0.981) 		0.242
(0.789) 		0.433
(0.922) 		0.557
(0.981)
TAF11 7 (2%) 388 0.787
(1.00) 		0.307
(0.84) 		0.238
(0.785) 		0.886
(1.00) 		0.791
(1.00) 		0.923
(1.00) 		0.527
(0.981) 		0.641
(1.00)
BCL2L1 4 (1%) 391 0.0201
(0.346) 		0.0473
(0.508) 		0.296
(0.837) 		0.694
(1.00) 		0.371
(0.891) 		0.404
(0.896) 		0.382
(0.893) 		0.906
(1.00)
TRERF1 21 (5%) 374 0.318
(0.847) 		0.928
(1.00) 		0.813
(1.00) 		0.768
(1.00) 		0.956
(1.00) 		0.674
(1.00) 		1
(1.00) 		0.591
(0.992) 		0.74
(1.00) 		0.687
(1.00)
CHD2 25 (6%) 370 0.118
(0.648) 		0.597
(0.993) 		0.905
(1.00) 		0.612
(0.998) 		0.523
(0.981) 		0.629
(0.998) 		0.347
(0.865) 		0.454
(0.939) 		0.374
(0.893) 		0.442
(0.934)
USP28 13 (3%) 382 0.856
(1.00) 		0.653
(1.00) 		0.146
(0.712) 		0.581
(0.987) 		0.718
(1.00) 		1
(1.00) 		0.619
(0.998) 		0.487
(0.958) 		0.95
(1.00) 		0.838
(1.00)
GPS2 10 (3%) 385 0.716
(1.00) 		0.867
(1.00) 		0.478
(0.946) 		0.354
(0.873) 		0.922
(1.00) 		0.558
(0.981) 		0.238
(0.785) 		0.303
(0.837) 		1
(1.00) 		0.955
(1.00)
F7 8 (2%) 387 0.559
(0.981) 		0.421
(0.916) 		0.902
(1.00) 		0.543
(0.981) 		0.893
(1.00) 		0.217
(0.776) 		0.0345
(0.442) 		0.421
(0.916)
IRX4 8 (2%) 387 0.325
(0.853) 		0.382
(0.893) 		0.598
(0.993) 		0.443
(0.934) 		0.342
(0.863) 		0.735
(1.00) 		0.732
(1.00) 		0.75
(1.00) 		1
(1.00) 		0.974
(1.00)
HSP90AA1 22 (6%) 373 0.392
(0.895) 		0.96
(1.00) 		0.0858
(0.574) 		0.0348
(0.442) 		0.851
(1.00) 		0.757
(1.00) 		0.0822
(0.574) 		0.159
(0.714) 		1
(1.00) 		0.946
(1.00)
TTYH1 7 (2%) 388 0.789
(1.00) 		0.769
(1.00) 		0.328
(0.853) 		0.212
(0.771) 		0.161
(0.714) 		0.238
(0.785) 		0.201
(0.76) 		0.027
(0.426) 		0.0514
(0.509) 		0.248
(0.793)
IL10RB 7 (2%) 388 0.247
(0.793) 		0.833
(1.00) 		0.235
(0.785) 		1
(1.00) 		0.159
(0.714) 		0.889
(1.00) 		1
(1.00) 		0.827
(1.00) 		0.247
(0.793) 		0.884
(1.00)
THSD4 10 (3%) 385 0.744
(1.00) 		0.87
(1.00) 		0.926
(1.00) 		0.467
(0.945) 		0.714
(1.00) 		0.363
(0.885) 		0.141
(0.704) 		0.757
(1.00) 		0.73
(1.00) 		0.246
(0.793)
DDX3X 15 (4%) 380 0.562
(0.981) 		0.515
(0.981) 		0.924
(1.00) 		0.687
(1.00) 		1
(1.00) 		0.846
(1.00) 		1
(1.00) 		0.538
(0.981) 		0.269
(0.812) 		0.651
(1.00)
DGKG 14 (4%) 381 0.0333
(0.442) 		0.265
(0.808) 		0.295
(0.837) 		0.0655
(0.552) 		0.886
(1.00) 		0.888
(1.00) 		0.124
(0.665) 		0.405
(0.897) 		0.369
(0.891) 		0.0816
(0.574)
TAS2R9 6 (2%) 389 0.0383
(0.45) 		0.236
(0.785) 		0.435
(0.923) 		0.882
(1.00) 		0.491
(0.96) 		0.973
(1.00) 		0.889
(1.00) 		0.858
(1.00)
COL7A1 30 (8%) 365 0.236
(0.785) 		0.562
(0.981) 		0.768
(1.00) 		0.301
(0.837) 		0.914
(1.00) 		0.256
(0.805) 		0.221
(0.776) 		0.391
(0.894) 		0.574
(0.982) 		0.637
(1.00)
ZNF513 11 (3%) 384 0.296
(0.837) 		0.972
(1.00) 		0.293
(0.837) 		0.937
(1.00) 		0.456
(0.939) 		0.538
(0.981) 		1
(1.00) 		0.722
(1.00) 		0.916
(1.00) 		0.759
(1.00)
ACSL5 6 (2%) 389 0.852
(1.00) 		0.771
(1.00) 		0.431
(0.922) 		0.0308
(0.441) 		0.282
(0.829) 		0.193
(0.744) 		0.262
(0.808) 		0.234
(0.785)
C18ORF8 6 (2%) 389 0.74
(1.00) 		0.143
(0.707) 		0.88
(1.00) 		0.58
(0.987) 		1
(1.00) 		0.524
(0.981) 		0.941
(1.00) 		0.497
(0.964)
PRB2 7 (2%) 388 0.0518
(0.509) 		0.111
(0.622) 		0.0558
(0.521) 		0.868
(1.00) 		0.716
(1.00) 		0.564
(0.981) 		0.292
(0.837) 		0.549
(0.981) 		0.682
(1.00) 		0.63
(0.998)
POU3F1 3 (1%) 392 0.141
(0.704) 		0.167
(0.714) 		0.172
(0.718) 		0.79
(1.00) 		0.246
(0.793) 		0.626
(0.998) 		0.0345
(0.442) 		0.119
(0.649)
EZR 12 (3%) 383 0.303
(0.837) 		0.894
(1.00) 		0.783
(1.00) 		0.719
(1.00) 		0.569
(0.981) 		0.869
(1.00) 		0.703
(1.00) 		0.322
(0.853) 		0.95
(1.00) 		0.744
(1.00)
ZEB2 16 (4%) 379 0.297
(0.837) 		0.122
(0.66) 		0.898
(1.00) 		0.808
(1.00) 		0.596
(0.993) 		0.0244
(0.4) 		0.867
(1.00) 		0.966
(1.00)
C12ORF43 8 (2%) 387 0.134
(0.7) 		0.52
(0.981) 		0.166
(0.714) 		0.0863
(0.574) 		1
(1.00) 		0.719
(1.00) 		0.0514
(0.509) 		0.252
(0.797) 		0.527
(0.981) 		0.551
(0.981)
NAP1L1 10 (3%) 385 0.0365
(0.45) 		0.269
(0.812) 		0.556
(0.981) 		0.231
(0.785) 		0.167
(0.714) 		0.0555
(0.521) 		0.475
(0.946) 		0.569
(0.981)
NAALADL1 7 (2%) 388 0.706
(1.00) 		0.909
(1.00) 		1
(1.00) 		0.8
(1.00) 		0.701
(1.00) 		0.941
(1.00) 		0.0828
(0.574) 		0.287
(0.832)
DENND5B 20 (5%) 375 0.387
(0.894) 		0.164
(0.714) 		0.11
(0.622) 		0.0099
(0.268) 		0.137
(0.704) 		0.453
(0.939) 		0.384
(0.893) 		0.872
(1.00) 		0.771
(1.00) 		0.807
(1.00)
SF3B3 21 (5%) 374 0.985
(1.00) 		0.957
(1.00) 		0.151
(0.714) 		0.4
(0.896) 		0.49
(0.959) 		0.2
(0.76) 		0.6
(0.993) 		0.95
(1.00) 		0.849
(1.00) 		0.158
(0.714)
KIAA1522 15 (4%) 380 0.087
(0.574) 		0.793
(1.00) 		0.229
(0.785) 		0.149
(0.713) 		0.141
(0.704) 		0.712
(1.00) 		0.152
(0.714) 		0.0755
(0.566) 		0.586
(0.99) 		0.24
(0.788)
GTF2I 16 (4%) 379 0.0092
(0.268) 		0.629
(0.998) 		0.109
(0.622) 		0.671
(1.00) 		0.849
(1.00) 		0.723
(1.00) 		0.517
(0.981) 		0.946
(1.00) 		0.517
(0.981) 		0.146
(0.712)
MOAP1 7 (2%) 388 0.628
(0.998) 		0.236
(0.785) 		0.807
(1.00) 		1
(1.00) 		0.066
(0.552) 		0.639
(1.00) 		0.549
(0.981) 		0.6
(0.993) 		0.866
(1.00) 		0.692
(1.00)
GAR1 4 (1%) 391 0.441
(0.934) 		0.118
(0.648) 		1
(1.00) 		0.693
(1.00) 		0.582
(0.987) 		0.95
(1.00) 		0.55
(0.981) 		0.323
(0.853)
RFTN2 11 (3%) 384 0.404
(0.896) 		0.0382
(0.45) 		0.476
(0.946) 		0.193
(0.744) 		0.74
(1.00) 		0.239
(0.785) 		0.927
(1.00) 		0.378
(0.893) 		0.665
(1.00) 		0.056
(0.521)
ZFP36L2 17 (4%) 378 0.523
(0.981) 		0.763
(1.00) 		0.558
(0.981) 		0.656
(1.00) 		0.737
(1.00) 		0.701
(1.00) 		0.819
(1.00) 		0.777
(1.00) 		0.839
(1.00) 		0.771
(1.00)
GUCY2C 13 (3%) 382 0.661
(1.00) 		0.733
(1.00) 		0.479
(0.946) 		0.444
(0.934) 		0.769
(1.00) 		0.77
(1.00) 		0.221
(0.776) 		0.993
(1.00) 		0.954
(1.00) 		0.209
(0.771)
COPZ2 3 (1%) 392 0.14
(0.704) 		0.074
(0.566) 		0.257
(0.805) 		0.11
(0.622) 		0.61
(0.998) 		0.468
(0.945)
ZNF791 10 (3%) 385 0.77
(1.00) 		0.805
(1.00) 		0.0153
(0.322) 		0.506
(0.975) 		0.385
(0.893) 		0.169
(0.714) 		0.0806
(0.574) 		0.389
(0.894)
BUD13 11 (3%) 384 0.304
(0.837) 		0.2
(0.76) 		0.951
(1.00) 		0.522
(0.981) 		0.462
(0.945) 		0.0993
(0.595) 		0.583
(0.987) 		0.358
(0.878) 		0.5
(0.967) 		0.499
(0.966)
HES1 11 (3%) 384 0.849
(1.00) 		0.825
(1.00) 		0.373
(0.893) 		0.125
(0.666) 		0.63
(0.998) 		0.63
(0.998) 		0.674
(1.00) 		0.47
(0.945) 		0.328
(0.853) 		0.57
(0.981)
HORMAD1 11 (3%) 384 0.033
(0.442) 		0.0266
(0.425) 		0.929
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.464
(0.945) 		0.0319
(0.442) 		0.772
(1.00) 		0.83
(1.00) 		0.917
(1.00)
SND1 9 (2%) 386 0.84
(1.00) 		0.907
(1.00) 		0.648
(1.00) 		0.352
(0.871) 		1
(1.00) 		0.528
(0.981) 		0.757
(1.00) 		0.878
(1.00) 		0.902
(1.00) 		0.978
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

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 = 1e-05 (Fisher's exact test), Q value = 0.00098

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 = 0.03 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
TP53 MUTATED 15 11 25 1 11
TP53 WILD-TYPE 22 18 11 4 9

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 = 0.00619 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
TP53 MUTATED 16 16 21 10
TP53 WILD-TYPE 27 22 6 9

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 = 0.0172 (Fisher's exact test), Q value = 0.34

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 = 2e-05 (Fisher's exact test), Q value = 0.0017

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 = 0.293 (Fisher's exact test), Q value = 0.84

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 = 0.00501 (Fisher's exact test), Q value = 0.22

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 = 0.0202 (Fisher's exact test), Q value = 0.35

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 = 4e-05 (Fisher's exact test), Q value = 0.0029

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'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.85

Table S11.  Gene #2: '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 S12.  Gene #2: '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 = 0.322 (Fisher's exact test), Q value = 0.85

Table S13.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
PIK3CA MUTATED 6 6 11 0 2
PIK3CA WILD-TYPE 31 23 25 5 18
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
PIK3CA MUTATED 9 9 5 2
PIK3CA WILD-TYPE 34 29 22 17
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S15.  Gene #2: '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 = 0.766 (Fisher's exact test), Q value = 1

Table S16.  Gene #2: '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 = 0.939 (Fisher's exact test), Q value = 1

Table S17.  Gene #2: '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 = 0.949 (Fisher's exact test), Q value = 1

Table S18.  Gene #2: '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 = 1

Table S19.  Gene #2: '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 = 0.602 (Fisher's exact test), Q value = 0.99

Table S20.  Gene #2: '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
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

Table S21.  Gene #3: '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 #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.031 (Fisher's exact test), Q value = 0.44

Table S22.  Gene #3: '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 #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RB1 MUTATED 4 6 7 0 3
RB1 WILD-TYPE 33 23 29 5 17
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0748 (Fisher's exact test), Q value = 0.57

Table S24.  Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RB1 MUTATED 3 7 8 2
RB1 WILD-TYPE 40 31 19 17
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0024

Table S25.  Gene #3: '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 S12.  Get High-res Image Gene #3: '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 = 0.00098

Table S26.  Gene #3: '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 S13.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.81

Table S27.  Gene #3: '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 = 0.14 (Fisher's exact test), Q value = 0.7

Table S28.  Gene #3: '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 = 0.00325 (Fisher's exact test), Q value = 0.15

Table S29.  Gene #3: '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 S14.  Get High-res Image Gene #3: '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 = 0.00098

Table S30.  Gene #3: '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 S15.  Get High-res Image Gene #3: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00098

Table S31.  Gene #4: '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 S16.  Get High-res Image Gene #4: '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 = 0.00098

Table S32.  Gene #4: '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 S17.  Get High-res Image Gene #4: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0677 (Fisher's exact test), Q value = 0.56

Table S33.  Gene #4: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
FGFR3 MUTATED 9 2 4 0 0
FGFR3 WILD-TYPE 28 27 32 5 20
'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0112 (Fisher's exact test), Q value = 0.28

Table S34.  Gene #4: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
FGFR3 MUTATED 9 0 4 2
FGFR3 WILD-TYPE 34 38 23 17

Figure S18.  Get High-res Image Gene #4: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0017

Table S35.  Gene #4: '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 S19.  Get High-res Image Gene #4: '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 = 0.00098

Table S36.  Gene #4: '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 S20.  Get High-res Image Gene #4: '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 = 0.00098

Table S37.  Gene #4: '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 S21.  Get High-res Image Gene #4: '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 = 0.00098

Table S38.  Gene #4: '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 S22.  Get High-res Image Gene #4: '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 = 0.00098

Table S39.  Gene #4: '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 S23.  Get High-res Image Gene #4: '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 = 0.00098

Table S40.  Gene #4: '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 S24.  Get High-res Image Gene #4: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.86

Table S41.  Gene #5: '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 = 0.0166 (Fisher's exact test), Q value = 0.33

Table S42.  Gene #5: '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 #5: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 0.91

Table S43.  Gene #5: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CDKN2A MUTATED 2 0 4 0 1
CDKN2A WILD-TYPE 35 29 32 5 19
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.77

Table S44.  Gene #5: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CDKN2A MUTATED 3 0 2 2
CDKN2A WILD-TYPE 40 38 25 17
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.74

Table S45.  Gene #5: '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 = 0.45 (Fisher's exact test), Q value = 0.94

Table S46.  Gene #5: '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 = 0.839 (Fisher's exact test), Q value = 1

Table S47.  Gene #5: '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 = 0.0542 (Fisher's exact test), Q value = 0.52

Table S48.  Gene #5: '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 = 0.0381 (Fisher's exact test), Q value = 0.45

Table S49.  Gene #5: '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 S26.  Get High-res Image Gene #5: '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 = 0.71

Table S50.  Gene #5: '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
'RHOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0385 (Fisher's exact test), Q value = 0.45

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 S27.  Get High-res Image Gene #6: 'RHOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RHOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 0.79

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 = 0.576 (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 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RHOB MUTATED 2 1 4 0 0
RHOB WILD-TYPE 35 28 32 5 20
'RHOB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.525 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RHOB MUTATED 2 2 3 0
RHOB WILD-TYPE 41 36 24 19
'RHOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.89

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 = 0.71

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 = 0.839 (Fisher's exact test), Q value = 1

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 = 0.639 (Fisher's exact test), Q value = 1

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 = 0.89 (Fisher's exact test), Q value = 1

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 = 0.88 (Fisher's exact test), Q value = 1

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
'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.89

Table S61.  Gene #7: '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 = 0.104 (Fisher's exact test), Q value = 0.61

Table S62.  Gene #7: '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 = 0.654 (Fisher's exact test), Q value = 1

Table S63.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ELF3 MUTATED 4 3 3 0 0
ELF3 WILD-TYPE 33 26 33 5 20
'ELF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.522 (Fisher's exact test), Q value = 0.98

Table S64.  Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ELF3 MUTATED 3 4 3 0
ELF3 WILD-TYPE 40 34 24 19
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0259 (Fisher's exact test), Q value = 0.42

Table S65.  Gene #7: '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 S28.  Get High-res Image Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.47

Table S66.  Gene #7: '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 S29.  Get High-res Image Gene #7: 'ELF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.83

Table S67.  Gene #7: '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 = 0.33 (Fisher's exact test), Q value = 0.85

Table S68.  Gene #7: '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 = 0.376 (Fisher's exact test), Q value = 0.89

Table S69.  Gene #7: '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 = 1

Table S70.  Gene #7: '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 = 0.333 (Fisher's exact test), Q value = 0.86

Table S71.  Gene #8: '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 = 1

Table S72.  Gene #8: '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 = 0.612 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'TSC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
TSC1 MUTATED 6 2 2 0 2
TSC1 WILD-TYPE 31 27 34 5 18
'TSC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 0.98

Table S74.  Gene #8: 'TSC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
TSC1 MUTATED 6 3 1 2
TSC1 WILD-TYPE 37 35 26 17
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.67

Table S75.  Gene #8: '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 = 0.234 (Fisher's exact test), Q value = 0.79

Table S76.  Gene #8: '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 = 0.144 (Fisher's exact test), Q value = 0.71

Table S77.  Gene #8: '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 = 0.0658 (Fisher's exact test), Q value = 0.55

Table S78.  Gene #8: '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 = 0.629 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: '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 = 0.708 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: '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
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.71

Table S81.  Gene #9: '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 = 0.00117 (Fisher's exact test), Q value = 0.077

Table S82.  Gene #9: '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 S30.  Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 0.99

Table S83.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
KDM6A MUTATED 9 5 10 2 3
KDM6A WILD-TYPE 28 24 26 3 17
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 0.83

Table S84.  Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
KDM6A MUTATED 9 7 10 3
KDM6A WILD-TYPE 34 31 17 16
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00292 (Fisher's exact test), Q value = 0.14

Table S85.  Gene #9: '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 S31.  Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.28

Table S86.  Gene #9: '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 S32.  Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.95

Table S87.  Gene #9: '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 = 0.149 (Fisher's exact test), Q value = 0.71

Table S88.  Gene #9: '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 = 0.0505 (Fisher's exact test), Q value = 0.51

Table S89.  Gene #9: '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 = 0.0295 (Fisher's exact test), Q value = 0.44

Table S90.  Gene #9: '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 S33.  Get High-res Image Gene #9: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: '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 = 0.203 (Fisher's exact test), Q value = 0.76

Table S92.  Gene #10: '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 = 0.731 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CDKN1A MUTATED 6 4 5 1 1
CDKN1A WILD-TYPE 31 25 31 4 19
'CDKN1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CDKN1A MUTATED 7 4 4 2
CDKN1A WILD-TYPE 36 34 23 17
'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.89

Table S95.  Gene #10: '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 = 0.87

Table S96.  Gene #10: '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 = 0.0292 (Fisher's exact test), Q value = 0.44

Table S97.  Gene #10: '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 S34.  Get High-res Image Gene #10: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.71

Table S98.  Gene #10: '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 = 0.677 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: '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 = 0.598 (Fisher's exact test), Q value = 0.99

Table S100.  Gene #10: '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 = 0.98

Table S101.  Gene #11: '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 = 0.877 (Fisher's exact test), Q value = 1

Table S102.  Gene #11: '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 = 0.384 (Fisher's exact test), Q value = 0.89

Table S103.  Gene #11: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
EP300 MUTATED 4 3 5 2 4
EP300 WILD-TYPE 33 26 31 3 16
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.89

Table S104.  Gene #11: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
EP300 MUTATED 8 3 3 4
EP300 WILD-TYPE 35 35 24 15
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 0.87

Table S105.  Gene #11: '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 = 0.31 (Fisher's exact test), Q value = 0.84

Table S106.  Gene #11: '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 = 1

Table S107.  Gene #11: '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 = 0.645 (Fisher's exact test), Q value = 1

Table S108.  Gene #11: '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 = 0.335 (Fisher's exact test), Q value = 0.86

Table S109.  Gene #11: '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 = 0.155 (Fisher's exact test), Q value = 0.71

Table S110.  Gene #11: '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
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: '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 = 0.86

Table S112.  Gene #12: '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 = 0.456 (Fisher's exact test), Q value = 0.94

Table S113.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ARID1A MUTATED 12 8 6 2 4
ARID1A WILD-TYPE 25 21 30 3 16
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.71

Table S114.  Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ARID1A MUTATED 11 14 5 2
ARID1A WILD-TYPE 32 24 22 17
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 0.98

Table S115.  Gene #12: '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 = 1

Table S116.  Gene #12: '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 = 0.0752 (Fisher's exact test), Q value = 0.57

Table S117.  Gene #12: '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 = 0.169 (Fisher's exact test), Q value = 0.71

Table S118.  Gene #12: '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 = 0.285 (Fisher's exact test), Q value = 0.83

Table S119.  Gene #12: '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 = 0.0404 (Fisher's exact test), Q value = 0.46

Table S120.  Gene #12: '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 S35.  Get High-res Image Gene #12: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.44

Table S121.  Gene #13: '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 S36.  Get High-res Image Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00354 (Fisher's exact test), Q value = 0.16

Table S122.  Gene #13: '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 S37.  Get High-res Image Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.7

Table S123.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
STAG2 MUTATED 8 4 3 0 0
STAG2 WILD-TYPE 29 25 33 5 20
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 0.94

Table S124.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
STAG2 MUTATED 8 3 2 2
STAG2 WILD-TYPE 35 35 25 17
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.9

Table S125.  Gene #13: '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 = 0.00635 (Fisher's exact test), Q value = 0.22

Table S126.  Gene #13: '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 S38.  Get High-res Image Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.49

Table S127.  Gene #13: '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 S39.  Get High-res Image Gene #13: '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 = 0.74

Table S128.  Gene #13: '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 = 0.02 (Fisher's exact test), Q value = 0.35

Table S129.  Gene #13: '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 S40.  Get High-res Image Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.047 (Fisher's exact test), Q value = 0.51

Table S130.  Gene #13: '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 S41.  Get High-res Image Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ERCC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00294 (Fisher's exact test), Q value = 0.14

Table S131.  Gene #14: '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 S42.  Get High-res Image Gene #14: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ERCC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0826 (Fisher's exact test), Q value = 0.57

Table S132.  Gene #14: '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 = 0.0954 (Fisher's exact test), Q value = 0.59

Table S133.  Gene #14: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ERCC2 MUTATED 3 0 6 1 1
ERCC2 WILD-TYPE 34 29 30 4 19
'ERCC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0589 (Fisher's exact test), Q value = 0.53

Table S134.  Gene #14: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ERCC2 MUTATED 3 1 6 1
ERCC2 WILD-TYPE 40 37 21 18
'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S135.  Gene #14: '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 = 0.706 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: '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 = 0.0966 (Fisher's exact test), Q value = 0.59

Table S137.  Gene #14: '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 = 0.403 (Fisher's exact test), Q value = 0.9

Table S138.  Gene #14: '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 = 0.284 (Fisher's exact test), Q value = 0.83

Table S139.  Gene #14: '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 = 0.00936 (Fisher's exact test), Q value = 0.27

Table S140.  Gene #14: '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 S43.  Get High-res Image Gene #14: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: '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 10 5 4
ZFP36L1 WILD-TYPE 152 127 54 30
'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.94

Table S142.  Gene #15: '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 7 10 4 8
ZFP36L1 WILD-TYPE 128 102 65 71
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S143.  Gene #15: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ZFP36L1 MUTATED 2 1 3 0 1
ZFP36L1 WILD-TYPE 35 28 33 5 19
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.79

Table S144.  Gene #15: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ZFP36L1 MUTATED 1 1 3 2
ZFP36L1 WILD-TYPE 42 37 24 17
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S145.  Gene #15: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZFP36L1 MUTATED 8 13 8
ZFP36L1 WILD-TYPE 106 160 96
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 0.85

Table S146.  Gene #15: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZFP36L1 MUTATED 11 9 9
ZFP36L1 WILD-TYPE 105 97 160
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S147.  Gene #15: 'ZFP36L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZFP36L1 MUTATED 9 7 13
ZFP36L1 WILD-TYPE 110 89 164
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.95

Table S148.  Gene #15: '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 5 5 6 7 6
ZFP36L1 WILD-TYPE 81 94 83 58 47
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.982 (Fisher's exact test), Q value = 1

Table S149.  Gene #15: '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 6 3 10 9
ZFP36L1 WILD-TYPE 87 40 117 110
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0974 (Fisher's exact test), Q value = 0.59

Table S150.  Gene #15: '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 12 2 0 4
ZFP36L1 WILD-TYPE 68 43 76 63 27 77
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.9

Table S151.  Gene #16: '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 16 8 6 1
FBXW7 WILD-TYPE 146 129 53 33
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.81

Table S152.  Gene #16: '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 8 3 5
FBXW7 WILD-TYPE 119 104 66 74
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 0.82

Table S153.  Gene #16: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
FBXW7 MUTATED 1 3 5 1 1
FBXW7 WILD-TYPE 36 26 31 4 19
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.666 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
FBXW7 MUTATED 2 4 3 2
FBXW7 WILD-TYPE 41 34 24 17
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S155.  Gene #16: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FBXW7 MUTATED 9 13 10
FBXW7 WILD-TYPE 105 160 94
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 0.79

Table S156.  Gene #16: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FBXW7 MUTATED 6 8 18
FBXW7 WILD-TYPE 110 98 151
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.68

Table S157.  Gene #16: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FBXW7 MUTATED 5 8 19
FBXW7 WILD-TYPE 114 88 158
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 0.78

Table S158.  Gene #16: '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 7 6 1
FBXW7 WILD-TYPE 75 92 82 59 52
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0796 (Fisher's exact test), Q value = 0.57

Table S159.  Gene #16: '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 10 5
FBXW7 WILD-TYPE 80 39 117 114
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.71

Table S160.  Gene #16: '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 7 4 2 11
FBXW7 WILD-TYPE 72 41 81 61 25 70
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 0.89

Table S161.  Gene #17: '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 = 0.015 (Fisher's exact test), Q value = 0.32

Table S162.  Gene #17: '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 S44.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0113 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
HRAS MUTATED 3 0 1 2 0
HRAS WILD-TYPE 34 29 35 3 20

Figure S45.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
HRAS MUTATED 4 0 1 1
HRAS WILD-TYPE 39 38 26 18
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: '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 = 0.776 (Fisher's exact test), Q value = 1

Table S166.  Gene #17: '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 S167.  Gene #17: '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 = 0.84

Table S168.  Gene #17: '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 = 0.316 (Fisher's exact test), Q value = 0.84

Table S169.  Gene #17: '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 = 0.74

Table S170.  Gene #17: '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
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.93

Table S171.  Gene #18: '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 = 0.92

Table S172.  Gene #18: '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 = 0.985 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CREBBP MUTATED 5 4 6 0 2
CREBBP WILD-TYPE 32 25 30 5 18
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CREBBP MUTATED 6 3 7 1
CREBBP WILD-TYPE 37 35 20 18
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.73

Table S175.  Gene #18: '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 = 0.544 (Fisher's exact test), Q value = 0.98

Table S176.  Gene #18: '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 = 0.00247 (Fisher's exact test), Q value = 0.13

Table S177.  Gene #18: '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 S46.  Get High-res Image Gene #18: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0339 (Fisher's exact test), Q value = 0.44

Table S178.  Gene #18: '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 S47.  Get High-res Image Gene #18: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0848 (Fisher's exact test), Q value = 0.57

Table S179.  Gene #18: '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 = 0.463 (Fisher's exact test), Q value = 0.94

Table S180.  Gene #18: '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
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0317 (Fisher's exact test), Q value = 0.44

Table S181.  Gene #19: '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 11 2 0 1
KRAS WILD-TYPE 151 135 59 33

Figure S48.  Get High-res Image Gene #19: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S182.  Gene #19: '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 6 2 2
KRAS WILD-TYPE 131 106 67 77
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.95

Table S183.  Gene #19: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
KRAS MUTATED 6 6 2
KRAS WILD-TYPE 108 167 102
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0982 (Fisher's exact test), Q value = 0.59

Table S184.  Gene #19: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
KRAS MUTATED 1 6 7
KRAS WILD-TYPE 115 100 162
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.84

Table S185.  Gene #19: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
KRAS MUTATED 4 1 8
KRAS WILD-TYPE 115 95 169
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.9

Table S186.  Gene #19: '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 4 2 1
KRAS WILD-TYPE 81 98 85 63 52
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S187.  Gene #19: '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 6 2
KRAS WILD-TYPE 90 42 121 117
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 0.96

Table S188.  Gene #19: '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 4 0 1 4
KRAS WILD-TYPE 72 46 84 65 26 77
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00018 (Fisher's exact test), Q value = 0.012

Table S189.  Gene #20: '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 S49.  Get High-res Image Gene #20: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0793 (Fisher's exact test), Q value = 0.57

Table S190.  Gene #20: '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 = 0.257 (Fisher's exact test), Q value = 0.8

Table S191.  Gene #20: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
NFE2L2 MUTATED 1 4 3 1 3
NFE2L2 WILD-TYPE 36 25 33 4 17
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S192.  Gene #20: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
NFE2L2 MUTATED 3 4 4 1
NFE2L2 WILD-TYPE 40 34 23 18
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00196 (Fisher's exact test), Q value = 0.11

Table S193.  Gene #20: '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 S50.  Get High-res Image Gene #20: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00806 (Fisher's exact test), Q value = 0.26

Table S194.  Gene #20: '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 S51.  Get High-res Image Gene #20: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0768 (Fisher's exact test), Q value = 0.57

Table S195.  Gene #20: '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 = 0.656 (Fisher's exact test), Q value = 1

Table S196.  Gene #20: '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 = 0.39 (Fisher's exact test), Q value = 0.89

Table S197.  Gene #20: '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 = 0.142 (Fisher's exact test), Q value = 0.71

Table S198.  Gene #20: '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
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.77

Table S199.  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 = 0.35 (Fisher's exact test), Q value = 0.87

Table S200.  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 = 0.18 (Fisher's exact test), Q value = 0.74

Table S201.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RHOA MUTATED 2 1 0 1 1
RHOA WILD-TYPE 35 28 36 4 19
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.403 (Fisher's exact test), Q value = 0.9

Table S202.  Gene #21: 'RHOA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RHOA MUTATED 1 3 0 1
RHOA WILD-TYPE 42 35 27 18
'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.9

Table S203.  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 = 0.483 (Fisher's exact test), Q value = 0.95

Table S204.  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 = 0.0515 (Fisher's exact test), Q value = 0.51

Table S205.  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 = 0.0896 (Fisher's exact test), Q value = 0.58

Table S206.  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 = 0.769 (Fisher's exact test), Q value = 1

Table S207.  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 = 1

Table S208.  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
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S209.  Gene #22: '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 = 0.094 (Fisher's exact test), Q value = 0.59

Table S210.  Gene #22: '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 = 0.424 (Fisher's exact test), Q value = 0.92

Table S211.  Gene #22: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
PTEN MUTATED 1 0 2 0 2
PTEN WILD-TYPE 36 29 34 5 18
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 0.92

Table S212.  Gene #22: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
PTEN MUTATED 1 1 1 2
PTEN WILD-TYPE 42 37 26 17
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 1

Table S213.  Gene #22: '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 = 0.159 (Fisher's exact test), Q value = 0.71

Table S214.  Gene #22: '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 S215.  Gene #22: '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 S216.  Gene #22: '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 = 0.697 (Fisher's exact test), Q value = 1

Table S217.  Gene #22: '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 = 0.756 (Fisher's exact test), Q value = 1

Table S218.  Gene #22: '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 = 0.682 (Fisher's exact test), Q value = 1

Table S219.  Gene #23: '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 = 0.169 (Fisher's exact test), Q value = 0.71

Table S220.  Gene #23: '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 = 0.188 (Fisher's exact test), Q value = 0.74

Table S221.  Gene #23: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
C3ORF70 MUTATED 2 0 2 1 0
C3ORF70 WILD-TYPE 35 29 34 4 20
'C3ORF70 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S222.  Gene #23: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
C3ORF70 MUTATED 2 1 1 1
C3ORF70 WILD-TYPE 41 37 26 18
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S223.  Gene #23: '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 = 0.568 (Fisher's exact test), Q value = 0.98

Table S224.  Gene #23: '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 = 0.774 (Fisher's exact test), Q value = 1

Table S225.  Gene #23: '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 = 0.98

Table S226.  Gene #23: '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 = 0.788 (Fisher's exact test), Q value = 1

Table S227.  Gene #23: '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 = 0.927 (Fisher's exact test), Q value = 1

Table S228.  Gene #23: '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
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S229.  Gene #24: '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 = 0.76

Table S230.  Gene #24: '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 = 0.471 (Fisher's exact test), Q value = 0.94

Table S231.  Gene #24: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RBM10 MUTATED 1 1 4 0 0
RBM10 WILD-TYPE 36 28 32 5 20
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S232.  Gene #24: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RBM10 MUTATED 3 2 1 0
RBM10 WILD-TYPE 40 36 26 19
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.98

Table S233.  Gene #24: '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 = 1

Table S234.  Gene #24: '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 = 0.424 (Fisher's exact test), Q value = 0.92

Table S235.  Gene #24: '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 = 0.805 (Fisher's exact test), Q value = 1

Table S236.  Gene #24: '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 = 0.3 (Fisher's exact test), Q value = 0.84

Table S237.  Gene #24: '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 = 0.72

Table S238.  Gene #24: '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
'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.92

Table S239.  Gene #25: '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 = 0.0229 (Fisher's exact test), Q value = 0.39

Table S240.  Gene #25: '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 S52.  Get High-res Image Gene #25: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0956 (Fisher's exact test), Q value = 0.59

Table S241.  Gene #25: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
PSIP1 MUTATED 3 2 0 1 0
PSIP1 WILD-TYPE 34 27 36 4 20
'PSIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.84

Table S242.  Gene #25: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
PSIP1 MUTATED 4 2 0 0
PSIP1 WILD-TYPE 39 36 27 19
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 0.72

Table S243.  Gene #25: '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 = 0.0165 (Fisher's exact test), Q value = 0.33

Table S244.  Gene #25: '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 S53.  Get High-res Image Gene #25: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0505 (Fisher's exact test), Q value = 0.51

Table S245.  Gene #25: '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 = 0.00971 (Fisher's exact test), Q value = 0.27

Table S246.  Gene #25: '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 S54.  Get High-res Image Gene #25: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0353 (Fisher's exact test), Q value = 0.44

Table S247.  Gene #25: '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 S55.  Get High-res Image Gene #25: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.34

Table S248.  Gene #25: '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 S56.  Get High-res Image Gene #25: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 0.74

Table S249.  Gene #26: '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 = 0.544 (Fisher's exact test), Q value = 0.98

Table S250.  Gene #26: '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 = 0.313 (Fisher's exact test), Q value = 0.84

Table S251.  Gene #26: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ASXL2 MUTATED 4 1 3 1 0
ASXL2 WILD-TYPE 33 28 33 4 20
'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 0.98

Table S252.  Gene #26: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ASXL2 MUTATED 4 2 3 0
ASXL2 WILD-TYPE 39 36 24 19
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 1

Table S253.  Gene #26: '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 = 0.59 (Fisher's exact test), Q value = 0.99

Table S254.  Gene #26: '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 = 0.89

Table S255.  Gene #26: '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 = 0.98

Table S256.  Gene #26: '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 = 0.389 (Fisher's exact test), Q value = 0.89

Table S257.  Gene #26: '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 = 1

Table S258.  Gene #26: '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
'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0711 (Fisher's exact test), Q value = 0.57

Table S259.  Gene #27: '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 = 0.0657 (Fisher's exact test), Q value = 0.55

Table S260.  Gene #27: '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 = 0.307 (Fisher's exact test), Q value = 0.84

Table S261.  Gene #27: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
FAT1 MUTATED 3 3 6 2 2
FAT1 WILD-TYPE 34 26 30 3 18
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S262.  Gene #27: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
FAT1 MUTATED 4 5 5 2
FAT1 WILD-TYPE 39 33 22 17
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.98

Table S263.  Gene #27: '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 = 0.196 (Fisher's exact test), Q value = 0.75

Table S264.  Gene #27: '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 = 0.106 (Fisher's exact test), Q value = 0.62

Table S265.  Gene #27: '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 = 0.654 (Fisher's exact test), Q value = 1

Table S266.  Gene #27: '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 = 0.187 (Fisher's exact test), Q value = 0.74

Table S267.  Gene #27: '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 = 0.0895 (Fisher's exact test), Q value = 0.58

Table S268.  Gene #27: '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
'SPTAN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.85

Table S269.  Gene #28: '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 = 0.78

Table S270.  Gene #28: '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 = 0.936 (Fisher's exact test), Q value = 1

Table S271.  Gene #28: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
SPTAN1 MUTATED 5 4 4 1 2
SPTAN1 WILD-TYPE 32 25 32 4 18
'SPTAN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.71

Table S272.  Gene #28: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
SPTAN1 MUTATED 9 5 1 1
SPTAN1 WILD-TYPE 34 33 26 18
'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.79

Table S273.  Gene #28: '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 = 0.204 (Fisher's exact test), Q value = 0.76

Table S274.  Gene #28: '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 = 0.239 (Fisher's exact test), Q value = 0.79

Table S275.  Gene #28: '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 = 0.0767 (Fisher's exact test), Q value = 0.57

Table S276.  Gene #28: '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 = 0.041 (Fisher's exact test), Q value = 0.46

Table S277.  Gene #28: '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 S57.  Get High-res Image Gene #28: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0659 (Fisher's exact test), Q value = 0.55

Table S278.  Gene #28: '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
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0885 (Fisher's exact test), Q value = 0.58

Table S279.  Gene #29: '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 = 0.826 (Fisher's exact test), Q value = 1

Table S280.  Gene #29: '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 = 0.396 (Fisher's exact test), Q value = 0.9

Table S281.  Gene #29: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ZBTB7B MUTATED 0 2 2 0 0
ZBTB7B WILD-TYPE 37 27 34 5 20
'ZBTB7B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.89

Table S282.  Gene #29: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ZBTB7B MUTATED 0 2 1 1
ZBTB7B WILD-TYPE 43 36 26 18
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.98

Table S283.  Gene #29: '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 = 0.399 (Fisher's exact test), Q value = 0.9

Table S284.  Gene #29: '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 = 0.359 (Fisher's exact test), Q value = 0.88

Table S285.  Gene #29: '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 = 0.79

Table S286.  Gene #29: '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 = 0.474 (Fisher's exact test), Q value = 0.95

Table S287.  Gene #29: '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 = 0.0181 (Fisher's exact test), Q value = 0.34

Table S288.  Gene #29: '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 S58.  Get High-res Image Gene #29: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CUL1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S289.  Gene #30: '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 = 0.92 (Fisher's exact test), Q value = 1

Table S290.  Gene #30: '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 = 0.683 (Fisher's exact test), Q value = 1

Table S291.  Gene #30: 'CUL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CUL1 MUTATED 3 1 1 0 2
CUL1 WILD-TYPE 34 28 35 5 18
'CUL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 0.71

Table S292.  Gene #30: 'CUL1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CUL1 MUTATED 4 0 1 2
CUL1 WILD-TYPE 39 38 26 17
'CUL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 0.98

Table S293.  Gene #30: '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 = 0.454 (Fisher's exact test), Q value = 0.94

Table S294.  Gene #30: '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 = 0.409 (Fisher's exact test), Q value = 0.9

Table S295.  Gene #30: '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 = 0.904 (Fisher's exact test), Q value = 1

Table S296.  Gene #30: '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 = 0.467 (Fisher's exact test), Q value = 0.94

Table S297.  Gene #30: '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 = 0.581 (Fisher's exact test), Q value = 0.99

Table S298.  Gene #30: '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
'KLF5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.7

Table S299.  Gene #31: '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 S300.  Gene #31: '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 = 0.271 (Fisher's exact test), Q value = 0.81

Table S301.  Gene #31: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
KLF5 MUTATED 4 1 4 1 0
KLF5 WILD-TYPE 33 28 32 4 20
'KLF5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 0.84

Table S302.  Gene #31: 'KLF5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
KLF5 MUTATED 6 2 2 0
KLF5 WILD-TYPE 37 36 25 19
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S303.  Gene #31: '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 = 0.706 (Fisher's exact test), Q value = 1

Table S304.  Gene #31: '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 = 0.96

Table S305.  Gene #31: '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 = 0.122 (Fisher's exact test), Q value = 0.66

Table S306.  Gene #31: '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 = 0.0196 (Fisher's exact test), Q value = 0.35

Table S307.  Gene #31: '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 S59.  Get High-res Image Gene #31: '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 = 0.79

Table S308.  Gene #31: '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
'RXRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0405 (Fisher's exact test), Q value = 0.46

Table S309.  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 S60.  Get High-res Image Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RXRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00859 (Fisher's exact test), Q value = 0.27

Table S310.  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 S61.  Get High-res Image Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RXRA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.7

Table S311.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RXRA MUTATED 7 1 2 1 1
RXRA WILD-TYPE 30 28 34 4 19
'RXRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S312.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RXRA MUTATED 5 4 1 2
RXRA WILD-TYPE 38 34 26 17
'RXRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 0.98

Table S313.  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 = 0.26 (Fisher's exact test), Q value = 0.81

Table S314.  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 = 0.346 (Fisher's exact test), Q value = 0.86

Table S315.  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 = 0.0616 (Fisher's exact test), Q value = 0.55

Table S316.  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 = 0.37 (Fisher's exact test), Q value = 0.89

Table S317.  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 = 0.0727 (Fisher's exact test), Q value = 0.57

Table S318.  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
'GNA13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S319.  Gene #33: '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 = 0.267 (Fisher's exact test), Q value = 0.81

Table S320.  Gene #33: '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 = 0.726 (Fisher's exact test), Q value = 1

Table S321.  Gene #33: 'GNA13 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
GNA13 MUTATED 2 0 2 0 1
GNA13 WILD-TYPE 35 29 34 5 19
'GNA13 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S322.  Gene #33: 'GNA13 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
GNA13 MUTATED 2 2 1 0
GNA13 WILD-TYPE 41 36 26 19
'GNA13 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0856 (Fisher's exact test), Q value = 0.57

Table S323.  Gene #33: '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 = 0.368 (Fisher's exact test), Q value = 0.89

Table S324.  Gene #33: '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 = 0.675 (Fisher's exact test), Q value = 1

Table S325.  Gene #33: '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 = 0.354 (Fisher's exact test), Q value = 0.87

Table S326.  Gene #33: '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 = 0.0725 (Fisher's exact test), Q value = 0.57

Table S327.  Gene #33: '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 = 0.809 (Fisher's exact test), Q value = 1

Table S328.  Gene #33: '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
'METTL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.79

Table S329.  Gene #34: '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 = 0.641 (Fisher's exact test), Q value = 1

Table S330.  Gene #34: '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 'MRNASEQ_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.86

Table S331.  Gene #34: '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 = 0.222 (Fisher's exact test), Q value = 0.78

Table S332.  Gene #34: '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 = 0.264 (Fisher's exact test), Q value = 0.81

Table S333.  Gene #34: '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 = 0.0402 (Fisher's exact test), Q value = 0.46

Table S334.  Gene #34: '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 S62.  Get High-res Image Gene #34: 'METTL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'METTL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S335.  Gene #34: '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 = 0.283 (Fisher's exact test), Q value = 0.83

Table S336.  Gene #34: '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
'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.84

Table S337.  Gene #35: '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 = 0.385 (Fisher's exact test), Q value = 0.89

Table S338.  Gene #35: '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 = 0.59 (Fisher's exact test), Q value = 0.99

Table S339.  Gene #35: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ERBB3 MUTATED 6 3 3 1 1
ERBB3 WILD-TYPE 31 26 33 4 19
'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.9

Table S340.  Gene #35: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ERBB3 MUTATED 6 6 1 1
ERBB3 WILD-TYPE 37 32 26 18
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.89

Table S341.  Gene #35: '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 = 0.219 (Fisher's exact test), Q value = 0.78

Table S342.  Gene #35: '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 = 0.791 (Fisher's exact test), Q value = 1

Table S343.  Gene #35: '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 = 0.898 (Fisher's exact test), Q value = 1

Table S344.  Gene #35: '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 = 0.877 (Fisher's exact test), Q value = 1

Table S345.  Gene #35: '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 = 1

Table S346.  Gene #35: '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
'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.44

Table S347.  Gene #36: '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 10 2 0
RUNX1 WILD-TYPE 160 127 57 34

Figure S63.  Get High-res Image Gene #36: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 0.95

Table S348.  Gene #36: '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 6 3 1
RUNX1 WILD-TYPE 131 106 66 78
'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S349.  Gene #36: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RUNX1 MUTATED 1 1 1 0 0
RUNX1 WILD-TYPE 36 28 35 5 20
'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.74

Table S350.  Gene #36: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RUNX1 MUTATED 0 1 2 0
RUNX1 WILD-TYPE 43 37 25 19
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.74

Table S351.  Gene #36: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RUNX1 MUTATED 6 3 5
RUNX1 WILD-TYPE 108 170 99
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.78

Table S352.  Gene #36: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RUNX1 MUTATED 5 1 8
RUNX1 WILD-TYPE 111 105 161
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S353.  Gene #36: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RUNX1 MUTATED 3 2 8
RUNX1 WILD-TYPE 116 94 169
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S354.  Gene #36: '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 3 2
RUNX1 WILD-TYPE 82 97 87 62 51
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S355.  Gene #36: '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 5 3
RUNX1 WILD-TYPE 89 42 122 116
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S356.  Gene #36: '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 3 4 0 4
RUNX1 WILD-TYPE 73 46 85 61 27 77
'MBD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0867 (Fisher's exact test), Q value = 0.57

Table S357.  Gene #37: '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 4 2
MBD1 WILD-TYPE 160 132 55 32
'MBD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S358.  Gene #37: '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 4 4 2 3
MBD1 WILD-TYPE 131 108 67 76
'MBD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S359.  Gene #37: 'MBD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
MBD1 MUTATED 1 1 3 0 1
MBD1 WILD-TYPE 36 28 33 5 19
'MBD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S360.  Gene #37: 'MBD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
MBD1 MUTATED 1 2 2 1
MBD1 WILD-TYPE 42 36 25 18
'MBD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.593 (Fisher's exact test), Q value = 0.99

Table S361.  Gene #37: 'MBD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
MBD1 MUTATED 5 4 4
MBD1 WILD-TYPE 109 169 100
'MBD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.98

Table S362.  Gene #37: 'MBD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MBD1 MUTATED 2 4 7
MBD1 WILD-TYPE 114 102 162
'MBD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.83

Table S363.  Gene #37: 'MBD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
MBD1 MUTATED 3 1 8
MBD1 WILD-TYPE 116 95 169
'MBD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 0.98

Table S364.  Gene #37: '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 3
MBD1 WILD-TYPE 83 98 86 63 50
'MBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.94

Table S365.  Gene #37: '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 2
MBD1 WILD-TYPE 88 42 124 117
'MBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 0.98

Table S366.  Gene #37: '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 3 1 3 0 0 4
MBD1 WILD-TYPE 71 46 85 65 27 77
'FOXQ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.98

Table S367.  Gene #38: '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 = 0.66 (Fisher's exact test), Q value = 1

Table S368.  Gene #38: '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 = 0.53 (Fisher's exact test), Q value = 0.98

Table S369.  Gene #38: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
FOXQ1 MUTATED 2 0 2 0 2
FOXQ1 WILD-TYPE 35 29 34 5 18
'FOXQ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 0.81

Table S370.  Gene #38: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
FOXQ1 MUTATED 3 1 0 2
FOXQ1 WILD-TYPE 40 37 27 17
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.84

Table S371.  Gene #38: '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 = 1

Table S372.  Gene #38: '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 = 0.935 (Fisher's exact test), Q value = 1

Table S373.  Gene #38: '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 = 0.904 (Fisher's exact test), Q value = 1

Table S374.  Gene #38: '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 = 0.933 (Fisher's exact test), Q value = 1

Table S375.  Gene #38: '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 = 0.985 (Fisher's exact test), Q value = 1

Table S376.  Gene #38: '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
'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S377.  Gene #39: '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 = 0.89 (Fisher's exact test), Q value = 1

Table S378.  Gene #39: '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 = 0.0902 (Fisher's exact test), Q value = 0.58

Table S379.  Gene #39: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RPTN MUTATED 1 1 0 0 3
RPTN WILD-TYPE 36 28 36 5 17
'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 0.85

Table S380.  Gene #39: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RPTN MUTATED 2 1 0 2
RPTN WILD-TYPE 41 37 27 17
'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S381.  Gene #39: '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 S382.  Gene #39: '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 = 0.75 (Fisher's exact test), Q value = 1

Table S383.  Gene #39: '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 = 0.62

Table S384.  Gene #39: '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 = 1

Table S385.  Gene #39: '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 = 0.653 (Fisher's exact test), Q value = 1

Table S386.  Gene #39: '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
'SF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.51

Table S387.  Gene #40: '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

Figure S64.  Get High-res Image Gene #40: 'SF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S388.  Gene #40: '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 = 1 (Fisher's exact test), Q value = 1

Table S389.  Gene #40: 'SF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
SF1 MUTATED 1 1 1 0 0
SF1 WILD-TYPE 36 28 35 5 20
'SF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.74

Table S390.  Gene #40: 'SF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
SF1 MUTATED 0 1 2 0
SF1 WILD-TYPE 43 37 25 19
'SF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S391.  Gene #40: '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 S392.  Gene #40: '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 = 0.00793 (Fisher's exact test), Q value = 0.26

Table S393.  Gene #40: '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 S65.  Get High-res Image Gene #40: '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 = 0.76

Table S394.  Gene #40: '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 = 0.167 (Fisher's exact test), Q value = 0.71

Table S395.  Gene #40: '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 = 0.0148 (Fisher's exact test), Q value = 0.32

Table S396.  Gene #40: '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 S66.  Get High-res Image Gene #40: 'SF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'DNAH6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S397.  Gene #41: '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 = 0.103 (Fisher's exact test), Q value = 0.61

Table S398.  Gene #41: '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 = 0.534 (Fisher's exact test), Q value = 0.98

Table S399.  Gene #41: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
DNAH6 MUTATED 1 2 0 0 1
DNAH6 WILD-TYPE 36 27 36 5 19
'DNAH6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S400.  Gene #41: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
DNAH6 MUTATED 1 2 0 1
DNAH6 WILD-TYPE 42 36 27 18
'DNAH6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.27

Table S401.  Gene #41: '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 S67.  Get High-res Image Gene #41: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'DNAH6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0114 (Fisher's exact test), Q value = 0.28

Table S402.  Gene #41: '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 S68.  Get High-res Image Gene #41: '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 S403.  Gene #41: '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 = 0.0337 (Fisher's exact test), Q value = 0.44

Table S404.  Gene #41: '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 S69.  Get High-res Image Gene #41: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'DNAH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.056 (Fisher's exact test), Q value = 0.52

Table S405.  Gene #41: '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 = 0.0167 (Fisher's exact test), Q value = 0.33

Table S406.  Gene #41: '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 S70.  Get High-res Image Gene #41: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF185 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0914 (Fisher's exact test), Q value = 0.58

Table S407.  Gene #42: '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 = 0.561 (Fisher's exact test), Q value = 0.98

Table S408.  Gene #42: '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 'MRNASEQ_CNMF'

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

Table S409.  Gene #42: '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 = 1

Table S410.  Gene #42: '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 = 0.94

Table S411.  Gene #42: '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 = 0.74

Table S412.  Gene #42: '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 = 1

Table S413.  Gene #42: '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 = 0.788 (Fisher's exact test), Q value = 1

Table S414.  Gene #42: '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
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.98

Table S415.  Gene #43: '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 = 0.687 (Fisher's exact test), Q value = 1

Table S416.  Gene #43: '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 = 0.18 (Fisher's exact test), Q value = 0.74

Table S417.  Gene #43: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ATM MUTATED 2 3 3 1 5
ATM WILD-TYPE 35 26 33 4 15
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S418.  Gene #43: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ATM MUTATED 5 4 2 3
ATM WILD-TYPE 38 34 25 16
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S419.  Gene #43: '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 = 0.654 (Fisher's exact test), Q value = 1

Table S420.  Gene #43: '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 = 0.0748 (Fisher's exact test), Q value = 0.57

Table S421.  Gene #43: '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 = 0.212 (Fisher's exact test), Q value = 0.77

Table S422.  Gene #43: '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 = 0.223 (Fisher's exact test), Q value = 0.78

Table S423.  Gene #43: '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 = 0.74

Table S424.  Gene #43: '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 = 0.82

Table S425.  Gene #44: '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 S426.  Gene #44: '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 'MRNASEQ_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.98

Table S427.  Gene #44: '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 = 0.889 (Fisher's exact test), Q value = 1

Table S428.  Gene #44: '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 = 1

Table S429.  Gene #44: '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 = 0.959 (Fisher's exact test), Q value = 1

Table S430.  Gene #44: '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 = 1

Table S431.  Gene #44: '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 = 0.718 (Fisher's exact test), Q value = 1

Table S432.  Gene #44: '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
'UBA52 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.96

Table S433.  Gene #45: 'UBA52 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
UBA52 MUTATED 4 1 1 1
UBA52 WILD-TYPE 158 136 58 33
'UBA52 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S434.  Gene #45: 'UBA52 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
UBA52 MUTATED 1 3 1 2
UBA52 WILD-TYPE 134 109 68 77
'UBA52 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S435.  Gene #45: 'UBA52 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
UBA52 MUTATED 3 3 1
UBA52 WILD-TYPE 111 170 103
'UBA52 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.77

Table S436.  Gene #45: 'UBA52 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
UBA52 MUTATED 4 2 1
UBA52 WILD-TYPE 112 104 168
'UBA52 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.83

Table S437.  Gene #45: 'UBA52 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
UBA52 MUTATED 2 0 5
UBA52 WILD-TYPE 117 96 172
'UBA52 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S438.  Gene #45: 'UBA52 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
UBA52 MUTATED 1 1 2 2 1
UBA52 WILD-TYPE 85 98 87 63 52
'UBA52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S439.  Gene #45: 'UBA52 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
UBA52 MUTATED 1 0 2 3
UBA52 WILD-TYPE 92 43 125 116
'UBA52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S440.  Gene #45: 'UBA52 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
UBA52 MUTATED 1 0 2 2 0 1
UBA52 WILD-TYPE 73 47 86 63 27 80
'CNOT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.66

Table S441.  Gene #46: '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 = 0.98

Table S442.  Gene #46: '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 = 0.415 (Fisher's exact test), Q value = 0.91

Table S443.  Gene #46: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CNOT1 MUTATED 2 0 4 0 1
CNOT1 WILD-TYPE 35 29 32 5 19
'CNOT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S444.  Gene #46: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CNOT1 MUTATED 3 1 2 1
CNOT1 WILD-TYPE 40 37 25 18
'CNOT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 1

Table S445.  Gene #46: '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 = 0.451 (Fisher's exact test), Q value = 0.94

Table S446.  Gene #46: '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 = 0.53 (Fisher's exact test), Q value = 0.98

Table S447.  Gene #46: '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 = 0.715 (Fisher's exact test), Q value = 1

Table S448.  Gene #46: '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 = 1

Table S449.  Gene #46: '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 = 0.965 (Fisher's exact test), Q value = 1

Table S450.  Gene #46: '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
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 0.92

Table S451.  Gene #47: '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 = 0.43 (Fisher's exact test), Q value = 0.92

Table S452.  Gene #47: '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 = 0.156 (Fisher's exact test), Q value = 0.71

Table S453.  Gene #47: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ERBB2 MUTATED 3 0 3 1 0
ERBB2 WILD-TYPE 34 29 33 4 20
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.408 (Fisher's exact test), Q value = 0.9

Table S454.  Gene #47: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ERBB2 MUTATED 4 1 2 0
ERBB2 WILD-TYPE 39 37 25 19
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.83

Table S455.  Gene #47: '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 = 0.76

Table S456.  Gene #47: '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 = 0.759 (Fisher's exact test), Q value = 1

Table S457.  Gene #47: '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 = 0.185 (Fisher's exact test), Q value = 0.74

Table S458.  Gene #47: '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 = 0.186 (Fisher's exact test), Q value = 0.74

Table S459.  Gene #47: '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 = 0.288 (Fisher's exact test), Q value = 0.83

Table S460.  Gene #47: '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
'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.98

Table S461.  Gene #48: '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 = 0.811 (Fisher's exact test), Q value = 1

Table S462.  Gene #48: '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 = 0.0574 (Fisher's exact test), Q value = 0.53

Table S463.  Gene #48: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
FAM47C MUTATED 0 1 5 0 3
FAM47C WILD-TYPE 37 28 31 5 17
'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.74

Table S464.  Gene #48: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
FAM47C MUTATED 1 2 4 2
FAM47C WILD-TYPE 42 36 23 17
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.77

Table S465.  Gene #48: '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 = 0.718 (Fisher's exact test), Q value = 1

Table S466.  Gene #48: '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 = 0.252 (Fisher's exact test), Q value = 0.8

Table S467.  Gene #48: '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 = 0.71

Table S468.  Gene #48: '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 = 1

Table S469.  Gene #48: '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 = 0.742 (Fisher's exact test), Q value = 1

Table S470.  Gene #48: '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
'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.68

Table S471.  Gene #49: '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 = 1

Table S472.  Gene #49: '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 = 0.267 (Fisher's exact test), Q value = 0.81

Table S473.  Gene #49: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
SF3B1 MUTATED 3 0 3 1 1
SF3B1 WILD-TYPE 34 29 33 4 19
'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.92

Table S474.  Gene #49: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
SF3B1 MUTATED 5 1 1 1
SF3B1 WILD-TYPE 38 37 26 18
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S475.  Gene #49: '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 = 0.615 (Fisher's exact test), Q value = 1

Table S476.  Gene #49: '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 = 0.962 (Fisher's exact test), Q value = 1

Table S477.  Gene #49: '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 = 1

Table S478.  Gene #49: '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 = 0.22 (Fisher's exact test), Q value = 0.78

Table S479.  Gene #49: '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 = 0.33 (Fisher's exact test), Q value = 0.85

Table S480.  Gene #49: '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
'EPS8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.62

Table S481.  Gene #50: 'EPS8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
EPS8 MUTATED 2 7 3 2
EPS8 WILD-TYPE 160 130 56 32
'EPS8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.98

Table S482.  Gene #50: 'EPS8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
EPS8 MUTATED 5 6 2 1
EPS8 WILD-TYPE 130 106 67 78
'EPS8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 1

Table S483.  Gene #50: 'EPS8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
EPS8 MUTATED 5 5 4
EPS8 WILD-TYPE 109 168 100
'EPS8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S484.  Gene #50: 'EPS8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EPS8 MUTATED 4 3 7
EPS8 WILD-TYPE 112 103 162
'EPS8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0634 (Fisher's exact test), Q value = 0.55

Table S485.  Gene #50: 'EPS8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
EPS8 MUTATED 8 2 3
EPS8 WILD-TYPE 111 94 174
'EPS8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S486.  Gene #50: 'EPS8 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
EPS8 MUTATED 4 2 2 2 3
EPS8 WILD-TYPE 82 97 87 63 50
'EPS8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.74

Table S487.  Gene #50: 'EPS8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
EPS8 MUTATED 3 0 2 7
EPS8 WILD-TYPE 90 43 125 112
'EPS8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.81

Table S488.  Gene #50: 'EPS8 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
EPS8 MUTATED 4 0 1 4 0 3
EPS8 WILD-TYPE 70 47 87 61 27 78
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S489.  Gene #51: '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 = 0.0196 (Fisher's exact test), Q value = 0.35

Table S490.  Gene #51: '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 S71.  Get High-res Image Gene #51: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 0.94

Table S491.  Gene #51: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
EPHA2 MUTATED 2 1 2 1 0
EPHA2 WILD-TYPE 35 28 34 4 20
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S492.  Gene #51: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
EPHA2 MUTATED 3 1 1 1
EPHA2 WILD-TYPE 40 37 26 18
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.71

Table S493.  Gene #51: '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 S494.  Gene #51: '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 = 0.94

Table S495.  Gene #51: '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 = 0.16 (Fisher's exact test), Q value = 0.71

Table S496.  Gene #51: '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 = 0.586 (Fisher's exact test), Q value = 0.99

Table S497.  Gene #51: '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 = 0.37 (Fisher's exact test), Q value = 0.89

Table S498.  Gene #51: '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 = 0.0559 (Fisher's exact test), Q value = 0.52

Table S499.  Gene #52: '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 = 0.247 (Fisher's exact test), Q value = 0.79

Table S500.  Gene #52: '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 = 0.144 (Fisher's exact test), Q value = 0.71

Table S501.  Gene #52: 'OGDH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
OGDH MUTATED 1 0 1 1 0
OGDH WILD-TYPE 36 29 35 4 20
'OGDH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.85

Table S502.  Gene #52: 'OGDH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
OGDH MUTATED 2 0 0 1
OGDH WILD-TYPE 41 38 27 18
'OGDH MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S503.  Gene #52: '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 = 0.866 (Fisher's exact test), Q value = 1

Table S504.  Gene #52: '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 = 0.446 (Fisher's exact test), Q value = 0.94

Table S505.  Gene #52: '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 = 0.315 (Fisher's exact test), Q value = 0.84

Table S506.  Gene #52: '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 = 0.81

Table S507.  Gene #52: '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 = 1

Table S508.  Gene #52: '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
'SCARF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.98

Table S509.  Gene #53: '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 = 0.0652 (Fisher's exact test), Q value = 0.55

Table S510.  Gene #53: '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 'MRNASEQ_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.44

Table S511.  Gene #53: '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 S72.  Get High-res Image Gene #53: '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 = 0.71

Table S512.  Gene #53: '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 = 0.661 (Fisher's exact test), Q value = 1

Table S513.  Gene #53: '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 = 0.22 (Fisher's exact test), Q value = 0.78

Table S514.  Gene #53: '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 = 0.336 (Fisher's exact test), Q value = 0.86

Table S515.  Gene #53: '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 = 0.569 (Fisher's exact test), Q value = 0.98

Table S516.  Gene #53: '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
'SSH3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.34

Table S517.  Gene #54: '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 S73.  Get High-res Image Gene #54: 'SSH3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SSH3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0955 (Fisher's exact test), Q value = 0.59

Table S518.  Gene #54: '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 = 0.533 (Fisher's exact test), Q value = 0.98

Table S519.  Gene #54: 'SSH3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
SSH3 MUTATED 2 1 0 0 0
SSH3 WILD-TYPE 35 28 36 5 20
'SSH3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S520.  Gene #54: 'SSH3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
SSH3 MUTATED 2 1 0 0
SSH3 WILD-TYPE 41 37 27 19
'SSH3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.51

Table S521.  Gene #54: '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 S74.  Get High-res Image Gene #54: 'SSH3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SSH3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.9

Table S522.  Gene #54: '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 = 0.0699 (Fisher's exact test), Q value = 0.57

Table S523.  Gene #54: '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 = 0.103 (Fisher's exact test), Q value = 0.61

Table S524.  Gene #54: '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 = 0.86

Table S525.  Gene #54: '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 = 0.256 (Fisher's exact test), Q value = 0.8

Table S526.  Gene #54: '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
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S527.  Gene #55: '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 = 0.303 (Fisher's exact test), Q value = 0.84

Table S528.  Gene #55: '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 = 0.864 (Fisher's exact test), Q value = 1

Table S529.  Gene #55: '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 S530.  Gene #55: '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 = 0.722 (Fisher's exact test), Q value = 1

Table S531.  Gene #55: '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 = 0.722 (Fisher's exact test), Q value = 1

Table S532.  Gene #55: '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 = 0.69 (Fisher's exact test), Q value = 1

Table S533.  Gene #55: '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 = 0.495 (Fisher's exact test), Q value = 0.96

Table S534.  Gene #55: '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
'PARD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 1

Table S535.  Gene #56: '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 4 3
PARD3 WILD-TYPE 154 129 55 31
'PARD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 0.98

Table S536.  Gene #56: '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 9 8 4 2
PARD3 WILD-TYPE 126 104 65 77
'PARD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S537.  Gene #56: 'PARD3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
PARD3 MUTATED 3 2 2 0 0
PARD3 WILD-TYPE 34 27 34 5 20
'PARD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.81

Table S538.  Gene #56: 'PARD3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
PARD3 MUTATED 3 4 0 0
PARD3 WILD-TYPE 40 34 27 19
'PARD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S539.  Gene #56: 'PARD3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
PARD3 MUTATED 7 11 5
PARD3 WILD-TYPE 107 162 99
'PARD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S540.  Gene #56: 'PARD3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PARD3 MUTATED 6 5 12
PARD3 WILD-TYPE 110 101 157
'PARD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.71

Table S541.  Gene #56: 'PARD3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
PARD3 MUTATED 3 8 10
PARD3 WILD-TYPE 116 88 167
'PARD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S542.  Gene #56: '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 5 7 2 4 3
PARD3 WILD-TYPE 81 92 87 61 50
'PARD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 0.98

Table S543.  Gene #56: '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 5 4 5 5
PARD3 WILD-TYPE 88 39 122 114
'PARD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S544.  Gene #56: '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 3
PARD3 WILD-TYPE 70 43 83 62 27 78
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0792 (Fisher's exact test), Q value = 0.57

Table S545.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
BAP1 MUTATED 2 9 2 1
BAP1 WILD-TYPE 160 128 57 33
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00593 (Fisher's exact test), Q value = 0.22

Table S546.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
BAP1 MUTATED 0 8 3 3
BAP1 WILD-TYPE 135 104 66 76

Figure S75.  Get High-res Image Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S547.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
BAP1 MUTATED 2 0 1 0 1
BAP1 WILD-TYPE 35 29 35 5 19
'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.94

Table S548.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
BAP1 MUTATED 2 0 1 1
BAP1 WILD-TYPE 41 38 26 18
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0969 (Fisher's exact test), Q value = 0.59

Table S549.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
BAP1 MUTATED 3 10 1
BAP1 WILD-TYPE 111 163 103
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00568 (Fisher's exact test), Q value = 0.22

Table S550.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
BAP1 MUTATED 8 5 1
BAP1 WILD-TYPE 108 101 168

Figure S76.  Get High-res Image Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.28

Table S551.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
BAP1 MUTATED 0 6 8
BAP1 WILD-TYPE 119 90 169

Figure S77.  Get High-res Image Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.9

Table S552.  Gene #57: 'BAP1 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
BAP1 MUTATED 2 5 5 2 0
BAP1 WILD-TYPE 84 94 84 63 53
'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00556 (Fisher's exact test), Q value = 0.22

Table S553.  Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
BAP1 MUTATED 0 4 8 2
BAP1 WILD-TYPE 93 39 119 117

Figure S78.  Get High-res Image Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00607 (Fisher's exact test), Q value = 0.22

Table S554.  Gene #57: 'BAP1 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
BAP1 MUTATED 0 4 6 2 2 0
BAP1 WILD-TYPE 74 43 82 63 25 81

Figure S79.  Get High-res Image Gene #57: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RIPK4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.531 (Fisher's exact test), Q value = 0.98

Table S555.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RIPK4 MUTATED 6 8 1 2
RIPK4 WILD-TYPE 156 129 58 32
'RIPK4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 0.57

Table S556.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RIPK4 MUTATED 2 9 2 4
RIPK4 WILD-TYPE 133 103 67 75
'RIPK4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S557.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RIPK4 MUTATED 2 1 1 0 1
RIPK4 WILD-TYPE 35 28 35 5 19
'RIPK4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S558.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RIPK4 MUTATED 2 1 1 1
RIPK4 WILD-TYPE 41 37 26 18
'RIPK4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0505 (Fisher's exact test), Q value = 0.51

Table S559.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RIPK4 MUTATED 4 12 1
RIPK4 WILD-TYPE 110 161 103
'RIPK4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.015 (Fisher's exact test), Q value = 0.32

Table S560.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RIPK4 MUTATED 7 8 2
RIPK4 WILD-TYPE 109 98 167

Figure S80.  Get High-res Image Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RIPK4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S561.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RIPK4 MUTATED 4 5 8
RIPK4 WILD-TYPE 115 91 169
'RIPK4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S562.  Gene #58: 'RIPK4 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
RIPK4 MUTATED 2 4 4 4 3
RIPK4 WILD-TYPE 84 95 85 61 50
'RIPK4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.81

Table S563.  Gene #58: 'RIPK4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RIPK4 MUTATED 1 2 7 7
RIPK4 WILD-TYPE 92 41 120 112
'RIPK4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.65

Table S564.  Gene #58: 'RIPK4 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
RIPK4 MUTATED 5 1 6 4 1 0
RIPK4 WILD-TYPE 69 46 82 61 26 81
'TMCO4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 0.95

Table S565.  Gene #59: '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 = 0.0367 (Fisher's exact test), Q value = 0.45

Table S566.  Gene #59: '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 S81.  Get High-res Image Gene #59: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TMCO4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.91

Table S567.  Gene #59: '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 = 0.073 (Fisher's exact test), Q value = 0.57

Table S568.  Gene #59: '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 = 0.393 (Fisher's exact test), Q value = 0.9

Table S569.  Gene #59: '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 = 0.301 (Fisher's exact test), Q value = 0.84

Table S570.  Gene #59: '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 = 0.0763 (Fisher's exact test), Q value = 0.57

Table S571.  Gene #59: '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 = 0.0856 (Fisher's exact test), Q value = 0.57

Table S572.  Gene #59: '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
'CDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.98

Table S573.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CDH1 MUTATED 5 4 3 2
CDH1 WILD-TYPE 157 133 56 32
'CDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 1

Table S574.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CDH1 MUTATED 4 4 4 2
CDH1 WILD-TYPE 131 108 65 77
'CDH1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S575.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CDH1 MUTATED 2 1 1 0 1
CDH1 WILD-TYPE 35 28 35 5 19
'CDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S576.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CDH1 MUTATED 2 2 0 1
CDH1 WILD-TYPE 41 36 27 18
'CDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S577.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CDH1 MUTATED 4 7 3
CDH1 WILD-TYPE 110 166 101
'CDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.9

Table S578.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CDH1 MUTATED 2 5 7
CDH1 WILD-TYPE 114 101 162
'CDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.81

Table S579.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CDH1 MUTATED 6 1 7
CDH1 WILD-TYPE 113 95 170
'CDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 0.53

Table S580.  Gene #60: 'CDH1 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
CDH1 MUTATED 5 1 6 0 2
CDH1 WILD-TYPE 81 98 83 65 51
'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 0.99

Table S581.  Gene #60: 'CDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CDH1 MUTATED 4 0 6 4
CDH1 WILD-TYPE 89 43 121 115
'CDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.85

Table S582.  Gene #60: 'CDH1 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
CDH1 MUTATED 2 0 4 1 1 6
CDH1 WILD-TYPE 72 47 84 64 26 75
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.86

Table S583.  Gene #61: '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 = 0.47 (Fisher's exact test), Q value = 0.94

Table S584.  Gene #61: '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 'MRNASEQ_CNMF'

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

Table S585.  Gene #61: '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 = 0.64 (Fisher's exact test), Q value = 1

Table S586.  Gene #61: '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 = 0.68

Table S587.  Gene #61: '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 = 0.464 (Fisher's exact test), Q value = 0.94

Table S588.  Gene #61: '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 = 0.0288 (Fisher's exact test), Q value = 0.44

Table S589.  Gene #61: '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 S82.  Get High-res Image Gene #61: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.085 (Fisher's exact test), Q value = 0.57

Table S590.  Gene #61: '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
'ARID1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00998 (Fisher's exact test), Q value = 0.27

Table S591.  Gene #62: '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 S83.  Get High-res Image Gene #62: 'ARID1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.77

Table S592.  Gene #62: '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 = 0.925 (Fisher's exact test), Q value = 1

Table S593.  Gene #62: 'ARID1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ARID1B MUTATED 2 1 1 0 0
ARID1B WILD-TYPE 35 28 35 5 20
'ARID1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 0.98

Table S594.  Gene #62: 'ARID1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ARID1B MUTATED 3 1 0 0
ARID1B WILD-TYPE 40 37 27 19
'ARID1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0856 (Fisher's exact test), Q value = 0.57

Table S595.  Gene #62: '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 = 0.0569 (Fisher's exact test), Q value = 0.52

Table S596.  Gene #62: '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 = 0.0838 (Fisher's exact test), Q value = 0.57

Table S597.  Gene #62: '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 = 0.0585 (Fisher's exact test), Q value = 0.53

Table S598.  Gene #62: '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 = 0.391 (Fisher's exact test), Q value = 0.89

Table S599.  Gene #62: '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 = 0.76

Table S600.  Gene #62: '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
'ZNF511 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.98

Table S601.  Gene #63: 'ZNF511 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZNF511 MUTATED 4 5 0 1
ZNF511 WILD-TYPE 158 132 59 33
'ZNF511 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.86

Table S602.  Gene #63: 'ZNF511 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZNF511 MUTATED 4 3 3 0
ZNF511 WILD-TYPE 131 109 66 79
'ZNF511 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S603.  Gene #63: 'ZNF511 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZNF511 MUTATED 3 4 2
ZNF511 WILD-TYPE 111 169 102
'ZNF511 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S604.  Gene #63: 'ZNF511 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZNF511 MUTATED 3 2 4
ZNF511 WILD-TYPE 113 104 165
'ZNF511 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S605.  Gene #63: 'ZNF511 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZNF511 MUTATED 3 1 5
ZNF511 WILD-TYPE 116 95 172
'ZNF511 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.71

Table S606.  Gene #63: 'ZNF511 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
ZNF511 MUTATED 4 1 0 2 2
ZNF511 WILD-TYPE 82 98 89 63 51
'ZNF511 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 0.98

Table S607.  Gene #63: 'ZNF511 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZNF511 MUTATED 4 1 2 2
ZNF511 WILD-TYPE 89 42 125 117
'ZNF511 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.94

Table S608.  Gene #63: 'ZNF511 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
ZNF511 MUTATED 3 1 1 0 1 3
ZNF511 WILD-TYPE 71 46 87 65 26 78
'TFG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 0.98

Table S609.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TFG MUTATED 3 6 1 0
TFG WILD-TYPE 159 131 58 34
'TFG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.086 (Fisher's exact test), Q value = 0.57

Table S610.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TFG MUTATED 1 5 4 1
TFG WILD-TYPE 134 107 65 78
'TFG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.89

Table S611.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
TFG MUTATED 1 0 1 0 2
TFG WILD-TYPE 36 29 35 5 18
'TFG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0915 (Fisher's exact test), Q value = 0.58

Table S612.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
TFG MUTATED 2 0 0 2
TFG WILD-TYPE 41 38 27 17
'TFG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00546 (Fisher's exact test), Q value = 0.22

Table S613.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TFG MUTATED 0 10 1
TFG WILD-TYPE 114 163 103

Figure S84.  Get High-res Image Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TFG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0976 (Fisher's exact test), Q value = 0.59

Table S614.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TFG MUTATED 3 6 2
TFG WILD-TYPE 113 100 167
'TFG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.74

Table S615.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TFG MUTATED 1 2 8
TFG WILD-TYPE 118 94 169
'TFG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.77

Table S616.  Gene #64: 'TFG 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
TFG MUTATED 1 2 4 4 0
TFG WILD-TYPE 85 97 85 61 53
'TFG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0754 (Fisher's exact test), Q value = 0.57

Table S617.  Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TFG MUTATED 1 0 8 2
TFG WILD-TYPE 92 43 119 117
'TFG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00176 (Fisher's exact test), Q value = 0.1

Table S618.  Gene #64: 'TFG 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
TFG MUTATED 1 0 9 1 0 0
TFG WILD-TYPE 73 47 79 64 27 81

Figure S85.  Get High-res Image Gene #64: 'TFG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FUS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.84

Table S619.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FUS MUTATED 3 2 2 2
FUS WILD-TYPE 159 135 57 32
'FUS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S620.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FUS MUTATED 3 2 1 3
FUS WILD-TYPE 132 110 68 76
'FUS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.71

Table S621.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
FUS MUTATED 1 0 2 1 0
FUS WILD-TYPE 36 29 34 4 20
'FUS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S622.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
FUS MUTATED 2 1 1 0
FUS WILD-TYPE 41 37 26 19
'FUS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S623.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FUS MUTATED 3 3 3
FUS WILD-TYPE 111 170 101
'FUS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.88

Table S624.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FUS MUTATED 1 2 6
FUS WILD-TYPE 115 104 163
'FUS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S625.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FUS MUTATED 3 3 3
FUS WILD-TYPE 116 93 174
'FUS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 0.86

Table S626.  Gene #65: 'FUS 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
FUS MUTATED 1 2 1 4 1
FUS WILD-TYPE 85 97 88 61 52
'FUS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S627.  Gene #65: 'FUS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FUS MUTATED 2 1 2 3
FUS WILD-TYPE 91 42 125 116
'FUS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.991 (Fisher's exact test), Q value = 1

Table S628.  Gene #65: 'FUS 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
FUS MUTATED 1 1 2 2 0 2
FUS WILD-TYPE 73 46 86 63 27 79
'ASXL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.7

Table S629.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ASXL1 MUTATED 6 11 5 0
ASXL1 WILD-TYPE 156 126 54 34
'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0376 (Fisher's exact test), Q value = 0.45

Table S630.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ASXL1 MUTATED 7 12 1 2
ASXL1 WILD-TYPE 128 100 68 77

Figure S86.  Get High-res Image Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ASXL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S631.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ASXL1 MUTATED 4 1 2 0 2
ASXL1 WILD-TYPE 33 28 34 5 18
'ASXL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.83

Table S632.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ASXL1 MUTATED 5 3 0 1
ASXL1 WILD-TYPE 38 35 27 18
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S633.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ASXL1 MUTATED 5 12 5
ASXL1 WILD-TYPE 109 161 99
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 0.89

Table S634.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ASXL1 MUTATED 5 9 8
ASXL1 WILD-TYPE 111 97 161
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0503 (Fisher's exact test), Q value = 0.51

Table S635.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ASXL1 MUTATED 2 8 12
ASXL1 WILD-TYPE 117 88 165
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.84

Table S636.  Gene #66: 'ASXL1 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
ASXL1 MUTATED 4 8 3 6 1
ASXL1 WILD-TYPE 82 91 86 59 52
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.94

Table S637.  Gene #66: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ASXL1 MUTATED 5 3 10 4
ASXL1 WILD-TYPE 88 40 117 115
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.71

Table S638.  Gene #66: 'ASXL1 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
ASXL1 MUTATED 1 3 10 3 1 4
ASXL1 WILD-TYPE 73 44 78 62 26 77
'CNOT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.6

Table S639.  Gene #67: '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 2
CNOT3 WILD-TYPE 157 136 56 32
'CNOT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S640.  Gene #67: '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 2 1 2
CNOT3 WILD-TYPE 129 110 68 77
'CNOT3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.65

Table S641.  Gene #67: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CNOT3 MUTATED 2 2 0 1 0
CNOT3 WILD-TYPE 35 27 36 4 20
'CNOT3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S642.  Gene #67: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CNOT3 MUTATED 3 1 1 0
CNOT3 WILD-TYPE 40 37 26 19
'CNOT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0911 (Fisher's exact test), Q value = 0.58

Table S643.  Gene #67: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CNOT3 MUTATED 3 2 6
CNOT3 WILD-TYPE 111 171 98
'CNOT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0895 (Fisher's exact test), Q value = 0.58

Table S644.  Gene #67: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CNOT3 MUTATED 4 0 7
CNOT3 WILD-TYPE 112 106 162
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S645.  Gene #67: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CNOT3 MUTATED 3 3 5
CNOT3 WILD-TYPE 116 93 172
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0674 (Fisher's exact test), Q value = 0.56

Table S646.  Gene #67: '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 2 0
CNOT3 WILD-TYPE 83 93 89 63 53
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00969 (Fisher's exact test), Q value = 0.27

Table S647.  Gene #67: '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 1 1
CNOT3 WILD-TYPE 87 40 126 118

Figure S87.  Get High-res Image Gene #67: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CNOT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.31

Table S648.  Gene #67: '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 3 0 6
CNOT3 WILD-TYPE 74 45 88 62 27 75

Figure S88.  Get High-res Image Gene #67: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.89

Table S649.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ARID2 MUTATED 9 13 6 1
ARID2 WILD-TYPE 153 124 53 33
'ARID2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.9

Table S650.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ARID2 MUTATED 7 12 4 6
ARID2 WILD-TYPE 128 100 65 73
'ARID2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.96

Table S651.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ARID2 MUTATED 2 3 5 1 1
ARID2 WILD-TYPE 35 26 31 4 19
'ARID2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.81

Table S652.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ARID2 MUTATED 3 6 3 0
ARID2 WILD-TYPE 40 32 24 19
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.79

Table S653.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ARID2 MUTATED 9 16 4
ARID2 WILD-TYPE 105 157 100
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.74

Table S654.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ARID2 MUTATED 11 10 8
ARID2 WILD-TYPE 105 96 161
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0126 (Fisher's exact test), Q value = 0.29

Table S655.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ARID2 MUTATED 11 12 6
ARID2 WILD-TYPE 108 84 171

Figure S89.  Get High-res Image Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ARID2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.84

Table S656.  Gene #68: 'ARID2 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
ARID2 MUTATED 3 8 7 4 7
ARID2 WILD-TYPE 83 91 82 61 46
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.35

Table S657.  Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ARID2 MUTATED 3 4 6 16
ARID2 WILD-TYPE 90 39 121 103

Figure S90.  Get High-res Image Gene #68: 'ARID2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.71

Table S658.  Gene #68: 'ARID2 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
ARID2 MUTATED 10 4 6 6 0 3
ARID2 WILD-TYPE 64 43 82 59 27 78
'ZNF773 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.99

Table S659.  Gene #69: 'ZNF773 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZNF773 MUTATED 2 3 2 0
ZNF773 WILD-TYPE 160 134 57 34
'ZNF773 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 0.99

Table S660.  Gene #69: 'ZNF773 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZNF773 MUTATED 3 3 1 0
ZNF773 WILD-TYPE 132 109 68 79
'ZNF773 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 0.92

Table S661.  Gene #69: 'ZNF773 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZNF773 MUTATED 2 4 0
ZNF773 WILD-TYPE 112 169 104
'ZNF773 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 0.97

Table S662.  Gene #69: 'ZNF773 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZNF773 MUTATED 1 3 2
ZNF773 WILD-TYPE 115 103 167
'ZNF773 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S663.  Gene #69: 'ZNF773 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZNF773 MUTATED 1 2 4
ZNF773 WILD-TYPE 118 94 173
'ZNF773 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S664.  Gene #69: 'ZNF773 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
ZNF773 MUTATED 2 3 2 0 0
ZNF773 WILD-TYPE 84 96 87 65 53
'ZNF773 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.74

Table S665.  Gene #69: 'ZNF773 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZNF773 MUTATED 3 1 3 0
ZNF773 WILD-TYPE 90 42 124 119
'ZNF773 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 0.85

Table S666.  Gene #69: 'ZNF773 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
ZNF773 MUTATED 0 1 3 0 0 3
ZNF773 WILD-TYPE 74 46 85 65 27 78
'DAZAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.741 (Fisher's exact test), Q value = 1

Table S667.  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 = 0.045 (Fisher's exact test), Q value = 0.49

Table S668.  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 S91.  Get High-res Image Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DAZAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 0.74

Table S669.  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 = 0.0104 (Fisher's exact test), Q value = 0.27

Table S670.  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 S92.  Get High-res Image Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.77

Table S671.  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 = 0.024 (Fisher's exact test), Q value = 0.4

Table S672.  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 S93.  Get High-res Image Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.86

Table S673.  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 = 0.428 (Fisher's exact test), Q value = 0.92

Table S674.  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
'ADC MUTATION STATUS' versus 'CN_CNMF'

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

Table S675.  Gene #71: '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 3 0 0
ADC WILD-TYPE 159 134 59 34
'ADC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S676.  Gene #71: '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 3 0 1
ADC WILD-TYPE 133 109 69 78
'ADC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S677.  Gene #71: 'ADC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ADC MUTATED 2 3 1
ADC WILD-TYPE 112 170 103
'ADC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.582 (Fisher's exact test), Q value = 0.99

Table S678.  Gene #71: 'ADC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ADC MUTATED 3 1 2
ADC WILD-TYPE 113 105 167
'ADC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S679.  Gene #71: 'ADC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ADC MUTATED 1 2 3
ADC WILD-TYPE 118 94 174
'ADC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 0.84

Table S680.  Gene #71: '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 3 1 2 0
ADC WILD-TYPE 86 96 88 63 53
'ADC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S681.  Gene #71: '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 1 2 2
ADC WILD-TYPE 92 42 125 117
'ADC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S682.  Gene #71: '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 2 0 0
ADC WILD-TYPE 73 46 86 63 27 81
'FUT5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S683.  Gene #72: 'FUT5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
FUT5 MUTATED 2 1 0 0
FUT5 WILD-TYPE 160 136 59 34
'FUT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.9

Table S684.  Gene #72: 'FUT5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
FUT5 MUTATED 0 1 1 1
FUT5 WILD-TYPE 135 111 68 78
'FUT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S685.  Gene #72: 'FUT5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
FUT5 MUTATED 1 2 0
FUT5 WILD-TYPE 113 171 104
'FUT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.62

Table S686.  Gene #72: 'FUT5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FUT5 MUTATED 1 2 0
FUT5 WILD-TYPE 115 104 169
'FUT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S687.  Gene #72: 'FUT5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
FUT5 MUTATED 1 0 2
FUT5 WILD-TYPE 118 96 175
'FUT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 0.86

Table S688.  Gene #72: 'FUT5 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
FUT5 MUTATED 0 0 1 1 1
FUT5 WILD-TYPE 86 99 88 64 52
'FUT5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S689.  Gene #72: 'FUT5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
FUT5 MUTATED 0 0 2 1
FUT5 WILD-TYPE 93 43 125 118
'FUT5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.81

Table S690.  Gene #72: 'FUT5 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
FUT5 MUTATED 0 0 1 1 1 0
FUT5 WILD-TYPE 74 47 87 64 26 81
'AHR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 0.98

Table S691.  Gene #73: '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 = 0.0533 (Fisher's exact test), Q value = 0.52

Table S692.  Gene #73: '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 = 0.543 (Fisher's exact test), Q value = 0.98

Table S693.  Gene #73: 'AHR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
AHR MUTATED 1 3 2 0 0
AHR WILD-TYPE 36 26 34 5 20
'AHR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.77

Table S694.  Gene #73: 'AHR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
AHR MUTATED 1 4 0 1
AHR WILD-TYPE 42 34 27 18
'AHR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0644 (Fisher's exact test), Q value = 0.55

Table S695.  Gene #73: '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 = 0.0755 (Fisher's exact test), Q value = 0.57

Table S696.  Gene #73: '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 = 1

Table S697.  Gene #73: '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 = 0.313 (Fisher's exact test), Q value = 0.84

Table S698.  Gene #73: '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 = 0.531 (Fisher's exact test), Q value = 0.98

Table S699.  Gene #73: '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 = 0.511 (Fisher's exact test), Q value = 0.98

Table S700.  Gene #73: '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
'THRAP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.98

Table S701.  Gene #74: '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 = 0.336 (Fisher's exact test), Q value = 0.86

Table S702.  Gene #74: '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 = 0.0723 (Fisher's exact test), Q value = 0.57

Table S703.  Gene #74: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
THRAP3 MUTATED 0 1 3 1 0
THRAP3 WILD-TYPE 37 28 33 4 20
'THRAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S704.  Gene #74: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
THRAP3 MUTATED 2 2 1 0
THRAP3 WILD-TYPE 41 36 26 19
'THRAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S705.  Gene #74: '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 = 0.785 (Fisher's exact test), Q value = 1

Table S706.  Gene #74: '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 S707.  Gene #74: '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 = 0.794 (Fisher's exact test), Q value = 1

Table S708.  Gene #74: '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 S709.  Gene #74: '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 = 0.902 (Fisher's exact test), Q value = 1

Table S710.  Gene #74: '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
'TFPI2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S711.  Gene #75: 'TFPI2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TFPI2 MUTATED 2 2 1 1
TFPI2 WILD-TYPE 160 135 58 33
'TFPI2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S712.  Gene #75: 'TFPI2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TFPI2 MUTATED 3 2 0 1
TFPI2 WILD-TYPE 132 110 69 78
'TFPI2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

Table S713.  Gene #75: 'TFPI2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TFPI2 MUTATED 2 2 2
TFPI2 WILD-TYPE 112 171 102
'TFPI2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S714.  Gene #75: 'TFPI2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TFPI2 MUTATED 1 2 3
TFPI2 WILD-TYPE 115 104 166
'TFPI2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S715.  Gene #75: 'TFPI2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TFPI2 MUTATED 1 1 4
TFPI2 WILD-TYPE 118 95 173
'TFPI2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.79

Table S716.  Gene #75: 'TFPI2 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
TFPI2 MUTATED 3 1 0 2 0
TFPI2 WILD-TYPE 83 98 89 63 53
'TFPI2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.76

Table S717.  Gene #75: 'TFPI2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TFPI2 MUTATED 4 0 1 1
TFPI2 WILD-TYPE 89 43 126 118
'TFPI2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 0.98

Table S718.  Gene #75: 'TFPI2 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
TFPI2 MUTATED 0 0 2 1 0 3
TFPI2 WILD-TYPE 74 47 86 64 27 78
'NPAS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.79

Table S719.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
NPAS4 MUTATED 3 7 1 2
NPAS4 WILD-TYPE 159 130 58 32
'NPAS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S720.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
NPAS4 MUTATED 3 4 3 3
NPAS4 WILD-TYPE 132 108 66 76
'NPAS4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S721.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
NPAS4 MUTATED 2 2 1 0 0
NPAS4 WILD-TYPE 35 27 35 5 20
'NPAS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S722.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
NPAS4 MUTATED 1 2 1 1
NPAS4 WILD-TYPE 42 36 26 18
'NPAS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S723.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
NPAS4 MUTATED 3 7 3
NPAS4 WILD-TYPE 111 166 101
'NPAS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 0.99

Table S724.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NPAS4 MUTATED 5 4 4
NPAS4 WILD-TYPE 111 102 165
'NPAS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.98

Table S725.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
NPAS4 MUTATED 3 5 5
NPAS4 WILD-TYPE 116 91 172
'NPAS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.79

Table S726.  Gene #76: 'NPAS4 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
NPAS4 MUTATED 1 5 1 4 2
NPAS4 WILD-TYPE 85 94 88 61 51
'NPAS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.92

Table S727.  Gene #76: 'NPAS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
NPAS4 MUTATED 1 2 6 4
NPAS4 WILD-TYPE 92 41 121 115
'NPAS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.557 (Fisher's exact test), Q value = 0.98

Table S728.  Gene #76: 'NPAS4 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
NPAS4 MUTATED 2 3 4 3 0 1
NPAS4 WILD-TYPE 72 44 84 62 27 80
'NFE2L3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.84

Table S729.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
NFE2L3 MUTATED 3 6 3 2
NFE2L3 WILD-TYPE 159 131 56 32
'NFE2L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00136 (Fisher's exact test), Q value = 0.084

Table S730.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
NFE2L3 MUTATED 1 10 0 3
NFE2L3 WILD-TYPE 134 102 69 76

Figure S94.  Get High-res Image Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.62

Table S731.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
NFE2L3 MUTATED 1 1 0 1 0
NFE2L3 WILD-TYPE 36 28 36 4 20
'NFE2L3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S732.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
NFE2L3 MUTATED 2 1 0 0
NFE2L3 WILD-TYPE 41 37 27 19
'NFE2L3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.65 (Fisher's exact test), Q value = 1

Table S733.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
NFE2L3 MUTATED 3 8 3
NFE2L3 WILD-TYPE 111 165 101
'NFE2L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 0.62

Table S734.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NFE2L3 MUTATED 4 7 3
NFE2L3 WILD-TYPE 112 99 166
'NFE2L3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S735.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
NFE2L3 MUTATED 4 3 7
NFE2L3 WILD-TYPE 115 93 170
'NFE2L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.98

Table S736.  Gene #77: 'NFE2L3 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
NFE2L3 MUTATED 1 4 3 4 2
NFE2L3 WILD-TYPE 85 95 86 61 51
'NFE2L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S737.  Gene #77: 'NFE2L3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
NFE2L3 MUTATED 3 2 5 3
NFE2L3 WILD-TYPE 90 41 122 116
'NFE2L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S738.  Gene #77: 'NFE2L3 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
NFE2L3 MUTATED 2 2 5 1 0 3
NFE2L3 WILD-TYPE 72 45 83 64 27 78
'TAF11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S739.  Gene #78: 'TAF11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TAF11 MUTATED 3 2 2 0
TAF11 WILD-TYPE 159 135 57 34
'TAF11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.84

Table S740.  Gene #78: 'TAF11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TAF11 MUTATED 5 1 0 1
TAF11 WILD-TYPE 130 111 69 78
'TAF11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.79

Table S741.  Gene #78: 'TAF11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TAF11 MUTATED 3 1 3
TAF11 WILD-TYPE 111 172 101
'TAF11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 1

Table S742.  Gene #78: 'TAF11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TAF11 MUTATED 2 1 4
TAF11 WILD-TYPE 114 105 165
'TAF11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S743.  Gene #78: 'TAF11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TAF11 MUTATED 3 1 3
TAF11 WILD-TYPE 116 95 174
'TAF11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S744.  Gene #78: 'TAF11 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
TAF11 MUTATED 1 3 1 1 1
TAF11 WILD-TYPE 85 96 88 64 52
'TAF11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 0.98

Table S745.  Gene #78: 'TAF11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TAF11 MUTATED 3 1 1 2
TAF11 WILD-TYPE 90 42 126 117
'TAF11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S746.  Gene #78: 'TAF11 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
TAF11 MUTATED 2 1 1 0 0 3
TAF11 WILD-TYPE 72 46 87 65 27 78
'BCL2L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.35

Table S747.  Gene #79: '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 S95.  Get High-res Image Gene #79: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'BCL2L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.51

Table S748.  Gene #79: '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 S96.  Get High-res Image Gene #79: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BCL2L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.84

Table S749.  Gene #79: '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 = 0.694 (Fisher's exact test), Q value = 1

Table S750.  Gene #79: '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 = 0.371 (Fisher's exact test), Q value = 0.89

Table S751.  Gene #79: '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 = 0.404 (Fisher's exact test), Q value = 0.9

Table S752.  Gene #79: '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 = 0.89

Table S753.  Gene #79: '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 = 0.906 (Fisher's exact test), Q value = 1

Table S754.  Gene #79: '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
'TRERF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.85

Table S755.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TRERF1 MUTATED 5 8 5 2
TRERF1 WILD-TYPE 157 129 54 32
'TRERF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S756.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TRERF1 MUTATED 6 7 4 4
TRERF1 WILD-TYPE 129 105 65 75
'TRERF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S757.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
TRERF1 MUTATED 4 1 4 0 2
TRERF1 WILD-TYPE 33 28 32 5 18
'TRERF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S758.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
TRERF1 MUTATED 5 2 2 2
TRERF1 WILD-TYPE 38 36 25 17
'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S759.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TRERF1 MUTATED 5 9 6
TRERF1 WILD-TYPE 109 164 98
'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S760.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TRERF1 MUTATED 6 7 7
TRERF1 WILD-TYPE 110 99 162
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S761.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TRERF1 MUTATED 6 5 10
TRERF1 WILD-TYPE 113 91 167
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 0.99

Table S762.  Gene #80: 'TRERF1 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
TRERF1 MUTATED 4 5 8 2 2
TRERF1 WILD-TYPE 82 94 81 63 51
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S763.  Gene #80: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TRERF1 MUTATED 3 3 7 6
TRERF1 WILD-TYPE 90 40 120 113
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S764.  Gene #80: 'TRERF1 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
TRERF1 MUTATED 5 3 6 2 0 3
TRERF1 WILD-TYPE 69 44 82 63 27 78
'CHD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.65

Table S765.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
CHD2 MUTATED 8 10 7 0
CHD2 WILD-TYPE 154 127 52 34
'CHD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 0.99

Table S766.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
CHD2 MUTATED 10 9 3 3
CHD2 WILD-TYPE 125 103 66 76
'CHD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S767.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
CHD2 MUTATED 4 3 2 0 2
CHD2 WILD-TYPE 33 26 34 5 18
'CHD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S768.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
CHD2 MUTATED 3 5 1 2
CHD2 WILD-TYPE 40 33 26 17
'CHD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.98

Table S769.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
CHD2 MUTATED 7 9 9
CHD2 WILD-TYPE 107 164 95
'CHD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S770.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CHD2 MUTATED 7 5 13
CHD2 WILD-TYPE 109 101 156
'CHD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 0.86

Table S771.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
CHD2 MUTATED 11 5 9
CHD2 WILD-TYPE 108 91 168
'CHD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.94

Table S772.  Gene #81: 'CHD2 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
CHD2 MUTATED 5 7 3 4 6
CHD2 WILD-TYPE 81 92 86 61 47
'CHD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.89

Table S773.  Gene #81: 'CHD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
CHD2 MUTATED 8 1 6 10
CHD2 WILD-TYPE 85 42 121 109
'CHD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.93

Table S774.  Gene #81: 'CHD2 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
CHD2 MUTATED 6 1 6 4 0 8
CHD2 WILD-TYPE 68 46 82 61 27 73
'USP28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S775.  Gene #82: '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 = 0.653 (Fisher's exact test), Q value = 1

Table S776.  Gene #82: '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 = 0.146 (Fisher's exact test), Q value = 0.71

Table S777.  Gene #82: 'USP28 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
USP28 MUTATED 1 0 1 1 0
USP28 WILD-TYPE 36 29 35 4 20
'USP28 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 0.99

Table S778.  Gene #82: 'USP28 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
USP28 MUTATED 2 0 1 0
USP28 WILD-TYPE 41 38 26 19
'USP28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S779.  Gene #82: '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 S780.  Gene #82: '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 = 0.619 (Fisher's exact test), Q value = 1

Table S781.  Gene #82: '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 = 0.96

Table S782.  Gene #82: '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 = 1

Table S783.  Gene #82: '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 = 1

Table S784.  Gene #82: '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
'GPS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S785.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
GPS2 MUTATED 3 5 1 1
GPS2 WILD-TYPE 159 132 58 33
'GPS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S786.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
GPS2 MUTATED 3 3 1 3
GPS2 WILD-TYPE 132 109 68 76
'GPS2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.95

Table S787.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
GPS2 MUTATED 3 0 1 0 0
GPS2 WILD-TYPE 34 29 35 5 20
'GPS2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.87

Table S788.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
GPS2 MUTATED 3 0 1 0
GPS2 WILD-TYPE 40 38 26 19
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.922 (Fisher's exact test), Q value = 1

Table S789.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
GPS2 MUTATED 3 5 2
GPS2 WILD-TYPE 111 168 102
'GPS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 0.98

Table S790.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
GPS2 MUTATED 3 4 3
GPS2 WILD-TYPE 113 102 166
'GPS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.79

Table S791.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
GPS2 MUTATED 4 4 2
GPS2 WILD-TYPE 115 92 175
'GPS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 0.84

Table S792.  Gene #83: 'GPS2 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
GPS2 MUTATED 3 5 1 0 1
GPS2 WILD-TYPE 83 94 88 65 52
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S793.  Gene #83: 'GPS2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
GPS2 MUTATED 2 1 4 3
GPS2 WILD-TYPE 91 42 123 116
'GPS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S794.  Gene #83: 'GPS2 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
GPS2 MUTATED 1 1 3 2 1 2
GPS2 WILD-TYPE 73 46 85 63 26 79
'F7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 0.98

Table S795.  Gene #84: 'F7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
F7 MUTATED 3 4 0 1
F7 WILD-TYPE 159 133 59 33
'F7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.92

Table S796.  Gene #84: 'F7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
F7 MUTATED 2 4 0 2
F7 WILD-TYPE 133 108 69 77
'F7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S797.  Gene #84: 'F7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
F7 MUTATED 3 3 2
F7 WILD-TYPE 111 170 102
'F7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.98

Table S798.  Gene #84: 'F7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
F7 MUTATED 1 2 5
F7 WILD-TYPE 115 104 164
'F7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S799.  Gene #84: 'F7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
F7 MUTATED 2 1 4
F7 WILD-TYPE 117 95 173
'F7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.78

Table S800.  Gene #84: 'F7 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
F7 MUTATED 4 1 2 0 0
F7 WILD-TYPE 82 98 87 65 53
'F7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.44

Table S801.  Gene #84: 'F7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
F7 MUTATED 1 0 6 0
F7 WILD-TYPE 92 43 121 119

Figure S97.  Get High-res Image Gene #84: 'F7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'F7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 0.92

Table S802.  Gene #84: 'F7 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
F7 MUTATED 1 0 4 0 0 2
F7 WILD-TYPE 73 47 84 65 27 79
'IRX4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.85

Table S803.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
IRX4 MUTATED 1 4 1 1
IRX4 WILD-TYPE 161 133 58 33
'IRX4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.89

Table S804.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
IRX4 MUTATED 1 3 1 3
IRX4 WILD-TYPE 134 109 68 76
'IRX4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 0.99

Table S805.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
IRX4 MUTATED 0 1 1 0 1
IRX4 WILD-TYPE 37 28 35 5 19
'IRX4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 0.93

Table S806.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
IRX4 MUTATED 0 1 1 1
IRX4 WILD-TYPE 43 37 26 18
'IRX4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.86

Table S807.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
IRX4 MUTATED 1 3 4
IRX4 WILD-TYPE 113 170 100
'IRX4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S808.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
IRX4 MUTATED 3 1 4
IRX4 WILD-TYPE 113 105 165
'IRX4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S809.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
IRX4 MUTATED 2 1 5
IRX4 WILD-TYPE 117 95 172
'IRX4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.75 (Fisher's exact test), Q value = 1

Table S810.  Gene #85: 'IRX4 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
IRX4 MUTATED 1 1 3 2 1
IRX4 WILD-TYPE 85 98 86 63 52
'IRX4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S811.  Gene #85: 'IRX4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
IRX4 MUTATED 2 1 3 2
IRX4 WILD-TYPE 91 42 124 117
'IRX4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.974 (Fisher's exact test), Q value = 1

Table S812.  Gene #85: 'IRX4 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
IRX4 MUTATED 1 1 3 1 0 2
IRX4 WILD-TYPE 73 46 85 64 27 79
'HSP90AA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.89

Table S813.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
HSP90AA1 MUTATED 6 10 3 3
HSP90AA1 WILD-TYPE 156 127 56 31
'HSP90AA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S814.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
HSP90AA1 MUTATED 8 6 3 5
HSP90AA1 WILD-TYPE 127 106 66 74
'HSP90AA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0858 (Fisher's exact test), Q value = 0.57

Table S815.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
HSP90AA1 MUTATED 0 4 3 0 0
HSP90AA1 WILD-TYPE 37 25 33 5 20
'HSP90AA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0348 (Fisher's exact test), Q value = 0.44

Table S816.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
HSP90AA1 MUTATED 0 5 2 0
HSP90AA1 WILD-TYPE 43 33 25 19

Figure S98.  Get High-res Image Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HSP90AA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S817.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
HSP90AA1 MUTATED 6 9 7
HSP90AA1 WILD-TYPE 108 164 97
'HSP90AA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S818.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
HSP90AA1 MUTATED 5 6 11
HSP90AA1 WILD-TYPE 111 100 158
'HSP90AA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0822 (Fisher's exact test), Q value = 0.57

Table S819.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
HSP90AA1 MUTATED 4 10 8
HSP90AA1 WILD-TYPE 115 86 169
'HSP90AA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.71

Table S820.  Gene #86: 'HSP90AA1 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
HSP90AA1 MUTATED 2 9 3 6 2
HSP90AA1 WILD-TYPE 84 90 86 59 51
'HSP90AA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S821.  Gene #86: 'HSP90AA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
HSP90AA1 MUTATED 5 2 8 7
HSP90AA1 WILD-TYPE 88 41 119 112
'HSP90AA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S822.  Gene #86: 'HSP90AA1 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
HSP90AA1 MUTATED 3 2 6 5 1 5
HSP90AA1 WILD-TYPE 71 45 82 60 26 76
'TTYH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S823.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TTYH1 MUTATED 3 2 2 0
TTYH1 WILD-TYPE 159 135 57 34
'TTYH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S824.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TTYH1 MUTATED 4 1 1 1
TTYH1 WILD-TYPE 131 111 68 78
'TTYH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.85

Table S825.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
TTYH1 MUTATED 0 1 3 0 0
TTYH1 WILD-TYPE 37 28 33 5 20
'TTYH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.77

Table S826.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
TTYH1 MUTATED 0 2 2 0
TTYH1 WILD-TYPE 43 36 25 19
'TTYH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 0.71

Table S827.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TTYH1 MUTATED 4 1 2
TTYH1 WILD-TYPE 110 172 102
'TTYH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.238 (Fisher's exact test), Q value = 0.79

Table S828.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TTYH1 MUTATED 2 0 5
TTYH1 WILD-TYPE 114 106 164
'TTYH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.76

Table S829.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TTYH1 MUTATED 4 2 1
TTYH1 WILD-TYPE 115 94 176
'TTYH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.027 (Fisher's exact test), Q value = 0.43

Table S830.  Gene #87: 'TTYH1 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
TTYH1 MUTATED 4 0 0 1 2
TTYH1 WILD-TYPE 82 99 89 64 51

Figure S99.  Get High-res Image Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TTYH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0514 (Fisher's exact test), Q value = 0.51

Table S831.  Gene #87: 'TTYH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TTYH1 MUTATED 1 0 0 5
TTYH1 WILD-TYPE 92 43 127 114
'TTYH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.79

Table S832.  Gene #87: 'TTYH1 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
TTYH1 MUTATED 2 0 0 3 0 1
TTYH1 WILD-TYPE 72 47 88 62 27 80
'IL10RB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.79

Table S833.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
IL10RB MUTATED 1 4 2 0
IL10RB WILD-TYPE 161 133 57 34
'IL10RB MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S834.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
IL10RB MUTATED 3 1 1 2
IL10RB WILD-TYPE 132 111 68 77
'IL10RB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.79

Table S835.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
IL10RB MUTATED 0 0 3 0 1
IL10RB WILD-TYPE 37 29 33 5 19
'IL10RB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S836.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
IL10RB MUTATED 2 1 1 0
IL10RB WILD-TYPE 41 37 26 19
'IL10RB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.71

Table S837.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
IL10RB MUTATED 4 1 2
IL10RB WILD-TYPE 110 172 102
'IL10RB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S838.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
IL10RB MUTATED 2 1 4
IL10RB WILD-TYPE 114 105 165
'IL10RB MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S839.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
IL10RB MUTATED 2 2 3
IL10RB WILD-TYPE 117 94 174
'IL10RB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S840.  Gene #88: 'IL10RB 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
IL10RB MUTATED 1 1 3 1 1
IL10RB WILD-TYPE 85 98 86 64 52
'IL10RB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.79

Table S841.  Gene #88: 'IL10RB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
IL10RB MUTATED 4 0 1 2
IL10RB WILD-TYPE 89 43 126 117
'IL10RB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S842.  Gene #88: 'IL10RB 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
IL10RB MUTATED 1 0 3 1 0 2
IL10RB WILD-TYPE 73 47 85 64 27 79
'THSD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S843.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
THSD4 MUTATED 6 3 1 0
THSD4 WILD-TYPE 156 134 58 34
'THSD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S844.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
THSD4 MUTATED 3 3 1 3
THSD4 WILD-TYPE 132 109 68 76
'THSD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S845.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
THSD4 MUTATED 2 1 1 0 0
THSD4 WILD-TYPE 35 28 35 5 20
'THSD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.94

Table S846.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
THSD4 MUTATED 2 0 1 1
THSD4 WILD-TYPE 41 38 26 18
'THSD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S847.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
THSD4 MUTATED 2 6 2
THSD4 WILD-TYPE 112 167 102
'THSD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.89

Table S848.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
THSD4 MUTATED 1 4 5
THSD4 WILD-TYPE 115 102 164
'THSD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.7

Table S849.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
THSD4 MUTATED 3 0 7
THSD4 WILD-TYPE 116 96 170
'THSD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S850.  Gene #89: 'THSD4 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
THSD4 MUTATED 2 1 3 2 2
THSD4 WILD-TYPE 84 98 86 63 51
'THSD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S851.  Gene #89: 'THSD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
THSD4 MUTATED 2 0 5 3
THSD4 WILD-TYPE 91 43 122 116
'THSD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 0.79

Table S852.  Gene #89: 'THSD4 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
THSD4 MUTATED 3 0 5 0 0 2
THSD4 WILD-TYPE 71 47 83 65 27 79
'DDX3X MUTATION STATUS' versus 'CN_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.98

Table S853.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
DDX3X MUTATED 8 4 3 0
DDX3X WILD-TYPE 154 133 56 34
'DDX3X MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.98

Table S854.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
DDX3X MUTATED 6 6 2 1
DDX3X WILD-TYPE 129 106 67 78
'DDX3X MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S855.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
DDX3X MUTATED 2 1 1 0 0
DDX3X WILD-TYPE 35 28 35 5 20
'DDX3X MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S856.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
DDX3X MUTATED 2 2 0 0
DDX3X WILD-TYPE 41 36 27 19
'DDX3X MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S857.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
DDX3X MUTATED 4 7 4
DDX3X WILD-TYPE 110 166 100
'DDX3X MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S858.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
DDX3X MUTATED 5 3 7
DDX3X WILD-TYPE 111 103 162
'DDX3X MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S859.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
DDX3X MUTATED 4 4 7
DDX3X WILD-TYPE 115 92 170
'DDX3X MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 0.98

Table S860.  Gene #90: 'DDX3X 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
DDX3X MUTATED 6 4 3 1 1
DDX3X WILD-TYPE 80 95 86 64 52
'DDX3X MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.81

Table S861.  Gene #90: 'DDX3X MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
DDX3X MUTATED 6 2 4 2
DDX3X WILD-TYPE 87 41 123 117
'DDX3X MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S862.  Gene #90: 'DDX3X 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
DDX3X MUTATED 1 2 4 2 0 5
DDX3X WILD-TYPE 73 45 84 63 27 76
'DGKG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.44

Table S863.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
DGKG MUTATED 3 5 6 0
DGKG WILD-TYPE 159 132 53 34

Figure S100.  Get High-res Image Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DGKG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.81

Table S864.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
DGKG MUTATED 5 6 0 3
DGKG WILD-TYPE 130 106 69 76
'DGKG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.84

Table S865.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
DGKG MUTATED 0 0 2 0 1
DGKG WILD-TYPE 37 29 34 5 19
'DGKG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0655 (Fisher's exact test), Q value = 0.55

Table S866.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
DGKG MUTATED 0 0 2 1
DGKG WILD-TYPE 43 38 25 18
'DGKG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 1

Table S867.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
DGKG MUTATED 5 6 3
DGKG WILD-TYPE 109 167 101
'DGKG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S868.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
DGKG MUTATED 5 3 6
DGKG WILD-TYPE 111 103 163
'DGKG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.66

Table S869.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
DGKG MUTATED 1 4 9
DGKG WILD-TYPE 118 92 168
'DGKG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.9

Table S870.  Gene #91: 'DGKG 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
DGKG MUTATED 5 4 2 3 0
DGKG WILD-TYPE 81 95 87 62 53
'DGKG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.89

Table S871.  Gene #91: 'DGKG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
DGKG MUTATED 2 1 7 2
DGKG WILD-TYPE 91 42 120 117
'DGKG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0816 (Fisher's exact test), Q value = 0.57

Table S872.  Gene #91: 'DGKG 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
DGKG MUTATED 0 1 7 1 0 3
DGKG WILD-TYPE 74 46 81 64 27 78
'TAS2R9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0383 (Fisher's exact test), Q value = 0.45

Table S873.  Gene #92: 'TAS2R9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
TAS2R9 MUTATED 2 0 3 1
TAS2R9 WILD-TYPE 160 137 56 33

Figure S101.  Get High-res Image Gene #92: 'TAS2R9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TAS2R9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.79

Table S874.  Gene #92: 'TAS2R9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
TAS2R9 MUTATED 2 0 2 2
TAS2R9 WILD-TYPE 133 112 67 77
'TAS2R9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 0.92

Table S875.  Gene #92: 'TAS2R9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
TAS2R9 MUTATED 2 4 0
TAS2R9 WILD-TYPE 112 169 104
'TAS2R9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S876.  Gene #92: 'TAS2R9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TAS2R9 MUTATED 2 2 2
TAS2R9 WILD-TYPE 114 104 167
'TAS2R9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.96

Table S877.  Gene #92: 'TAS2R9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
TAS2R9 MUTATED 2 0 4
TAS2R9 WILD-TYPE 117 96 173
'TAS2R9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.973 (Fisher's exact test), Q value = 1

Table S878.  Gene #92: 'TAS2R9 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
TAS2R9 MUTATED 1 1 2 1 1
TAS2R9 WILD-TYPE 85 98 87 64 52
'TAS2R9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S879.  Gene #92: 'TAS2R9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
TAS2R9 MUTATED 1 0 3 2
TAS2R9 WILD-TYPE 92 43 124 117
'TAS2R9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S880.  Gene #92: 'TAS2R9 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
TAS2R9 MUTATED 1 0 3 1 0 1
TAS2R9 WILD-TYPE 73 47 85 64 27 80
'COL7A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.79

Table S881.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
COL7A1 MUTATED 14 13 1 2
COL7A1 WILD-TYPE 148 124 58 32
'COL7A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.98

Table S882.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
COL7A1 MUTATED 9 11 3 7
COL7A1 WILD-TYPE 126 101 66 72
'COL7A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S883.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
COL7A1 MUTATED 4 3 3 1 3
COL7A1 WILD-TYPE 33 26 33 4 17
'COL7A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.84

Table S884.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
COL7A1 MUTATED 4 2 5 3
COL7A1 WILD-TYPE 39 36 22 16
'COL7A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S885.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
COL7A1 MUTATED 8 13 9
COL7A1 WILD-TYPE 106 160 95
'COL7A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.8

Table S886.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
COL7A1 MUTATED 13 6 11
COL7A1 WILD-TYPE 103 100 158
'COL7A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.78

Table S887.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
COL7A1 MUTATED 6 11 13
COL7A1 WILD-TYPE 113 85 164
'COL7A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.89

Table S888.  Gene #93: 'COL7A1 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
COL7A1 MUTATED 9 10 4 5 2
COL7A1 WILD-TYPE 77 89 85 60 51
'COL7A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.98

Table S889.  Gene #93: 'COL7A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
COL7A1 MUTATED 10 4 9 7
COL7A1 WILD-TYPE 83 39 118 112
'COL7A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S890.  Gene #93: 'COL7A1 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
COL7A1 MUTATED 3 5 7 7 1 7
COL7A1 WILD-TYPE 71 42 81 58 26 74
'ZNF513 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.84

Table S891.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZNF513 MUTATED 4 5 0 2
ZNF513 WILD-TYPE 158 132 59 32
'ZNF513 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.972 (Fisher's exact test), Q value = 1

Table S892.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZNF513 MUTATED 3 4 2 2
ZNF513 WILD-TYPE 132 108 67 77
'ZNF513 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.84

Table S893.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ZNF513 MUTATED 2 0 2 1 1
ZNF513 WILD-TYPE 35 29 34 4 19
'ZNF513 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S894.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ZNF513 MUTATED 3 1 1 1
ZNF513 WILD-TYPE 40 37 26 18
'ZNF513 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 0.94

Table S895.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZNF513 MUTATED 4 6 1
ZNF513 WILD-TYPE 110 167 103
'ZNF513 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.538 (Fisher's exact test), Q value = 0.98

Table S896.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZNF513 MUTATED 4 4 3
ZNF513 WILD-TYPE 112 102 166
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S897.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZNF513 MUTATED 3 3 5
ZNF513 WILD-TYPE 116 93 172
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S898.  Gene #94: 'ZNF513 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
ZNF513 MUTATED 2 3 1 3 2
ZNF513 WILD-TYPE 84 96 88 62 51
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S899.  Gene #94: 'ZNF513 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZNF513 MUTATED 2 1 5 3
ZNF513 WILD-TYPE 91 42 122 116
'ZNF513 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S900.  Gene #94: 'ZNF513 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
ZNF513 MUTATED 2 1 5 1 0 2
ZNF513 WILD-TYPE 72 46 83 64 27 79
'ACSL5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S901.  Gene #95: 'ACSL5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ACSL5 MUTATED 3 3 0 0
ACSL5 WILD-TYPE 159 134 59 34
'ACSL5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S902.  Gene #95: 'ACSL5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ACSL5 MUTATED 1 2 1 2
ACSL5 WILD-TYPE 134 110 68 77
'ACSL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 0.92

Table S903.  Gene #95: 'ACSL5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ACSL5 MUTATED 2 4 0
ACSL5 WILD-TYPE 112 169 104
'ACSL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0308 (Fisher's exact test), Q value = 0.44

Table S904.  Gene #95: 'ACSL5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ACSL5 MUTATED 2 4 0
ACSL5 WILD-TYPE 114 102 169

Figure S102.  Get High-res Image Gene #95: 'ACSL5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ACSL5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.83

Table S905.  Gene #95: 'ACSL5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ACSL5 MUTATED 0 2 4
ACSL5 WILD-TYPE 119 94 173
'ACSL5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.74

Table S906.  Gene #95: 'ACSL5 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
ACSL5 MUTATED 0 2 1 3 0
ACSL5 WILD-TYPE 86 97 88 62 53
'ACSL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.81

Table S907.  Gene #95: 'ACSL5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ACSL5 MUTATED 0 1 4 1
ACSL5 WILD-TYPE 93 42 123 118
'ACSL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 0.79

Table S908.  Gene #95: 'ACSL5 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
ACSL5 MUTATED 0 1 3 1 1 0
ACSL5 WILD-TYPE 74 46 85 64 26 81
'C18ORF8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S909.  Gene #96: 'C18ORF8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
C18ORF8 MUTATED 2 2 1 1
C18ORF8 WILD-TYPE 160 135 58 33
'C18ORF8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.71

Table S910.  Gene #96: 'C18ORF8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
C18ORF8 MUTATED 0 3 2 1
C18ORF8 WILD-TYPE 135 109 67 78
'C18ORF8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S911.  Gene #96: 'C18ORF8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
C18ORF8 MUTATED 1 3 2
C18ORF8 WILD-TYPE 113 170 102
'C18ORF8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 0.99

Table S912.  Gene #96: 'C18ORF8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
C18ORF8 MUTATED 3 1 2
C18ORF8 WILD-TYPE 113 105 167
'C18ORF8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S913.  Gene #96: 'C18ORF8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
C18ORF8 MUTATED 2 1 3
C18ORF8 WILD-TYPE 117 95 174
'C18ORF8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 0.98

Table S914.  Gene #96: 'C18ORF8 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
C18ORF8 MUTATED 2 1 1 0 2
C18ORF8 WILD-TYPE 84 98 88 65 51
'C18ORF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S915.  Gene #96: 'C18ORF8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
C18ORF8 MUTATED 1 1 2 2
C18ORF8 WILD-TYPE 92 42 125 117
'C18ORF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 0.96

Table S916.  Gene #96: 'C18ORF8 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
C18ORF8 MUTATED 2 0 3 1 0 0
C18ORF8 WILD-TYPE 72 47 85 64 27 81
'PRB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0518 (Fisher's exact test), Q value = 0.51

Table S917.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
PRB2 MUTATED 0 5 1 1
PRB2 WILD-TYPE 162 132 58 33
'PRB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.62

Table S918.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
PRB2 MUTATED 1 5 0 1
PRB2 WILD-TYPE 134 107 69 78
'PRB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0558 (Fisher's exact test), Q value = 0.52

Table S919.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
PRB2 MUTATED 0 0 1 1 1
PRB2 WILD-TYPE 37 29 35 4 19
'PRB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S920.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
PRB2 MUTATED 2 1 0 0
PRB2 WILD-TYPE 41 37 27 19
'PRB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S921.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
PRB2 MUTATED 3 3 1
PRB2 WILD-TYPE 111 170 103
'PRB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.98

Table S922.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PRB2 MUTATED 2 3 2
PRB2 WILD-TYPE 114 103 167
'PRB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.84

Table S923.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
PRB2 MUTATED 2 0 5
PRB2 WILD-TYPE 117 96 172
'PRB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.549 (Fisher's exact test), Q value = 0.98

Table S924.  Gene #97: 'PRB2 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
PRB2 MUTATED 2 1 2 0 2
PRB2 WILD-TYPE 84 98 87 65 51
'PRB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S925.  Gene #97: 'PRB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
PRB2 MUTATED 1 0 4 2
PRB2 WILD-TYPE 92 43 123 117
'PRB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S926.  Gene #97: 'PRB2 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
PRB2 MUTATED 1 0 4 1 0 1
PRB2 WILD-TYPE 73 47 84 64 27 80
'POU3F1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.7

Table S927.  Gene #98: '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 = 0.167 (Fisher's exact test), Q value = 0.71

Table S928.  Gene #98: '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 'MRNASEQ_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.72

Table S929.  Gene #98: '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 = 1

Table S930.  Gene #98: '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 = 0.246 (Fisher's exact test), Q value = 0.79

Table S931.  Gene #98: '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 = 0.626 (Fisher's exact test), Q value = 1

Table S932.  Gene #98: '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 = 0.0345 (Fisher's exact test), Q value = 0.44

Table S933.  Gene #98: '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 S103.  Get High-res Image Gene #98: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'POU3F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.65

Table S934.  Gene #98: '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
'EZR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.84

Table S935.  Gene #99: '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 = 1

Table S936.  Gene #99: '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 = 0.783 (Fisher's exact test), Q value = 1

Table S937.  Gene #99: 'EZR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
EZR MUTATED 3 1 2 0 0
EZR WILD-TYPE 34 28 34 5 20
'EZR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S938.  Gene #99: 'EZR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
EZR MUTATED 1 2 2 1
EZR WILD-TYPE 42 36 25 18
'EZR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.98

Table S939.  Gene #99: '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 = 0.869 (Fisher's exact test), Q value = 1

Table S940.  Gene #99: '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 = 0.703 (Fisher's exact test), Q value = 1

Table S941.  Gene #99: '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 = 0.322 (Fisher's exact test), Q value = 0.85

Table S942.  Gene #99: '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 = 0.95 (Fisher's exact test), Q value = 1

Table S943.  Gene #99: '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 = 0.744 (Fisher's exact test), Q value = 1

Table S944.  Gene #99: '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
'ZEB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.84

Table S945.  Gene #100: 'ZEB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZEB2 MUTATED 6 9 1 0
ZEB2 WILD-TYPE 156 128 58 34
'ZEB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.66

Table S946.  Gene #100: 'ZEB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZEB2 MUTATED 6 7 3 0
ZEB2 WILD-TYPE 129 105 66 79
'ZEB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S947.  Gene #100: 'ZEB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZEB2 MUTATED 4 7 5
ZEB2 WILD-TYPE 110 166 99
'ZEB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S948.  Gene #100: 'ZEB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZEB2 MUTATED 6 4 6
ZEB2 WILD-TYPE 110 102 163
'ZEB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.596 (Fisher's exact test), Q value = 0.99

Table S949.  Gene #100: 'ZEB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZEB2 MUTATED 6 4 5
ZEB2 WILD-TYPE 113 92 172
'ZEB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0244 (Fisher's exact test), Q value = 0.4

Table S950.  Gene #100: 'ZEB2 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
ZEB2 MUTATED 4 2 0 5 4
ZEB2 WILD-TYPE 82 97 89 60 49

Figure S104.  Get High-res Image Gene #100: 'ZEB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ZEB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S951.  Gene #100: 'ZEB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZEB2 MUTATED 5 1 5 4
ZEB2 WILD-TYPE 88 42 122 115
'ZEB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S952.  Gene #100: 'ZEB2 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
ZEB2 MUTATED 3 2 4 2 0 4
ZEB2 WILD-TYPE 71 45 84 63 27 77
'C12ORF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.7

Table S953.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
C12ORF43 MUTATED 1 6 1 0
C12ORF43 WILD-TYPE 161 131 58 34
'C12ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 0.98

Table S954.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
C12ORF43 MUTATED 4 3 1 0
C12ORF43 WILD-TYPE 131 109 68 79
'C12ORF43 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.166 (Fisher's exact test), Q value = 0.71

Table S955.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
C12ORF43 MUTATED 0 0 1 0 2
C12ORF43 WILD-TYPE 37 29 35 5 18
'C12ORF43 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0863 (Fisher's exact test), Q value = 0.57

Table S956.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
C12ORF43 MUTATED 1 0 0 2
C12ORF43 WILD-TYPE 42 38 27 17
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S957.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
C12ORF43 MUTATED 2 3 2
C12ORF43 WILD-TYPE 112 170 102
'C12ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S958.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
C12ORF43 MUTATED 1 2 4
C12ORF43 WILD-TYPE 115 104 165
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0514 (Fisher's exact test), Q value = 0.51

Table S959.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
C12ORF43 MUTATED 0 4 3
C12ORF43 WILD-TYPE 119 92 174
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 0.8

Table S960.  Gene #101: 'C12ORF43 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
C12ORF43 MUTATED 2 4 0 1 0
C12ORF43 WILD-TYPE 84 95 89 64 53
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 0.98

Table S961.  Gene #101: 'C12ORF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
C12ORF43 MUTATED 3 1 1 2
C12ORF43 WILD-TYPE 90 42 126 117
'C12ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 0.98

Table S962.  Gene #101: 'C12ORF43 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
C12ORF43 MUTATED 0 1 1 2 0 3
C12ORF43 WILD-TYPE 74 46 87 63 27 78
'NAP1L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.45

Table S963.  Gene #102: 'NAP1L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
NAP1L1 MUTATED 2 2 3 3
NAP1L1 WILD-TYPE 160 135 56 31

Figure S105.  Get High-res Image Gene #102: 'NAP1L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NAP1L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.81

Table S964.  Gene #102: 'NAP1L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
NAP1L1 MUTATED 6 3 0 1
NAP1L1 WILD-TYPE 129 109 69 78
'NAP1L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.98

Table S965.  Gene #102: 'NAP1L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
NAP1L1 MUTATED 3 3 4
NAP1L1 WILD-TYPE 111 170 100
'NAP1L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 0.79

Table S966.  Gene #102: 'NAP1L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NAP1L1 MUTATED 1 2 7
NAP1L1 WILD-TYPE 115 104 162
'NAP1L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.71

Table S967.  Gene #102: 'NAP1L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
NAP1L1 MUTATED 6 1 3
NAP1L1 WILD-TYPE 113 95 174
'NAP1L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0555 (Fisher's exact test), Q value = 0.52

Table S968.  Gene #102: 'NAP1L1 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
NAP1L1 MUTATED 1 3 0 2 4
NAP1L1 WILD-TYPE 85 96 89 63 49
'NAP1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.95

Table S969.  Gene #102: 'NAP1L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
NAP1L1 MUTATED 3 0 2 5
NAP1L1 WILD-TYPE 90 43 125 114
'NAP1L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 0.98

Table S970.  Gene #102: 'NAP1L1 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
NAP1L1 MUTATED 4 0 2 1 0 3
NAP1L1 WILD-TYPE 70 47 86 64 27 78
'NAALADL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 1

Table S971.  Gene #103: 'NAALADL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
NAALADL1 MUTATED 2 4 1 0
NAALADL1 WILD-TYPE 160 133 58 34
'NAALADL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S972.  Gene #103: 'NAALADL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
NAALADL1 MUTATED 2 3 1 1
NAALADL1 WILD-TYPE 133 109 68 78
'NAALADL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S973.  Gene #103: 'NAALADL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
NAALADL1 MUTATED 2 3 2
NAALADL1 WILD-TYPE 112 170 102
'NAALADL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S974.  Gene #103: 'NAALADL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NAALADL1 MUTATED 3 1 3
NAALADL1 WILD-TYPE 113 105 166
'NAALADL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S975.  Gene #103: 'NAALADL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
NAALADL1 MUTATED 1 2 4
NAALADL1 WILD-TYPE 118 94 173
'NAALADL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S976.  Gene #103: 'NAALADL1 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
NAALADL1 MUTATED 2 2 2 1 0
NAALADL1 WILD-TYPE 84 97 87 64 53
'NAALADL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0828 (Fisher's exact test), Q value = 0.57

Table S977.  Gene #103: 'NAALADL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
NAALADL1 MUTATED 3 2 2 0
NAALADL1 WILD-TYPE 90 41 125 119
'NAALADL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.83

Table S978.  Gene #103: 'NAALADL1 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
NAALADL1 MUTATED 0 2 3 0 0 2
NAALADL1 WILD-TYPE 74 45 85 65 27 79
'DENND5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.89

Table S979.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
DENND5B MUTATED 7 10 3 0
DENND5B WILD-TYPE 155 127 56 34
'DENND5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.71

Table S980.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
DENND5B MUTATED 8 9 1 2
DENND5B WILD-TYPE 127 103 68 77
'DENND5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.62

Table S981.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
DENND5B MUTATED 5 1 1 1 0
DENND5B WILD-TYPE 32 28 35 4 20
'DENND5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0099 (Fisher's exact test), Q value = 0.27

Table S982.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
DENND5B MUTATED 7 0 1 0
DENND5B WILD-TYPE 36 38 26 19

Figure S106.  Get High-res Image Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'DENND5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.7

Table S983.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
DENND5B MUTATED 9 9 2
DENND5B WILD-TYPE 105 164 102
'DENND5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.94

Table S984.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
DENND5B MUTATED 5 8 7
DENND5B WILD-TYPE 111 98 162
'DENND5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.89

Table S985.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
DENND5B MUTATED 9 4 7
DENND5B WILD-TYPE 110 92 170
'DENND5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S986.  Gene #104: 'DENND5B 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
DENND5B MUTATED 4 4 4 4 4
DENND5B WILD-TYPE 82 95 85 61 49
'DENND5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S987.  Gene #104: 'DENND5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
DENND5B MUTATED 4 1 7 8
DENND5B WILD-TYPE 89 42 120 111
'DENND5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S988.  Gene #104: 'DENND5B 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
DENND5B MUTATED 6 2 5 3 0 4
DENND5B WILD-TYPE 68 45 83 62 27 77
'SF3B3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.985 (Fisher's exact test), Q value = 1

Table S989.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SF3B3 MUTATED 9 8 3 1
SF3B3 WILD-TYPE 153 129 56 33
'SF3B3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.957 (Fisher's exact test), Q value = 1

Table S990.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SF3B3 MUTATED 8 5 4 4
SF3B3 WILD-TYPE 127 107 65 75
'SF3B3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.71

Table S991.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
SF3B3 MUTATED 2 0 3 1 0
SF3B3 WILD-TYPE 35 29 33 4 20
'SF3B3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.9

Table S992.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
SF3B3 MUTATED 2 1 3 0
SF3B3 WILD-TYPE 41 37 24 19
'SF3B3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.96

Table S993.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SF3B3 MUTATED 7 10 3
SF3B3 WILD-TYPE 107 163 101
'SF3B3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.76

Table S994.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SF3B3 MUTATED 7 8 5
SF3B3 WILD-TYPE 109 98 164
'SF3B3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 0.99

Table S995.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SF3B3 MUTATED 5 4 12
SF3B3 WILD-TYPE 114 92 165
'SF3B3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S996.  Gene #105: 'SF3B3 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
SF3B3 MUTATED 4 7 4 3 3
SF3B3 WILD-TYPE 82 92 85 62 50
'SF3B3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S997.  Gene #105: 'SF3B3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SF3B3 MUTATED 4 2 9 6
SF3B3 WILD-TYPE 89 41 118 113
'SF3B3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.71

Table S998.  Gene #105: 'SF3B3 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
SF3B3 MUTATED 2 1 4 6 4 4
SF3B3 WILD-TYPE 72 46 84 59 23 77
'KIAA1522 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.087 (Fisher's exact test), Q value = 0.57

Table S999.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
KIAA1522 MUTATED 3 8 1 3
KIAA1522 WILD-TYPE 159 129 58 31
'KIAA1522 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S1000.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
KIAA1522 MUTATED 4 6 2 3
KIAA1522 WILD-TYPE 131 106 67 76
'KIAA1522 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.79

Table S1001.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
KIAA1522 MUTATED 3 0 0 0 0
KIAA1522 WILD-TYPE 34 29 36 5 20
'KIAA1522 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.71

Table S1002.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
KIAA1522 MUTATED 3 0 0 0
KIAA1522 WILD-TYPE 40 38 27 19
'KIAA1522 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.7

Table S1003.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
KIAA1522 MUTATED 4 10 1
KIAA1522 WILD-TYPE 110 163 103
'KIAA1522 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.712 (Fisher's exact test), Q value = 1

Table S1004.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
KIAA1522 MUTATED 5 5 5
KIAA1522 WILD-TYPE 111 101 164
'KIAA1522 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.71

Table S1005.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
KIAA1522 MUTATED 3 7 5
KIAA1522 WILD-TYPE 116 89 172
'KIAA1522 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0755 (Fisher's exact test), Q value = 0.57

Table S1006.  Gene #106: 'KIAA1522 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
KIAA1522 MUTATED 1 8 3 3 0
KIAA1522 WILD-TYPE 85 91 86 62 53
'KIAA1522 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 0.99

Table S1007.  Gene #106: 'KIAA1522 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
KIAA1522 MUTATED 3 3 5 3
KIAA1522 WILD-TYPE 90 40 122 116
'KIAA1522 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 0.79

Table S1008.  Gene #106: 'KIAA1522 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
KIAA1522 MUTATED 0 2 5 4 0 3
KIAA1522 WILD-TYPE 74 45 83 61 27 78
'GTF2I MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0092 (Fisher's exact test), Q value = 0.27

Table S1009.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
GTF2I MUTATED 2 8 6 0
GTF2I WILD-TYPE 160 129 53 34

Figure S107.  Get High-res Image Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'GTF2I MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

Table S1010.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
GTF2I MUTATED 5 7 2 2
GTF2I WILD-TYPE 130 105 67 77
'GTF2I MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.62

Table S1011.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
GTF2I MUTATED 1 1 0 1 0
GTF2I WILD-TYPE 36 28 36 4 20
'GTF2I MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S1012.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
GTF2I MUTATED 1 2 0 0
GTF2I WILD-TYPE 42 36 27 19
'GTF2I MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S1013.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
GTF2I MUTATED 5 6 5
GTF2I WILD-TYPE 109 167 99
'GTF2I MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.723 (Fisher's exact test), Q value = 1

Table S1014.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
GTF2I MUTATED 6 3 7
GTF2I WILD-TYPE 110 103 162
'GTF2I MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.98

Table S1015.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
GTF2I MUTATED 7 3 6
GTF2I WILD-TYPE 112 93 171
'GTF2I MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S1016.  Gene #107: 'GTF2I 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
GTF2I MUTATED 5 4 3 2 2
GTF2I WILD-TYPE 81 95 86 63 51
'GTF2I MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 0.98

Table S1017.  Gene #107: 'GTF2I MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
GTF2I MUTATED 5 0 5 6
GTF2I WILD-TYPE 88 43 122 113
'GTF2I MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.71

Table S1018.  Gene #107: 'GTF2I 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
GTF2I MUTATED 1 0 7 3 0 5
GTF2I WILD-TYPE 73 47 81 62 27 76
'MOAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S1019.  Gene #108: '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 = 0.236 (Fisher's exact test), Q value = 0.79

Table S1020.  Gene #108: '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 = 0.807 (Fisher's exact test), Q value = 1

Table S1021.  Gene #108: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
MOAP1 MUTATED 2 0 1 0 0
MOAP1 WILD-TYPE 35 29 35 5 20
'MOAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S1022.  Gene #108: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
MOAP1 MUTATED 1 1 1 0
MOAP1 WILD-TYPE 42 37 26 19
'MOAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.066 (Fisher's exact test), Q value = 0.55

Table S1023.  Gene #108: '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 = 0.639 (Fisher's exact test), Q value = 1

Table S1024.  Gene #108: '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 = 0.549 (Fisher's exact test), Q value = 0.98

Table S1025.  Gene #108: '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 = 0.6 (Fisher's exact test), Q value = 0.99

Table S1026.  Gene #108: '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 = 0.866 (Fisher's exact test), Q value = 1

Table S1027.  Gene #108: '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 = 0.692 (Fisher's exact test), Q value = 1

Table S1028.  Gene #108: '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
'GAR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.93

Table S1029.  Gene #109: 'GAR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
GAR1 MUTATED 1 2 0 1
GAR1 WILD-TYPE 161 135 59 33
'GAR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.65

Table S1030.  Gene #109: 'GAR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
GAR1 MUTATED 0 3 0 1
GAR1 WILD-TYPE 135 109 69 78
'GAR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S1031.  Gene #109: 'GAR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
GAR1 MUTATED 1 2 1
GAR1 WILD-TYPE 113 171 103
'GAR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S1032.  Gene #109: 'GAR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
GAR1 MUTATED 1 2 1
GAR1 WILD-TYPE 115 104 168
'GAR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 0.99

Table S1033.  Gene #109: 'GAR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
GAR1 MUTATED 1 0 3
GAR1 WILD-TYPE 118 96 174
'GAR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S1034.  Gene #109: 'GAR1 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
GAR1 MUTATED 1 1 1 0 1
GAR1 WILD-TYPE 85 98 88 65 52
'GAR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.98

Table S1035.  Gene #109: 'GAR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
GAR1 MUTATED 0 0 3 1
GAR1 WILD-TYPE 93 43 124 118
'GAR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 0.85

Table S1036.  Gene #109: 'GAR1 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
GAR1 MUTATED 1 0 2 0 1 0
GAR1 WILD-TYPE 73 47 86 65 26 81
'RFTN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.404 (Fisher's exact test), Q value = 0.9

Table S1037.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
RFTN2 MUTATED 7 2 2 0
RFTN2 WILD-TYPE 155 135 57 34
'RFTN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.45

Table S1038.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
RFTN2 MUTATED 2 4 5 0
RFTN2 WILD-TYPE 133 108 64 79

Figure S108.  Get High-res Image Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RFTN2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.95

Table S1039.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
RFTN2 MUTATED 0 1 2 0 0
RFTN2 WILD-TYPE 37 28 34 5 20
'RFTN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.74

Table S1040.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
RFTN2 MUTATED 0 1 2 0
RFTN2 WILD-TYPE 43 37 25 19
'RFTN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S1041.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
RFTN2 MUTATED 2 6 3
RFTN2 WILD-TYPE 112 167 101
'RFTN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.79

Table S1042.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RFTN2 MUTATED 6 2 3
RFTN2 WILD-TYPE 110 104 166
'RFTN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S1043.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
RFTN2 MUTATED 4 2 5
RFTN2 WILD-TYPE 115 94 172
'RFTN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 0.89

Table S1044.  Gene #110: 'RFTN2 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
RFTN2 MUTATED 2 1 5 1 2
RFTN2 WILD-TYPE 84 98 84 64 51
'RFTN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S1045.  Gene #110: 'RFTN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
RFTN2 MUTATED 2 0 4 5
RFTN2 WILD-TYPE 91 43 123 114
'RFTN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.056 (Fisher's exact test), Q value = 0.52

Table S1046.  Gene #110: 'RFTN2 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
RFTN2 MUTATED 2 0 4 5 0 0
RFTN2 WILD-TYPE 72 47 84 60 27 81
'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.98

Table S1047.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZFP36L2 MUTATED 6 8 3 0
ZFP36L2 WILD-TYPE 156 129 56 34
'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 1

Table S1048.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZFP36L2 MUTATED 5 5 2 5
ZFP36L2 WILD-TYPE 130 107 67 74
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.98

Table S1049.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
ZFP36L2 MUTATED 1 0 3 0 1
ZFP36L2 WILD-TYPE 36 29 33 5 19
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 1

Table S1050.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
ZFP36L2 MUTATED 1 1 2 1
ZFP36L2 WILD-TYPE 42 37 25 18
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 1

Table S1051.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZFP36L2 MUTATED 5 9 3
ZFP36L2 WILD-TYPE 109 164 101
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S1052.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZFP36L2 MUTATED 5 6 6
ZFP36L2 WILD-TYPE 111 100 163
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 1

Table S1053.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZFP36L2 MUTATED 4 4 9
ZFP36L2 WILD-TYPE 115 92 168
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S1054.  Gene #111: 'ZFP36L2 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
ZFP36L2 MUTATED 2 4 4 4 3
ZFP36L2 WILD-TYPE 84 95 85 61 50
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S1055.  Gene #111: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZFP36L2 MUTATED 3 1 7 6
ZFP36L2 WILD-TYPE 90 42 120 113
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 1

Table S1056.  Gene #111: 'ZFP36L2 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
ZFP36L2 MUTATED 2 1 6 4 1 3
ZFP36L2 WILD-TYPE 72 46 82 61 26 78
'GUCY2C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S1057.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
GUCY2C MUTATED 5 5 3 0
GUCY2C WILD-TYPE 157 132 56 34
'GUCY2C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S1058.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
GUCY2C MUTATED 5 4 3 1
GUCY2C WILD-TYPE 130 108 66 78
'GUCY2C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.95

Table S1059.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
GUCY2C MUTATED 0 1 2 0 0
GUCY2C WILD-TYPE 37 28 34 5 20
'GUCY2C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.93

Table S1060.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
GUCY2C MUTATED 0 1 1 1
GUCY2C WILD-TYPE 43 37 26 18
'GUCY2C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

Table S1061.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
GUCY2C MUTATED 5 5 3
GUCY2C WILD-TYPE 109 168 101
'GUCY2C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S1062.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
GUCY2C MUTATED 5 3 5
GUCY2C WILD-TYPE 111 103 164
'GUCY2C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.78

Table S1063.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
GUCY2C MUTATED 7 2 4
GUCY2C WILD-TYPE 112 94 173
'GUCY2C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.993 (Fisher's exact test), Q value = 1

Table S1064.  Gene #112: 'GUCY2C 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
GUCY2C MUTATED 3 4 3 2 1
GUCY2C WILD-TYPE 83 95 86 63 52
'GUCY2C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.954 (Fisher's exact test), Q value = 1

Table S1065.  Gene #112: 'GUCY2C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
GUCY2C MUTATED 4 1 4 4
GUCY2C WILD-TYPE 89 42 123 115
'GUCY2C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.77

Table S1066.  Gene #112: 'GUCY2C 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
GUCY2C MUTATED 0 1 3 2 2 5
GUCY2C WILD-TYPE 74 46 85 63 25 76
'COPZ2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.7

Table S1067.  Gene #113: 'COPZ2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
COPZ2 MUTATED 0 2 0 1
COPZ2 WILD-TYPE 162 135 59 33
'COPZ2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.074 (Fisher's exact test), Q value = 0.57

Table S1068.  Gene #113: 'COPZ2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
COPZ2 MUTATED 0 3 0 0
COPZ2 WILD-TYPE 135 109 69 79
'COPZ2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.8

Table S1069.  Gene #113: 'COPZ2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
COPZ2 MUTATED 0 3 0
COPZ2 WILD-TYPE 114 170 104
'COPZ2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.62

Table S1070.  Gene #113: 'COPZ2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
COPZ2 MUTATED 1 2 0
COPZ2 WILD-TYPE 115 104 169
'COPZ2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S1071.  Gene #113: 'COPZ2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
COPZ2 MUTATED 0 1 2
COPZ2 WILD-TYPE 119 95 175
'COPZ2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.94

Table S1072.  Gene #113: 'COPZ2 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
COPZ2 MUTATED 0 1 0 1 1
COPZ2 WILD-TYPE 86 98 89 64 52
'ZNF791 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S1073.  Gene #114: 'ZNF791 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
ZNF791 MUTATED 3 4 2 1
ZNF791 WILD-TYPE 159 133 57 33
'ZNF791 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S1074.  Gene #114: 'ZNF791 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
ZNF791 MUTATED 5 2 1 2
ZNF791 WILD-TYPE 130 110 68 77
'ZNF791 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0153 (Fisher's exact test), Q value = 0.32

Table S1075.  Gene #114: 'ZNF791 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
ZNF791 MUTATED 7 1 2
ZNF791 WILD-TYPE 107 172 102

Figure S109.  Get High-res Image Gene #114: 'ZNF791 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF791 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 0.98

Table S1076.  Gene #114: 'ZNF791 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZNF791 MUTATED 4 1 5
ZNF791 WILD-TYPE 112 105 164
'ZNF791 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.89

Table S1077.  Gene #114: 'ZNF791 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
ZNF791 MUTATED 5 1 4
ZNF791 WILD-TYPE 114 95 173
'ZNF791 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.71

Table S1078.  Gene #114: 'ZNF791 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
ZNF791 MUTATED 2 2 2 0 4
ZNF791 WILD-TYPE 84 97 87 65 49
'ZNF791 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0806 (Fisher's exact test), Q value = 0.57

Table S1079.  Gene #114: 'ZNF791 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
ZNF791 MUTATED 2 0 1 7
ZNF791 WILD-TYPE 91 43 126 112
'ZNF791 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.89

Table S1080.  Gene #114: 'ZNF791 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
ZNF791 MUTATED 4 0 1 3 0 2
ZNF791 WILD-TYPE 70 47 87 62 27 79
'BUD13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.84

Table S1081.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
BUD13 MUTATED 2 6 2 1
BUD13 WILD-TYPE 160 131 57 33
'BUD13 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.76

Table S1082.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
BUD13 MUTATED 3 6 0 2
BUD13 WILD-TYPE 132 106 69 77
'BUD13 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.951 (Fisher's exact test), Q value = 1

Table S1083.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
BUD13 MUTATED 2 2 1 0 1
BUD13 WILD-TYPE 35 27 35 5 19
'BUD13 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.522 (Fisher's exact test), Q value = 0.98

Table S1084.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
BUD13 MUTATED 1 2 1 2
BUD13 WILD-TYPE 42 36 26 17
'BUD13 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.94

Table S1085.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
BUD13 MUTATED 4 6 1
BUD13 WILD-TYPE 110 167 103
'BUD13 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0993 (Fisher's exact test), Q value = 0.6

Table S1086.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
BUD13 MUTATED 3 6 2
BUD13 WILD-TYPE 113 100 167
'BUD13 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 0.99

Table S1087.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
BUD13 MUTATED 2 4 5
BUD13 WILD-TYPE 117 92 172
'BUD13 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.358 (Fisher's exact test), Q value = 0.88

Table S1088.  Gene #115: 'BUD13 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
BUD13 MUTATED 1 5 1 3 1
BUD13 WILD-TYPE 85 94 88 62 52
'BUD13 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.97

Table S1089.  Gene #115: 'BUD13 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
BUD13 MUTATED 1 2 5 3
BUD13 WILD-TYPE 92 41 122 116
'BUD13 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.499 (Fisher's exact test), Q value = 0.97

Table S1090.  Gene #115: 'BUD13 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
BUD13 MUTATED 1 2 5 2 0 1
BUD13 WILD-TYPE 73 45 83 63 27 80
'HES1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S1091.  Gene #116: '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 = 1

Table S1092.  Gene #116: '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 = 0.373 (Fisher's exact test), Q value = 0.89

Table S1093.  Gene #116: 'HES1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
HES1 MUTATED 1 0 1 0 2
HES1 WILD-TYPE 36 29 35 5 18
'HES1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.67

Table S1094.  Gene #116: 'HES1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
HES1 MUTATED 0 1 1 2
HES1 WILD-TYPE 43 37 26 17
'HES1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S1095.  Gene #116: '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 = 1

Table S1096.  Gene #116: '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 = 0.674 (Fisher's exact test), Q value = 1

Table S1097.  Gene #116: '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 = 0.47 (Fisher's exact test), Q value = 0.94

Table S1098.  Gene #116: '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 = 0.328 (Fisher's exact test), Q value = 0.85

Table S1099.  Gene #116: '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 = 0.57 (Fisher's exact test), Q value = 0.98

Table S1100.  Gene #116: '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
'HORMAD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.44

Table S1101.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
HORMAD1 MUTATED 2 6 0 3
HORMAD1 WILD-TYPE 160 131 59 31

Figure S110.  Get High-res Image Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HORMAD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.42

Table S1102.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
HORMAD1 MUTATED 0 5 2 4
HORMAD1 WILD-TYPE 135 107 67 75

Figure S111.  Get High-res Image Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HORMAD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S1103.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
HORMAD1 MUTATED 2 1 3 0 1
HORMAD1 WILD-TYPE 35 28 33 5 19
'HORMAD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S1104.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
HORMAD1 MUTATED 3 2 1 1
HORMAD1 WILD-TYPE 40 36 26 18
'HORMAD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S1105.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
HORMAD1 MUTATED 2 6 3
HORMAD1 WILD-TYPE 112 167 101
'HORMAD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 0.94

Table S1106.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
HORMAD1 MUTATED 5 3 3
HORMAD1 WILD-TYPE 111 103 166
'HORMAD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.44

Table S1107.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
HORMAD1 MUTATED 0 5 6
HORMAD1 WILD-TYPE 119 91 171

Figure S112.  Get High-res Image Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HORMAD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S1108.  Gene #117: 'HORMAD1 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
HORMAD1 MUTATED 2 5 2 1 1
HORMAD1 WILD-TYPE 84 94 87 64 52
'HORMAD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S1109.  Gene #117: 'HORMAD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
HORMAD1 MUTATED 3 2 3 3
HORMAD1 WILD-TYPE 90 41 124 116
'HORMAD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S1110.  Gene #117: 'HORMAD1 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
HORMAD1 MUTATED 2 2 2 1 1 3
HORMAD1 WILD-TYPE 72 45 86 64 26 78
'SND1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S1111.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 162 137 59 34
SND1 MUTATED 3 4 1 1
SND1 WILD-TYPE 159 133 58 33
'SND1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S1112.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 112 69 79
SND1 MUTATED 3 3 2 1
SND1 WILD-TYPE 132 109 67 78
'SND1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S1113.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 37 29 36 5 20
SND1 MUTATED 2 0 2 0 0
SND1 WILD-TYPE 35 29 34 5 20
'SND1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 0.87

Table S1114.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 38 27 19
SND1 MUTATED 3 0 1 0
SND1 WILD-TYPE 40 38 26 19
'SND1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S1115.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 114 173 104
SND1 MUTATED 3 4 2
SND1 WILD-TYPE 111 169 102
'SND1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 0.98

Table S1116.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SND1 MUTATED 4 1 4
SND1 WILD-TYPE 112 105 165
'SND1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S1117.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 119 96 177
SND1 MUTATED 3 1 5
SND1 WILD-TYPE 116 95 172
'SND1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S1118.  Gene #118: 'SND1 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
SND1 MUTATED 1 3 2 1 2
SND1 WILD-TYPE 85 96 87 64 51
'SND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S1119.  Gene #118: 'SND1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 93 43 127 119
SND1 MUTATED 3 1 2 3
SND1 WILD-TYPE 90 42 125 116
'SND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S1120.  Gene #118: 'SND1 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
SND1 MUTATED 2 1 2 1 0 3
SND1 WILD-TYPE 72 46 86 64 27 78
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/15190394/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/15111049/BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 395

  • Number of significantly mutated genes = 118

  • 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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