Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 81 genes and 10 molecular subtypes across 395 patients, 53 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

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

  • CDKN2A mutation correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • CREBBP mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • MLL mutation correlated to 'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • PSIP1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • MLL3 mutation correlated to 'CN_CNMF'.

  • RXRA mutation correlated to 'METHLYATION_CNMF'.

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

  • NUDT11 mutation correlated to 'RPPA_CNMF'.

  • FAM47C mutation correlated to 'RPPA_CNMF'.

  • SF1 mutation correlated to 'MIRSEQ_CNMF'.

  • DNAH6 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • TXNIP mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • RUNX1 mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • DAZAP1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 81 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 53 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
(0.000736) 		1e-05
(0.000736) 		1e-05
(0.000736) 		1e-05
(0.000736) 		1e-05
(0.000736) 		1e-05
(0.000736) 		1e-05
(0.000736) 		0.00041
(0.0166) 		1e-05
(0.000736) 		1e-05
(0.000736)
TP53 196 (50%) 199 1e-05
(0.000736) 		0.00084
(0.0283) 		0.0003
(0.0128) 		0.0242
(0.316) 		5e-05
(0.0027) 		2e-05
(0.00125) 		0.00155
(0.0448) 		0.144
(0.618) 		0.00562
(0.126) 		0.00141
(0.0439)
RB1 70 (18%) 325 1e-05
(0.000736) 		0.0406
(0.397) 		5e-05
(0.0027) 		0.00021
(0.00945) 		9e-05
(0.00456) 		2e-05
(0.00125) 		0.00011
(0.00524) 		0.368
(0.781) 		0.00068
(0.025) 		0.00154
(0.0448)
KDM6A 103 (26%) 292 0.387
(0.795) 		0.00222
(0.0607) 		0.0517
(0.414) 		0.222
(0.669) 		0.00446
(0.106) 		0.0113
(0.183) 		0.117
(0.558) 		0.169
(0.638) 		0.0373
(0.382) 		0.17
(0.638)
MLL 44 (11%) 351 0.0427
(0.399) 		0.708
(0.928) 		0.0644
(0.46) 		0.171
(0.638) 		0.401
(0.795) 		0.0731
(0.47) 		0.00646
(0.14) 		0.0109
(0.18) 		0.0322
(0.35) 		0.00471
(0.109)
NFE2L2 24 (6%) 371 0.0594
(0.437) 		0.0145
(0.226) 		0.12
(0.562) 		0.0687
(0.46) 		0.00844
(0.157) 		0.0083
(0.157) 		0.089
(0.5) 		0.656
(0.914) 		0.551
(0.873) 		0.0446
(0.399)
CNOT3 10 (3%) 385 0.11
(0.541) 		0.327
(0.754) 		0.702
(0.928) 		0.174
(0.638) 		0.0483
(0.399) 		0.116
(0.555) 		0.00871
(0.157) 		0.446
(0.823) 		0.00735
(0.145) 		0.0006
(0.0231)
CDKN2A 26 (7%) 369 0.856
(0.977) 		0.0386
(0.391) 		0.681
(0.919) 		0.0275
(0.343) 		0.284
(0.726) 		0.447
(0.823) 		0.00667
(0.14) 		0.19
(0.664) 		0.079
(0.478) 		0.00077
(0.0271)
RUNX1 13 (3%) 382 0.652
(0.914) 		0.675
(0.919) 		0.261
(0.713) 		0.518
(0.854) 		0.00225
(0.0607) 		0.0465
(0.399) 		0.192
(0.664) 		0.917
(0.987) 		0.813
(0.966) 		0.00109
(0.0353)
STAG2 56 (14%) 339 0.053
(0.414) 		0.03
(0.348) 		0.106
(0.541) 		0.19
(0.664) 		0.508
(0.85) 		0.00673
(0.14) 		0.102
(0.541) 		0.222
(0.669) 		0.0452
(0.399) 		0.0302
(0.348)
CREBBP 48 (12%) 347 0.472
(0.848) 		0.494
(0.85) 		0.644
(0.914) 		0.819
(0.967) 		0.264
(0.714) 		0.543
(0.866) 		0.087
(0.499) 		0.00348
(0.0854) 		0.139
(0.6) 		0.0542
(0.414)
PSIP1 20 (5%) 375 0.75
(0.945) 		0.0481
(0.399) 		0.0178
(0.257) 		0.167
(0.638) 		0.752
(0.945) 		0.0163
(0.249) 		0.107
(0.541) 		0.942
(0.992) 		0.028
(0.344) 		0.0257
(0.331)
MLL3 74 (19%) 321 0.00949
(0.167) 		0.628
(0.911) 		0.116
(0.555) 		0.225
(0.669) 		0.402
(0.795) 		0.479
(0.85) 		0.369
(0.781) 		0.0288
(0.345) 		0.124
(0.575) 		0.297
(0.727)
RXRA 24 (6%) 371 0.135
(0.6) 		0.0104
(0.177) 		0.583
(0.88) 		0.277
(0.721) 		0.31
(0.727) 		0.258
(0.713) 		0.287
(0.727) 		0.345
(0.776) 		0.541
(0.865) 		0.371
(0.781)
NUDT11 7 (2%) 388 0.811
(0.966) 		0.406
(0.797) 		0.00323
(0.0835) 		0.812
(0.966) 		0.244
(0.701) 		0.716
(0.931) 		0.758
(0.95) 		0.37
(0.781) 		0.344
(0.776) 		0.578
(0.88)
FAM47C 21 (5%) 374 0.397
(0.795) 		0.821
(0.967) 		0.00698
(0.141) 		0.743
(0.945) 		0.389
(0.795) 		0.718
(0.932) 		0.305
(0.727) 		0.155
(0.638) 		0.677
(0.919) 		0.408
(0.797)
SF1 10 (3%) 385 0.365
(0.781) 		0.638
(0.911) 		0.306
(0.727) 		0.0172
(0.254) 		0.895
(0.982) 		1
(1.00) 		0.0033
(0.0835) 		0.0167
(0.251) 		0.0927
(0.511) 		0.49
(0.85)
DNAH6 16 (4%) 379 0.734
(0.941) 		0.139
(0.6) 		0.452
(0.826) 		0.191
(0.664) 		0.0205
(0.287) 		0.0123
(0.196) 		0.33
(0.758) 		0.137
(0.6) 		0.0685
(0.46) 		0.0861
(0.499)
TXNIP 17 (4%) 378 0.725
(0.933) 		0.494
(0.85) 		0.128
(0.583) 		0.746
(0.945) 		0.31
(0.727) 		0.00862
(0.157) 		0.719
(0.932) 		0.429
(0.807) 		0.927
(0.992) 		0.779
(0.956)
DAZAP1 6 (2%) 389 0.365
(0.781) 		0.0875
(0.499) 		0.556
(0.874) 		0.32
(0.745) 		0.46
(0.831) 		0.0105
(0.177) 		0.192
(0.664) 		0.378
(0.792) 		0.475
(0.85) 		0.586
(0.88)
ELF3 46 (12%) 349 0.849
(0.975) 		0.109
(0.541) 		0.627
(0.911) 		0.0638
(0.46) 		0.0767
(0.474) 		0.0403
(0.397) 		0.416
(0.806) 		0.639
(0.911) 		0.259
(0.713) 		0.585
(0.88)
TSC1 33 (8%) 362 0.216
(0.669) 		0.931
(0.992) 		0.313
(0.732) 		0.205
(0.669) 		0.32
(0.745) 		0.234
(0.678) 		0.527
(0.854) 		0.0725
(0.47) 		0.591
(0.883) 		0.86
(0.978)
PIK3CA 86 (22%) 309 0.801
(0.966) 		0.949
(0.992) 		0.842
(0.974) 		0.947
(0.992) 		0.024
(0.316) 		0.765
(0.95) 		0.743
(0.945) 		0.685
(0.924) 		0.97
(1.00) 		0.839
(0.974)
RHOB 26 (7%) 369 0.371
(0.781) 		0.294
(0.727) 		0.918
(0.987) 		0.677
(0.919) 		0.248
(0.702) 		0.159
(0.638) 		0.42
(0.807) 		0.829
(0.97) 		0.771
(0.953) 		0.806
(0.966)
ARID1A 97 (25%) 298 0.245
(0.701) 		0.488
(0.85) 		0.766
(0.95) 		0.523
(0.854) 		0.148
(0.626) 		0.782
(0.956) 		0.0493
(0.399) 		0.0661
(0.46) 		0.11
(0.541) 		0.66
(0.914)
ZFP36L1 25 (6%) 370 0.961
(0.998) 		0.384
(0.795) 		0.307
(0.727) 		0.932
(0.992) 		0.509
(0.851) 		0.235
(0.678) 		0.723
(0.933) 		0.327
(0.754) 		0.567
(0.88) 		0.246
(0.702)
CDKN1A 35 (9%) 360 0.95
(0.992) 		0.17
(0.638) 		0.305
(0.727) 		0.0329
(0.35) 		0.72
(0.932) 		0.356
(0.781) 		0.172
(0.638) 		0.0874
(0.499) 		0.296
(0.727) 		0.504
(0.85)
EP300 61 (15%) 334 0.13
(0.587) 		0.813
(0.966) 		0.421
(0.807) 		0.663
(0.914) 		0.273
(0.717) 		0.31
(0.727) 		0.579
(0.88) 		0.842
(0.974) 		0.468
(0.843) 		0.866
(0.98)
MLL2 114 (29%) 281 0.156
(0.638) 		0.608
(0.897) 		0.908
(0.986) 		0.103
(0.541) 		0.68
(0.919) 		0.937
(0.992) 		0.448
(0.823) 		0.346
(0.776) 		0.505
(0.85) 		0.068
(0.46)
ERCC2 38 (10%) 357 0.548
(0.871) 		0.424
(0.807) 		0.0462
(0.399) 		0.254
(0.711) 		0.4
(0.795) 		0.705
(0.928) 		0.169
(0.638) 		0.428
(0.807) 		0.147
(0.624) 		0.396
(0.795)
HRAS 17 (4%) 378 0.244
(0.701) 		0.199
(0.669) 		0.506
(0.85) 		0.846
(0.975) 		0.843
(0.974) 		0.777
(0.956) 		0.341
(0.773) 		0.429
(0.807) 		0.358
(0.781) 		0.271
(0.717)
FOXA1 14 (4%) 381 0.745
(0.945) 		0.52
(0.854) 		0.814
(0.966) 		0.166
(0.638) 		0.366
(0.781) 		0.228
(0.672) 		0.273
(0.717) 		0.158
(0.638) 		0.021
(0.288) 		0.271
(0.717)
KRAS 13 (3%) 382 0.0718
(0.469) 		0.622
(0.909) 		0.584
(0.88) 		0.152
(0.638) 		0.108
(0.541) 		0.173
(0.638) 		0.639
(0.911) 		0.562
(0.879) 		0.703
(0.928) 		0.586
(0.88)
RHOA 18 (5%) 377 0.496
(0.85) 		0.353
(0.781) 		0.403
(0.796) 		0.178
(0.647) 		0.886
(0.98) 		0.48
(0.85) 		0.181
(0.648) 		0.111
(0.541) 		0.676
(0.919) 		0.816
(0.966)
KIAA1267 24 (6%) 371 0.406
(0.797) 		0.0491
(0.399) 		0.955
(0.994) 		0.647
(0.914) 		0.339
(0.771) 		0.212
(0.669) 		0.251
(0.706) 		0.781
(0.956) 		0.0563
(0.426) 		0.527
(0.854)
FAT1 50 (13%) 345 0.807
(0.966) 		0.0674
(0.46) 		0.23
(0.676) 		0.124
(0.575) 		0.392
(0.795) 		0.194
(0.665) 		0.113
(0.547) 		0.0324
(0.35) 		0.349
(0.78) 		0.0815
(0.486)
KLF5 23 (6%) 372 0.661
(0.914) 		0.952
(0.992) 		0.0492
(0.399) 		0.657
(0.914) 		0.582
(0.88) 		0.708
(0.928) 		0.248
(0.702) 		0.0624
(0.455) 		0.157
(0.638) 		0.0845
(0.496)
PTEN 14 (4%) 381 0.834
(0.97) 		0.135
(0.6) 		0.478
(0.85) 		0.371
(0.781) 		0.138
(0.6) 		0.162
(0.638) 		0.434
(0.812) 		1
(1.00) 		0.938
(0.992) 		0.667
(0.915)
C3ORF70 17 (4%) 378 0.57
(0.88) 		0.249
(0.702) 		1
(1.00) 		0.668
(0.915) 		0.872
(0.98) 		0.569
(0.88) 		0.875
(0.98) 		0.494
(0.85) 		0.951
(0.992) 		0.914
(0.987)
ASXL2 36 (9%) 359 0.82
(0.967) 		0.785
(0.956) 		0.0925
(0.511) 		0.217
(0.669) 		0.522
(0.854) 		0.593
(0.883) 		0.328
(0.756) 		0.213
(0.669) 		0.428
(0.807) 		0.49
(0.85)
ZBTB7B 11 (3%) 384 0.906
(0.986) 		0.88
(0.98) 		0.787
(0.956) 		0.534
(0.859) 		0.42
(0.807) 		0.397
(0.795) 		0.526
(0.854) 		0.214
(0.669) 		0.672
(0.919) 		0.407
(0.797)
FBXW7 30 (8%) 365 0.0219
(0.296) 		0.067
(0.46) 		0.711
(0.929) 		0.441
(0.819) 		0.49
(0.85) 		0.171
(0.638) 		0.365
(0.781) 		0.198
(0.669) 		0.209
(0.669) 		0.0469
(0.399)
RBM10 22 (6%) 373 0.288
(0.727) 		0.454
(0.828) 		0.484
(0.85) 		0.905
(0.986) 		0.304
(0.727) 		0.886
(0.98) 		0.209
(0.669) 		0.21
(0.669) 		0.309
(0.727) 		0.28
(0.724)
CUL1 19 (5%) 376 0.812
(0.966) 		0.601
(0.891) 		0.107
(0.541) 		0.298
(0.727) 		0.79
(0.957) 		0.458
(0.829) 		0.854
(0.977) 		0.831
(0.97) 		0.806
(0.966) 		0.301
(0.727)
HLA-A 5 (1%) 390 0.49
(0.85) 		1
(1.00) 		0.297
(0.727) 		1
(1.00) 		0.907
(0.986) 		0.291
(0.727) 		0.93
(0.992) 		0.693
(0.926)
GNA13 12 (3%) 383 0.798
(0.963) 		0.22
(0.669) 		0.366
(0.781) 		0.775
(0.956) 		0.694
(0.926) 		0.365
(0.781) 		0.542
(0.865) 		0.217
(0.669) 		0.0674
(0.46) 		0.535
(0.859)
MBD1 12 (3%) 383 0.193
(0.664) 		0.875
(0.98) 		0.508
(0.85) 		0.294
(0.727) 		0.207
(0.669) 		0.661
(0.914) 		0.796
(0.963) 		0.597
(0.888) 		0.575
(0.88) 		0.769
(0.951)
SCARF2 8 (2%) 387 0.385
(0.795) 		0.0534
(0.414) 		0.325
(0.754) 		0.199
(0.669) 		0.0702
(0.462) 		0.163
(0.638) 		0.871
(0.98) 		0.496
(0.85) 		0.279
(0.724) 		0.555
(0.874)
FOXQ1 14 (4%) 381 0.737
(0.943) 		0.767
(0.95) 		0.618
(0.906) 		0.268
(0.717) 		0.733
(0.941) 		0.887
(0.98) 		0.831
(0.97) 		0.841
(0.974) 		1
(1.00) 		0.968
(1.00)
METTL3 17 (4%) 378 0.761
(0.95) 		0.722
(0.933) 		1
(1.00) 		0.691
(0.926) 		0.558
(0.876) 		0.218
(0.669) 		0.412
(0.802) 		0.299
(0.727) 		0.575
(0.88) 		0.11
(0.541)
ZNF185 5 (1%) 390 0.869
(0.98) 		0.708
(0.928) 		0.0763
(0.474) 		0.356
(0.781) 		0.378
(0.792) 		0.864
(0.98) 		0.657
(0.914) 		0.652
(0.914) 		0.745
(0.945) 		0.258
(0.713)
ERBB2 48 (12%) 347 0.762
(0.95) 		0.223
(0.669) 		0.53
(0.854) 		0.679
(0.919) 		0.449
(0.823) 		0.207
(0.669) 		0.0701
(0.462) 		0.233
(0.678) 		0.362
(0.781) 		0.393
(0.795)
ATM 53 (13%) 342 0.482
(0.85) 		0.179
(0.647) 		0.172
(0.638) 		0.0183
(0.26) 		0.631
(0.911) 		0.654
(0.914) 		0.269
(0.717) 		0.207
(0.669) 		0.276
(0.721) 		0.0976
(0.534)
UNC93B1 7 (2%) 388 0.564
(0.88) 		0.657
(0.914) 		0.511
(0.852) 		0.896
(0.982) 		0.93
(0.992) 		0.888
(0.98) 		1
(1.00) 		1
(1.00) 		0.673
(0.919) 		0.663
(0.914)
BCL2L1 4 (1%) 391 0.0662
(0.46) 		0.0326
(0.35) 		0.0769
(0.474) 		0.525
(0.854) 		0.712
(0.929) 		0.692
(0.926) 		0.749
(0.945) 		1
(1.00) 		0.396
(0.795) 		0.816
(0.966)
HES1 11 (3%) 384 1
(1.00) 		0.948
(0.992) 		0.582
(0.88) 		0.127
(0.583) 		0.92
(0.987) 		0.632
(0.911) 		0.354
(0.781) 		0.308
(0.727) 		0.878
(0.98) 		0.498
(0.85)
ERBB3 41 (10%) 354 0.479
(0.85) 		0.359
(0.781) 		0.901
(0.985) 		0.268
(0.717) 		0.522
(0.854) 		0.219
(0.669) 		0.858
(0.977) 		0.856
(0.977) 		0.944
(0.992) 		0.301
(0.727)
THRAP3 14 (4%) 381 0.847
(0.975) 		0.646
(0.914) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.784
(0.956) 		0.336
(0.766) 		0.92
(0.987) 		0.96
(0.998) 		0.847
(0.975)
SPTAN1 45 (11%) 350 0.652
(0.914) 		0.157
(0.638) 		0.262
(0.713) 		0.12
(0.562) 		0.267
(0.717) 		0.203
(0.669) 		0.224
(0.669) 		0.586
(0.88) 		0.309
(0.727) 		0.172
(0.638)
ARID1B 23 (6%) 372 0.529
(0.854) 		0.0895
(0.5) 		0.187
(0.664) 		0.585
(0.88) 		0.0992
(0.539) 		0.0579
(0.431) 		0.21
(0.669) 		0.163
(0.638) 		0.175
(0.64) 		0.109
(0.541)
NRAS 7 (2%) 388 0.295
(0.727) 		0.44
(0.819) 		1
(1.00) 		0.638
(0.911) 		0.658
(0.914) 		0.638
(0.911) 		0.423
(0.807) 		0.368
(0.781) 		0.0434
(0.399) 		0.225
(0.669)
RPTN 15 (4%) 380 0.938
(0.992) 		0.35
(0.781) 		0.872
(0.98) 		0.764
(0.95) 		0.494
(0.85) 		1
(1.00) 		0.214
(0.669) 		0.22
(0.669) 		0.786
(0.956) 		0.782
(0.956)
RAI1 21 (5%) 374 0.654
(0.914) 		0.137
(0.6) 		0.119
(0.562) 		0.0772
(0.474) 		0.027
(0.341) 		0.0324
(0.35) 		0.174
(0.638) 		0.43
(0.807) 		0.396
(0.795) 		0.565
(0.88)
TMCO4 12 (3%) 383 0.753
(0.945) 		0.0532
(0.414) 		0.554
(0.874) 		0.287
(0.727) 		0.0479
(0.399) 		0.0753
(0.474) 		0.215
(0.669) 		1
(1.00) 		0.0492
(0.399) 		0.203
(0.669)
CNOT1 21 (5%) 374 0.442
(0.819) 		0.162
(0.638) 		0.363
(0.781) 		0.389
(0.795) 		0.605
(0.895) 		0.455
(0.828) 		0.555
(0.874) 		0.895
(0.982) 		0.91
(0.986) 		0.881
(0.98)
PARD3 22 (6%) 373 0.108
(0.541) 		0.647
(0.914) 		0.419
(0.807) 		0.367
(0.781) 		0.0885
(0.5) 		0.852
(0.977) 		0.971
(1.00) 		0.261
(0.713) 		0.876
(0.98) 		0.261
(0.713)
EZR 12 (3%) 383 0.446
(0.823) 		0.486
(0.85) 		1
(1.00) 		0.384
(0.795) 		0.413
(0.802) 		0.871
(0.98) 		0.936
(0.992) 		0.18
(0.647) 		0.892
(0.982) 		0.731
(0.94)
MOAP1 7 (2%) 388 0.807
(0.966) 		0.301
(0.727) 		0.523
(0.854) 		0.602
(0.891) 		0.227
(0.672) 		0.637
(0.911) 		0.272
(0.717) 		0.857
(0.977) 		0.908
(0.986) 		0.753
(0.945)
SF3B1 24 (6%) 371 0.343
(0.776) 		0.885
(0.98) 		0.506
(0.85) 		0.457
(0.829) 		0.701
(0.928) 		0.616
(0.904) 		0.947
(0.992) 		0.592
(0.883) 		0.385
(0.795) 		0.147
(0.624)
MEGF8 20 (5%) 375 0.664
(0.914) 		0.441
(0.819) 		0.689
(0.926) 		1
(1.00) 		0.137
(0.6) 		0.54
(0.865) 		0.215
(0.669) 		0.587
(0.88) 		0.909
(0.986) 		0.889
(0.98)
CASP8 14 (4%) 381 0.497
(0.85) 		0.488
(0.85) 		0.0822
(0.486) 		0.101
(0.541) 		0.879
(0.98) 		0.577
(0.88) 		0.163
(0.638) 		0.402
(0.795) 		0.547
(0.87) 		0.283
(0.726)
USP28 13 (3%) 382 0.397
(0.795) 		0.939
(0.992) 		0.583
(0.88) 		0.397
(0.795) 		0.833
(0.97) 		1
(1.00) 		0.752
(0.945) 		1
(1.00) 		0.613
(0.901) 		0.41
(0.799)
SETD2 27 (7%) 368 0.705
(0.928) 		0.712
(0.929) 		0.502
(0.85) 		0.826
(0.97) 		1
(1.00) 		0.819
(0.967) 		0.263
(0.714) 		0.43
(0.807) 		0.832
(0.97) 		0.865
(0.98)
EME1 5 (1%) 390 0.628
(0.911) 		0.287
(0.727) 		0.697
(0.928) 		0.282
(0.726) 		0.523
(0.854) 		0.335
(0.766) 		0.493
(0.85) 		0.105
(0.541) 		0.16
(0.638) 		0.109
(0.541)
ADC 5 (1%) 390 0.0817
(0.486) 		0.934
(0.992) 		0.694
(0.926) 		0.7
(0.928) 		0.917
(0.987) 		1
(1.00) 		1
(1.00) 		0.526
(0.854) 		0.569
(0.88) 		0.762
(0.95)
SSH3 15 (4%) 380 0.207
(0.669) 		0.058
(0.431) 		0.0342
(0.359) 		0.0438
(0.399) 		0.0779
(0.474) 		0.395
(0.795) 		0.125
(0.577) 		0.22
(0.669) 		0.0369
(0.382) 		0.029
(0.345)
AHR 22 (6%) 373 0.631
(0.911) 		0.103
(0.541) 		0.157
(0.638) 		0.778
(0.956) 		0.521
(0.854) 		0.0741
(0.473) 		0.705
(0.928) 		0.948
(0.992) 		0.504
(0.85) 		0.206
(0.669)
EIF4A2 11 (3%) 384 0.518
(0.854) 		0.714
(0.929) 		0.399
(0.795) 		0.611
(0.9) 		0.738
(0.943) 		0.261
(0.713) 		0.427
(0.807) 		0.188
(0.664) 		0.623
(0.909) 		0.0541
(0.414)
EPHA2 19 (5%) 376 0.942
(0.992) 		0.0398
(0.397) 		0.641
(0.913) 		0.494
(0.85) 		0.901
(0.985) 		1
(1.00) 		0.752
(0.945) 		0.508
(0.85) 		0.914
(0.987) 		0.295
(0.727)
OGDH 19 (5%) 376 0.219
(0.669) 		0.13
(0.587) 		0.882
(0.98) 		0.56
(0.878) 		0.823
(0.968) 		0.867
(0.98) 		0.467
(0.842) 		0.231
(0.676) 		0.43
(0.807) 		0.273
(0.717)
POU3F1 3 (1%) 392 0.577
(0.88) 		0.189
(0.664) 		0.0305
(0.348) 		0.633
(0.911) 		0.0446
(0.399) 		0.792
(0.958) 		0.282
(0.726) 		0.168
(0.638) 		0.0442
(0.399) 		0.228
(0.672)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
TP53 MUTATED 37 85 21 50 2
TP53 WILD-TYPE 37 57 93 10 0

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00084 (Fisher's exact test), Q value = 0.028

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
TP53 MUTATED 72 73 19 32
TP53 WILD-TYPE 63 49 43 44

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 = 3e-04 (Fisher's exact test), Q value = 0.013

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

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

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

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0242 (Fisher's exact test), Q value = 0.32

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

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

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
TP53 MUTATED 30 52 12 61 39
TP53 WILD-TYPE 41 78 23 38 17

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 = 0.0012

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 = 0.00155 (Fisher's exact test), Q value = 0.045

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
TP53 MUTATED 63 31 44 18 39
TP53 WILD-TYPE 37 43 61 7 49

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
TP53 MUTATED 135 34 26
TP53 WILD-TYPE 119 49 29
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00562 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
TP53 MUTATED 60 19 53 56
TP53 WILD-TYPE 63 33 67 31

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 = 0.00141 (Fisher's exact test), Q value = 0.044

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
ALL 87 61 41 122 71
TP53 MUTATED 38 24 24 53 49
TP53 WILD-TYPE 49 37 17 69 22

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

'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RB1 MUTATED 13 26 3 27 1
RB1 WILD-TYPE 61 116 111 33 1

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

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RB1 MUTATED 31 16 6 17
RB1 WILD-TYPE 104 106 56 59

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

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.0027

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

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

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

'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00021 (Fisher's exact test), Q value = 0.0094

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

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

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

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RB1 MUTATED 17 13 0 27 11
RB1 WILD-TYPE 54 117 35 72 45

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

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.0012

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

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

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

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0052

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RB1 MUTATED 32 10 9 7 11
RB1 WILD-TYPE 68 64 96 18 77

Figure S16.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RB1 MUTATED 50 12 7
RB1 WILD-TYPE 204 71 48
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.025

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RB1 MUTATED 17 5 17 29
RB1 WILD-TYPE 106 47 103 58

Figure S17.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00154 (Fisher's exact test), Q value = 0.045

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
RB1 MUTATED 10 7 8 18 25
RB1 WILD-TYPE 77 54 33 104 46

Figure S18.  Get High-res Image Gene #2: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ELF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ELF3 MUTATED 10 17 11 8 0
ELF3 WILD-TYPE 64 125 103 52 2
'ELF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ELF3 MUTATED 9 19 7 11
ELF3 WILD-TYPE 126 103 55 65
'ELF3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 0.91

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

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

P value = 0.0638 (Fisher's exact test), Q value = 0.46

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

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

P value = 0.0767 (Fisher's exact test), Q value = 0.47

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ELF3 MUTATED 6 24 3 7 5
ELF3 WILD-TYPE 65 106 32 92 51
'ELF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.4

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

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

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

'ELF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ELF3 MUTATED 10 11 16 1 8
ELF3 WILD-TYPE 90 63 89 24 80
'ELF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ELF3 MUTATED 29 12 5
ELF3 WILD-TYPE 225 71 50
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ELF3 MUTATED 13 10 15 7
ELF3 WILD-TYPE 110 42 105 80
'ELF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ELF3 MUTATED 9 9 5 17 5
ELF3 WILD-TYPE 78 52 36 105 66
'TSC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
TSC1 MUTATED 8 12 12 1 0
TSC1 WILD-TYPE 66 130 102 59 2
'TSC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
TSC1 MUTATED 10 11 6 6
TSC1 WILD-TYPE 125 111 56 70
'TSC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.73

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

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

P value = 0.205 (Fisher's exact test), Q value = 0.67

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

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

P value = 0.32 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
TSC1 MUTATED 8 15 1 6 3
TSC1 WILD-TYPE 63 115 34 93 53
'TSC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.527 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
TSC1 MUTATED 5 9 8 2 8
TSC1 WILD-TYPE 95 65 97 23 80
'TSC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0725 (Fisher's exact test), Q value = 0.47

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
TSC1 MUTATED 15 10 7
TSC1 WILD-TYPE 239 73 48
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
TSC1 MUTATED 12 6 9 5
TSC1 WILD-TYPE 111 46 111 82
'TSC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
TSC1 MUTATED 9 5 4 10 4
TSC1 WILD-TYPE 78 56 37 112 67
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
PIK3CA MUTATED 18 27 26 15 0
PIK3CA WILD-TYPE 56 115 88 45 2
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.949 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
PIK3CA MUTATED 29 25 14 18
PIK3CA WILD-TYPE 106 97 48 58
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 0.97

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

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

P value = 0.947 (Fisher's exact test), Q value = 0.99

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

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

P value = 0.024 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
PIK3CA MUTATED 17 21 15 22 10
PIK3CA WILD-TYPE 54 109 20 77 46

Figure S20.  Get High-res Image Gene #5: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 0.95

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

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

P value = 0.743 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
PIK3CA MUTATED 24 13 21 7 20
PIK3CA WILD-TYPE 76 61 84 18 68
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.685 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
PIK3CA MUTATED 58 15 12
PIK3CA WILD-TYPE 196 68 43
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
PIK3CA MUTATED 27 10 27 20
PIK3CA WILD-TYPE 96 42 93 67
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.839 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
PIK3CA MUTATED 17 11 9 30 17
PIK3CA WILD-TYPE 70 50 32 92 54
'RHOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RHOB MUTATED 4 13 4 5 0
RHOB WILD-TYPE 70 129 110 55 2
'RHOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RHOB MUTATED 9 12 2 3
RHOB WILD-TYPE 126 110 60 73
'RHOB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 0.99

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

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

P value = 0.677 (Fisher's exact test), Q value = 0.92

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

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

P value = 0.248 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RHOB MUTATED 4 12 4 5 1
RHOB WILD-TYPE 67 118 31 94 55
'RHOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.64

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 = 0.42 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RHOB MUTATED 8 3 10 0 5
RHOB WILD-TYPE 92 71 95 25 83
'RHOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.829 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RHOB MUTATED 18 4 4
RHOB WILD-TYPE 236 79 51
'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RHOB MUTATED 8 2 10 5
RHOB WILD-TYPE 115 50 110 82
'RHOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.806 (Fisher's exact test), Q value = 0.97

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
ALL 87 61 41 122 71
RHOB MUTATED 6 2 2 10 5
RHOB WILD-TYPE 81 59 39 112 66
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
KDM6A MUTATED 21 39 33 10 0
KDM6A WILD-TYPE 53 103 81 50 2
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
KDM6A MUTATED 25 40 24 14
KDM6A WILD-TYPE 110 82 38 62

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

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0517 (Fisher's exact test), Q value = 0.41

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

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

P value = 0.222 (Fisher's exact test), Q value = 0.67

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

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

P value = 0.00446 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
KDM6A MUTATED 10 42 15 20 15
KDM6A WILD-TYPE 61 88 20 79 41

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

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.18

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

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

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

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.117 (Fisher's exact test), Q value = 0.56

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
KDM6A MUTATED 22 19 37 6 17
KDM6A WILD-TYPE 78 55 68 19 71
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
KDM6A MUTATED 72 20 9
KDM6A WILD-TYPE 182 63 46
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0373 (Fisher's exact test), Q value = 0.38

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
KDM6A MUTATED 24 17 39 17
KDM6A WILD-TYPE 99 35 81 70

Figure S24.  Get High-res Image Gene #7: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
KDM6A MUTATED 19 18 7 39 14
KDM6A WILD-TYPE 68 43 34 83 57
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
CDKN2A MUTATED 6 8 7 5 0
CDKN2A WILD-TYPE 68 134 107 55 2
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
CDKN2A MUTATED 11 7 0 8
CDKN2A WILD-TYPE 124 115 62 68

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

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.681 (Fisher's exact test), Q value = 0.92

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

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

P value = 0.0275 (Fisher's exact test), Q value = 0.34

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

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

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

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
CDKN2A MUTATED 2 7 2 11 4
CDKN2A WILD-TYPE 69 123 33 88 52
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 0.82

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

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

P value = 0.00667 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
CDKN2A MUTATED 14 3 4 3 2
CDKN2A WILD-TYPE 86 71 101 22 86

Figure S27.  Get High-res Image Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
CDKN2A MUTATED 21 4 1
CDKN2A WILD-TYPE 233 79 54
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.079 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
CDKN2A MUTATED 5 2 6 11
CDKN2A WILD-TYPE 118 50 114 76
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00077 (Fisher's exact test), Q value = 0.027

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
CDKN2A MUTATED 1 0 4 9 10
CDKN2A WILD-TYPE 86 61 37 113 61

Figure S28.  Get High-res Image Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ARID1A MUTATED 24 35 22 15 1
ARID1A WILD-TYPE 50 107 92 45 1
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ARID1A MUTATED 30 36 15 16
ARID1A WILD-TYPE 105 86 47 60
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 0.95

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

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

P value = 0.523 (Fisher's exact test), Q value = 0.85

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

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

P value = 0.148 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ARID1A MUTATED 14 39 4 24 16
ARID1A WILD-TYPE 57 91 31 75 40
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 0.96

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

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

P value = 0.0493 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ARID1A MUTATED 15 25 26 8 22
ARID1A WILD-TYPE 85 49 79 17 66

Figure S29.  Get High-res Image Gene #9: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0661 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ARID1A MUTATED 53 25 18
ARID1A WILD-TYPE 201 58 37
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ARID1A MUTATED 32 19 27 16
ARID1A WILD-TYPE 91 33 93 71
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.66 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ARID1A MUTATED 22 18 10 31 13
ARID1A WILD-TYPE 65 43 31 91 58
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.053 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
STAG2 MUTATED 14 17 22 3 0
STAG2 WILD-TYPE 60 125 92 57 2
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.03 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
STAG2 MUTATED 19 15 16 6
STAG2 WILD-TYPE 116 107 46 70

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

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.54

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

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

P value = 0.19 (Fisher's exact test), Q value = 0.66

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

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

P value = 0.508 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
STAG2 MUTATED 10 17 8 11 9
STAG2 WILD-TYPE 61 113 27 88 47
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00673 (Fisher's exact test), Q value = 0.14

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

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

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

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
STAG2 MUTATED 12 5 21 5 12
STAG2 WILD-TYPE 88 69 84 20 76
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
STAG2 MUTATED 41 7 7
STAG2 WILD-TYPE 213 76 48
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
STAG2 MUTATED 15 2 23 11
STAG2 WILD-TYPE 108 50 97 76

Figure S32.  Get High-res Image Gene #10: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0302 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
STAG2 MUTATED 10 2 5 24 10
STAG2 WILD-TYPE 77 59 36 98 61

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

'ZFP36L1 MUTATION STATUS' versus 'CN_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ZFP36L1 MUTATED 5 8 8 4 0
ZFP36L1 WILD-TYPE 69 134 106 56 2
'ZFP36L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ZFP36L1 MUTATED 5 9 4 7
ZFP36L1 WILD-TYPE 130 113 58 69
'ZFP36L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.73

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

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

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

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

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

P value = 0.509 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ZFP36L1 MUTATED 8 8 1 5 3
ZFP36L1 WILD-TYPE 63 122 34 94 53
'ZFP36L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.723 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ZFP36L1 MUTATED 6 5 5 3 6
ZFP36L1 WILD-TYPE 94 69 100 22 82
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.327 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ZFP36L1 MUTATED 15 4 6
ZFP36L1 WILD-TYPE 239 79 49
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.567 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ZFP36L1 MUTATED 9 5 6 4
ZFP36L1 WILD-TYPE 114 47 114 83
'ZFP36L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ZFP36L1 MUTATED 7 3 2 11 1
ZFP36L1 WILD-TYPE 80 58 39 111 70
'CDKN1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.95 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
CDKN1A MUTATED 6 12 12 5 0
CDKN1A WILD-TYPE 68 130 102 55 2
'CDKN1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
CDKN1A MUTATED 10 9 4 12
CDKN1A WILD-TYPE 125 113 58 64
'CDKN1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.73

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

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

P value = 0.0329 (Fisher's exact test), Q value = 0.35

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

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

Figure S34.  Get High-res Image Gene #12: 'CDKN1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
CDKN1A MUTATED 5 15 3 8 3
CDKN1A WILD-TYPE 66 115 32 91 53
'CDKN1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.78

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

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

P value = 0.172 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
CDKN1A MUTATED 7 10 10 4 4
CDKN1A WILD-TYPE 93 64 95 21 84
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0874 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
CDKN1A MUTATED 21 12 2
CDKN1A WILD-TYPE 233 71 53
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
CDKN1A MUTATED 11 7 12 4
CDKN1A WILD-TYPE 112 45 108 83
'CDKN1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.504 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
CDKN1A MUTATED 7 9 2 11 5
CDKN1A WILD-TYPE 80 52 39 111 66
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
EP300 MUTATED 9 20 16 15 1
EP300 WILD-TYPE 65 122 98 45 1
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
EP300 MUTATED 24 17 8 12
EP300 WILD-TYPE 111 105 54 64
'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.81

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

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

P value = 0.663 (Fisher's exact test), Q value = 0.91

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

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

P value = 0.273 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
EP300 MUTATED 13 15 3 20 10
EP300 WILD-TYPE 58 115 32 79 46
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.73

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

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

P value = 0.579 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
EP300 MUTATED 19 10 19 3 10
EP300 WILD-TYPE 81 64 86 22 78
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
EP300 MUTATED 41 11 9
EP300 WILD-TYPE 213 72 46
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
EP300 MUTATED 15 6 21 16
EP300 WILD-TYPE 108 46 99 71
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.866 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
EP300 MUTATED 11 8 6 20 13
EP300 WILD-TYPE 76 53 35 102 58
'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
MLL2 MUTATED 25 41 24 21 1
MLL2 WILD-TYPE 49 101 90 39 1
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
MLL2 MUTATED 43 37 15 19
MLL2 WILD-TYPE 92 85 47 57
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 0.99

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

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

P value = 0.103 (Fisher's exact test), Q value = 0.54

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

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

P value = 0.68 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
MLL2 MUTATED 19 35 8 30 20
MLL2 WILD-TYPE 52 95 27 69 36
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

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

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
MLL2 MUTATED 33 21 28 10 21
MLL2 WILD-TYPE 67 53 77 15 67
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
MLL2 MUTATED 79 22 12
MLL2 WILD-TYPE 175 61 43
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
MLL2 MUTATED 32 11 38 26
MLL2 WILD-TYPE 91 41 82 61
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.068 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
MLL2 MUTATED 17 14 17 35 24
MLL2 WILD-TYPE 70 47 24 87 47
'FGFR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
FGFR3 MUTATED 10 9 35 2 0
FGFR3 WILD-TYPE 64 133 79 58 2

Figure S35.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FGFR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
FGFR3 MUTATED 8 10 22 16
FGFR3 WILD-TYPE 127 112 40 60

Figure S36.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FGFR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

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

Figure S37.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FGFR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

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

Figure S38.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
FGFR3 MUTATED 3 25 17 4 6
FGFR3 WILD-TYPE 68 105 18 95 50

Figure S39.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FGFR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

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

Figure S40.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
FGFR3 MUTATED 9 5 36 2 4
FGFR3 WILD-TYPE 91 69 69 23 84

Figure S41.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00041 (Fisher's exact test), Q value = 0.017

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
FGFR3 MUTATED 48 7 1
FGFR3 WILD-TYPE 206 76 54

Figure S42.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
FGFR3 MUTATED 11 3 35 3
FGFR3 WILD-TYPE 112 49 85 84

Figure S43.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FGFR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00074

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
FGFR3 MUTATED 6 4 6 33 3
FGFR3 WILD-TYPE 81 57 35 89 68

Figure S44.  Get High-res Image Gene #15: 'FGFR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ERCC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ERCC2 MUTATED 8 16 7 7 0
ERCC2 WILD-TYPE 66 126 107 53 2
'ERCC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ERCC2 MUTATED 12 15 3 8
ERCC2 WILD-TYPE 123 107 59 68
'ERCC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0462 (Fisher's exact test), Q value = 0.4

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

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

Figure S45.  Get High-res Image Gene #16: 'ERCC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ERCC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 0.71

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

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

P value = 0.4 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ERCC2 MUTATED 4 14 1 12 6
ERCC2 WILD-TYPE 67 116 34 87 50
'ERCC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 0.93

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

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

P value = 0.169 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ERCC2 MUTATED 11 12 7 2 5
ERCC2 WILD-TYPE 89 62 98 23 83
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ERCC2 MUTATED 22 11 4
ERCC2 WILD-TYPE 232 72 51
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ERCC2 MUTATED 7 8 11 11
ERCC2 WILD-TYPE 116 44 109 76
'ERCC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.396 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ERCC2 MUTATED 5 8 2 14 8
ERCC2 WILD-TYPE 82 53 39 108 63
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
CREBBP MUTATED 13 13 14 7 0
CREBBP WILD-TYPE 61 129 100 53 2
'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
CREBBP MUTATED 20 16 5 7
CREBBP WILD-TYPE 115 106 57 69
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 0.91

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

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

P value = 0.819 (Fisher's exact test), Q value = 0.97

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

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

P value = 0.264 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
CREBBP MUTATED 11 13 1 15 7
CREBBP WILD-TYPE 60 117 34 84 49
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.87

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

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

P value = 0.087 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
CREBBP MUTATED 16 3 15 4 9
CREBBP WILD-TYPE 84 71 90 21 79
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00348 (Fisher's exact test), Q value = 0.085

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
CREBBP MUTATED 38 2 7
CREBBP WILD-TYPE 216 81 48

Figure S46.  Get High-res Image Gene #17: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
CREBBP MUTATED 14 2 17 14
CREBBP WILD-TYPE 109 50 103 73
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0542 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
CREBBP MUTATED 11 2 6 14 14
CREBBP WILD-TYPE 76 59 35 108 57
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.7

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
HRAS MUTATED 3 3 9 2 0
HRAS WILD-TYPE 71 139 105 58 2
'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
HRAS MUTATED 4 4 2 7
HRAS WILD-TYPE 131 118 60 69
'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.85

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

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

P value = 0.846 (Fisher's exact test), Q value = 0.97

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

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

P value = 0.843 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
HRAS MUTATED 3 6 1 6 1
HRAS WILD-TYPE 68 124 34 93 55
'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.777 (Fisher's exact test), Q value = 0.96

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

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

P value = 0.341 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
HRAS MUTATED 8 3 3 1 2
HRAS WILD-TYPE 92 71 102 24 86
'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
HRAS MUTATED 14 2 1
HRAS WILD-TYPE 240 81 54
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
HRAS MUTATED 3 3 4 6
HRAS WILD-TYPE 120 49 116 81
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.271 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
HRAS MUTATED 3 1 0 9 3
HRAS WILD-TYPE 84 60 41 113 68
'FOXA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
FOXA1 MUTATED 4 5 4 1 0
FOXA1 WILD-TYPE 70 137 110 59 2
'FOXA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
FOXA1 MUTATED 3 7 2 2
FOXA1 WILD-TYPE 132 115 60 74
'FOXA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 0.97

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

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

P value = 0.166 (Fisher's exact test), Q value = 0.64

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

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

P value = 0.366 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
FOXA1 MUTATED 3 7 1 2 0
FOXA1 WILD-TYPE 68 123 34 97 56
'FOXA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.67

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

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

P value = 0.273 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
FOXA1 MUTATED 1 5 3 1 4
FOXA1 WILD-TYPE 99 69 102 24 84
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
FOXA1 MUTATED 6 5 3
FOXA1 WILD-TYPE 248 78 52
'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.29

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
FOXA1 MUTATED 5 5 3 0
FOXA1 WILD-TYPE 118 47 117 87

Figure S47.  Get High-res Image Gene #19: 'FOXA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FOXA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.271 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
FOXA1 MUTATED 3 4 1 5 0
FOXA1 WILD-TYPE 84 57 40 117 71
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0718 (Fisher's exact test), Q value = 0.47

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
KRAS MUTATED 4 1 7 1 0
KRAS WILD-TYPE 70 141 107 59 2
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
KRAS MUTATED 4 6 2 1
KRAS WILD-TYPE 131 116 60 75
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 0.88

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

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

P value = 0.152 (Fisher's exact test), Q value = 0.64

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

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

P value = 0.108 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
KRAS MUTATED 2 5 0 1 5
KRAS WILD-TYPE 69 125 35 98 51
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.64

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

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

P value = 0.639 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
KRAS MUTATED 2 1 5 1 3
KRAS WILD-TYPE 98 73 100 24 85
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.562 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
KRAS MUTATED 10 1 1
KRAS WILD-TYPE 244 82 54
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.703 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
KRAS MUTATED 2 1 5 3
KRAS WILD-TYPE 121 51 115 84
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
KRAS MUTATED 2 1 0 4 4
KRAS WILD-TYPE 85 60 41 118 67
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RHOA MUTATED 5 6 3 4 0
RHOA WILD-TYPE 69 136 111 56 2
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RHOA MUTATED 3 8 3 4
RHOA WILD-TYPE 132 114 59 72
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.8

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

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

P value = 0.178 (Fisher's exact test), Q value = 0.65

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

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

P value = 0.886 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RHOA MUTATED 2 8 1 5 2
RHOA WILD-TYPE 69 122 34 94 54
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.85

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

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

P value = 0.181 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RHOA MUTATED 1 6 5 1 5
RHOA WILD-TYPE 99 68 100 24 83
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RHOA MUTATED 8 7 3
RHOA WILD-TYPE 246 76 52
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RHOA MUTATED 5 4 6 3
RHOA WILD-TYPE 118 48 114 84
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.816 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
RHOA MUTATED 4 4 1 7 2
RHOA WILD-TYPE 83 57 40 115 69
'KIAA1267 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
KIAA1267 MUTATED 2 12 8 2 0
KIAA1267 WILD-TYPE 72 130 106 58 2
'KIAA1267 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
KIAA1267 MUTATED 5 9 8 2
KIAA1267 WILD-TYPE 130 113 54 74

Figure S48.  Get High-res Image Gene #22: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KIAA1267 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.955 (Fisher's exact test), Q value = 0.99

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

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

P value = 0.647 (Fisher's exact test), Q value = 0.91

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

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

P value = 0.339 (Fisher's exact test), Q value = 0.77

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
KIAA1267 MUTATED 5 9 1 3 6
KIAA1267 WILD-TYPE 66 121 34 96 50
'KIAA1267 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.67

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

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

P value = 0.251 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
KIAA1267 MUTATED 4 3 10 3 4
KIAA1267 WILD-TYPE 96 71 95 22 84
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
KIAA1267 MUTATED 17 5 2
KIAA1267 WILD-TYPE 237 78 53
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0563 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
KIAA1267 MUTATED 5 2 14 3
KIAA1267 WILD-TYPE 118 50 106 84
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.527 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
KIAA1267 MUTATED 4 3 2 12 3
KIAA1267 WILD-TYPE 83 58 39 110 68
'MLL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.4

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
MLL MUTATED 5 19 7 12 0
MLL WILD-TYPE 69 123 107 48 2

Figure S49.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.708 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
MLL MUTATED 18 14 5 7
MLL WILD-TYPE 117 108 57 69
'MLL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0644 (Fisher's exact test), Q value = 0.46

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

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

P value = 0.171 (Fisher's exact test), Q value = 0.64

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

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

P value = 0.401 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
MLL MUTATED 8 10 3 15 8
MLL WILD-TYPE 63 120 32 84 48
'MLL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0731 (Fisher's exact test), Q value = 0.47

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

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

P value = 0.00646 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
MLL MUTATED 14 13 3 2 12
MLL WILD-TYPE 86 61 102 23 76

Figure S50.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MLL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0109 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
MLL MUTATED 20 16 8
MLL WILD-TYPE 234 67 47

Figure S51.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0322 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
MLL MUTATED 14 9 6 13
MLL WILD-TYPE 109 43 114 74

Figure S52.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MLL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00471 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
MLL MUTATED 8 13 6 5 10
MLL WILD-TYPE 79 48 35 117 61

Figure S53.  Get High-res Image Gene #23: 'MLL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
FAT1 MUTATED 8 17 18 7 0
FAT1 WILD-TYPE 66 125 96 53 2
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0674 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
FAT1 MUTATED 24 13 3 10
FAT1 WILD-TYPE 111 109 59 66
'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.68

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

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

P value = 0.124 (Fisher's exact test), Q value = 0.58

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

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

P value = 0.392 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
FAT1 MUTATED 10 11 3 16 8
FAT1 WILD-TYPE 61 119 32 83 48
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.66

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

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

P value = 0.113 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
FAT1 MUTATED 19 4 14 3 10
FAT1 WILD-TYPE 81 70 91 22 78
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.35

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
FAT1 MUTATED 39 4 7
FAT1 WILD-TYPE 215 79 48

Figure S54.  Get High-res Image Gene #24: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.349 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
FAT1 MUTATED 15 3 18 13
FAT1 WILD-TYPE 108 49 102 74
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0815 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
FAT1 MUTATED 12 2 4 19 12
FAT1 WILD-TYPE 75 59 37 103 59
'KLF5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
KLF5 MUTATED 6 7 8 2 0
KLF5 WILD-TYPE 68 135 106 58 2
'KLF5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.952 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
KLF5 MUTATED 7 8 4 4
KLF5 WILD-TYPE 128 114 58 72
'KLF5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.4

Table S243.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
KLF5 MUTATED 3 11 7
KLF5 WILD-TYPE 117 95 96

Figure S55.  Get High-res Image Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KLF5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.657 (Fisher's exact test), Q value = 0.91

Table S244.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
KLF5 MUTATED 4 10 6 1
KLF5 WILD-TYPE 83 104 92 29
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 0.88

Table S245.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
KLF5 MUTATED 5 11 1 4 2
KLF5 WILD-TYPE 66 119 34 95 54
'KLF5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 0.93

Table S246.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
KLF5 MUTATED 6 8 9
KLF5 WILD-TYPE 110 98 160
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.7

Table S247.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
KLF5 MUTATED 2 7 7 1 6
KLF5 WILD-TYPE 98 67 98 24 82
'KLF5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0624 (Fisher's exact test), Q value = 0.46

Table S248.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
KLF5 MUTATED 10 8 5
KLF5 WILD-TYPE 244 75 50
'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.64

Table S249.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
KLF5 MUTATED 8 6 6 2
KLF5 WILD-TYPE 115 46 114 85
'KLF5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0845 (Fisher's exact test), Q value = 0.5

Table S250.  Gene #25: 'KLF5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
KLF5 MUTATED 5 8 2 6 1
KLF5 WILD-TYPE 82 53 39 116 70
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 0.97

Table S251.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
PTEN MUTATED 2 7 3 2 0
PTEN WILD-TYPE 72 135 111 58 2
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.6

Table S252.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
PTEN MUTATED 7 6 1 0
PTEN WILD-TYPE 128 116 61 76
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.478 (Fisher's exact test), Q value = 0.85

Table S253.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
PTEN MUTATED 4 4 1
PTEN WILD-TYPE 116 102 102
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 0.78

Table S254.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
PTEN MUTATED 1 3 3 2
PTEN WILD-TYPE 86 111 95 28
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.6

Table S255.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
PTEN MUTATED 0 4 0 6 3
PTEN WILD-TYPE 71 126 35 93 53
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.64

Table S256.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PTEN MUTATED 1 4 8
PTEN WILD-TYPE 115 102 161
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.81

Table S257.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
PTEN MUTATED 4 2 4 2 1
PTEN WILD-TYPE 96 72 101 23 87
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S258.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
PTEN MUTATED 9 3 1
PTEN WILD-TYPE 245 80 54
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 0.99

Table S259.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
PTEN MUTATED 5 2 4 2
PTEN WILD-TYPE 118 50 116 85
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 0.91

Table S260.  Gene #26: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
PTEN MUTATED 3 1 2 3 4
PTEN WILD-TYPE 84 60 39 119 67
'C3ORF70 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.88

Table S261.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
C3ORF70 MUTATED 5 4 5 3 0
C3ORF70 WILD-TYPE 69 138 109 57 2
'C3ORF70 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.7

Table S262.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
C3ORF70 MUTATED 8 6 0 3
C3ORF70 WILD-TYPE 127 116 62 73
'C3ORF70 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S263.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
C3ORF70 MUTATED 4 4 4
C3ORF70 WILD-TYPE 116 102 99
'C3ORF70 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.91

Table S264.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
C3ORF70 MUTATED 3 3 4 2
C3ORF70 WILD-TYPE 84 111 94 28
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 0.98

Table S265.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
C3ORF70 MUTATED 3 5 1 4 4
C3ORF70 WILD-TYPE 68 125 34 95 52
'C3ORF70 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 0.88

Table S266.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
C3ORF70 MUTATED 3 5 9
C3ORF70 WILD-TYPE 113 101 160
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.875 (Fisher's exact test), Q value = 0.98

Table S267.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
C3ORF70 MUTATED 6 3 4 0 4
C3ORF70 WILD-TYPE 94 71 101 25 84
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.85

Table S268.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
C3ORF70 MUTATED 10 3 4
C3ORF70 WILD-TYPE 244 80 51
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.951 (Fisher's exact test), Q value = 0.99

Table S269.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
C3ORF70 MUTATED 6 2 4 4
C3ORF70 WILD-TYPE 117 50 116 83
'C3ORF70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.914 (Fisher's exact test), Q value = 0.99

Table S270.  Gene #27: 'C3ORF70 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
C3ORF70 MUTATED 4 2 2 4 4
C3ORF70 WILD-TYPE 83 59 39 118 67
'PSIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.75 (Fisher's exact test), Q value = 0.94

Table S271.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
PSIP1 MUTATED 3 10 5 2 0
PSIP1 WILD-TYPE 71 132 109 58 2
'PSIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.4

Table S272.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
PSIP1 MUTATED 3 12 2 3
PSIP1 WILD-TYPE 132 110 60 73

Figure S56.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PSIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0178 (Fisher's exact test), Q value = 0.26

Table S273.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
PSIP1 MUTATED 4 11 2
PSIP1 WILD-TYPE 116 95 101

Figure S57.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'PSIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.64

Table S274.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
PSIP1 MUTATED 4 10 2 1
PSIP1 WILD-TYPE 83 104 96 29
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 0.94

Table S275.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
PSIP1 MUTATED 3 8 2 3 4
PSIP1 WILD-TYPE 68 122 33 96 52
'PSIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0163 (Fisher's exact test), Q value = 0.25

Table S276.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PSIP1 MUTATED 5 11 4
PSIP1 WILD-TYPE 111 95 165

Figure S58.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.54

Table S277.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
PSIP1 MUTATED 3 3 9 3 2
PSIP1 WILD-TYPE 97 71 96 22 86
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.942 (Fisher's exact test), Q value = 0.99

Table S278.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
PSIP1 MUTATED 14 4 2
PSIP1 WILD-TYPE 240 79 53
'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.028 (Fisher's exact test), Q value = 0.34

Table S279.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
PSIP1 MUTATED 6 1 12 1
PSIP1 WILD-TYPE 117 51 108 86

Figure S59.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PSIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0257 (Fisher's exact test), Q value = 0.33

Table S280.  Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
PSIP1 MUTATED 1 3 4 11 1
PSIP1 WILD-TYPE 86 58 37 111 70

Figure S60.  Get High-res Image Gene #28: 'PSIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00949 (Fisher's exact test), Q value = 0.17

Table S281.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
MLL3 MUTATED 13 29 27 3 1
MLL3 WILD-TYPE 61 113 87 57 1

Figure S61.  Get High-res Image Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 0.91

Table S282.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
MLL3 MUTATED 22 27 10 15
MLL3 WILD-TYPE 113 95 52 61
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.56

Table S283.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MLL3 MUTATED 19 28 18
MLL3 WILD-TYPE 101 78 85
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 0.67

Table S284.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MLL3 MUTATED 12 29 18 6
MLL3 WILD-TYPE 75 85 80 24
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 0.8

Table S285.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
MLL3 MUTATED 8 25 7 21 13
MLL3 WILD-TYPE 63 105 28 78 43
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.479 (Fisher's exact test), Q value = 0.85

Table S286.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MLL3 MUTATED 19 24 31
MLL3 WILD-TYPE 97 82 138
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.78

Table S287.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
MLL3 MUTATED 23 13 19 7 12
MLL3 WILD-TYPE 77 61 86 18 76
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0288 (Fisher's exact test), Q value = 0.35

Table S288.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
MLL3 MUTATED 56 14 4
MLL3 WILD-TYPE 198 69 51

Figure S62.  Get High-res Image Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.58

Table S289.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
MLL3 MUTATED 16 8 28 20
MLL3 WILD-TYPE 107 44 92 67
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.73

Table S290.  Gene #29: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
MLL3 MUTATED 12 8 8 29 15
MLL3 WILD-TYPE 75 53 33 93 56
'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 0.97

Table S291.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ASXL2 MUTATED 6 16 10 4 0
ASXL2 WILD-TYPE 68 126 104 56 2
'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 0.96

Table S292.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ASXL2 MUTATED 11 14 5 6
ASXL2 WILD-TYPE 124 108 57 70
'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0925 (Fisher's exact test), Q value = 0.51

Table S293.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ASXL2 MUTATED 5 10 12
ASXL2 WILD-TYPE 115 96 91
'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.67

Table S294.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ASXL2 MUTATED 6 13 8 0
ASXL2 WILD-TYPE 81 101 90 30
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.85

Table S295.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ASXL2 MUTATED 3 12 3 12 5
ASXL2 WILD-TYPE 68 118 32 87 51
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 0.88

Table S296.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ASXL2 MUTATED 13 8 14
ASXL2 WILD-TYPE 103 98 155
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.76

Table S297.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ASXL2 MUTATED 5 10 9 3 9
ASXL2 WILD-TYPE 95 64 96 22 79
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.67

Table S298.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ASXL2 MUTATED 19 11 6
ASXL2 WILD-TYPE 235 72 49
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.81

Table S299.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ASXL2 MUTATED 11 8 9 7
ASXL2 WILD-TYPE 112 44 111 80
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 0.85

Table S300.  Gene #30: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ASXL2 MUTATED 7 9 3 12 4
ASXL2 WILD-TYPE 80 52 38 110 67
'ZBTB7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 0.99

Table S301.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ZBTB7B MUTATED 2 3 4 2 0
ZBTB7B WILD-TYPE 72 139 110 58 2
'ZBTB7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.88 (Fisher's exact test), Q value = 0.98

Table S302.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ZBTB7B MUTATED 4 4 2 1
ZBTB7B WILD-TYPE 131 118 60 75
'ZBTB7B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.787 (Fisher's exact test), Q value = 0.96

Table S303.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ZBTB7B MUTATED 4 4 2
ZBTB7B WILD-TYPE 116 102 101
'ZBTB7B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 0.86

Table S304.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ZBTB7B MUTATED 2 4 2 2
ZBTB7B WILD-TYPE 85 110 96 28
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.81

Table S305.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ZBTB7B MUTATED 1 5 2 3 0
ZBTB7B WILD-TYPE 70 125 33 96 56
'ZBTB7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.8

Table S306.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZBTB7B MUTATED 2 5 4
ZBTB7B WILD-TYPE 114 101 165
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.85

Table S307.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ZBTB7B MUTATED 4 2 1 0 4
ZBTB7B WILD-TYPE 96 72 104 25 84
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.214 (Fisher's exact test), Q value = 0.67

Table S308.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ZBTB7B MUTATED 5 3 3
ZBTB7B WILD-TYPE 249 80 52
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 0.92

Table S309.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ZBTB7B MUTATED 5 2 2 2
ZBTB7B WILD-TYPE 118 50 118 85
'ZBTB7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.407 (Fisher's exact test), Q value = 0.8

Table S310.  Gene #31: 'ZBTB7B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ZBTB7B MUTATED 5 2 0 2 2
ZBTB7B WILD-TYPE 82 59 41 120 69
'RXRA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.6

Table S311.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RXRA MUTATED 3 15 4 2 0
RXRA WILD-TYPE 71 127 110 58 2
'RXRA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0104 (Fisher's exact test), Q value = 0.18

Table S312.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RXRA MUTATED 7 14 0 3
RXRA WILD-TYPE 128 108 62 73

Figure S63.  Get High-res Image Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RXRA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S313.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RXRA MUTATED 6 9 6
RXRA WILD-TYPE 114 97 97
'RXRA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.72

Table S314.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RXRA MUTATED 3 8 6 4
RXRA WILD-TYPE 84 106 92 26
'RXRA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.73

Table S315.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RXRA MUTATED 3 9 0 6 6
RXRA WILD-TYPE 68 121 35 93 50
'RXRA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 0.71

Table S316.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RXRA MUTATED 5 10 9
RXRA WILD-TYPE 111 96 160
'RXRA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.73

Table S317.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RXRA MUTATED 3 8 6 2 5
RXRA WILD-TYPE 97 66 99 23 83
'RXRA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.345 (Fisher's exact test), Q value = 0.78

Table S318.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RXRA MUTATED 13 8 3
RXRA WILD-TYPE 241 75 52
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.87

Table S319.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RXRA MUTATED 6 5 9 4
RXRA WILD-TYPE 117 47 111 83
'RXRA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 0.78

Table S320.  Gene #32: 'RXRA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
RXRA MUTATED 5 5 0 10 4
RXRA WILD-TYPE 82 56 41 112 67
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0219 (Fisher's exact test), Q value = 0.3

Table S321.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
FBXW7 MUTATED 1 10 13 4 1
FBXW7 WILD-TYPE 73 132 101 56 1

Figure S64.  Get High-res Image Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.067 (Fisher's exact test), Q value = 0.46

Table S322.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
FBXW7 MUTATED 16 9 1 4
FBXW7 WILD-TYPE 119 113 61 72
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.711 (Fisher's exact test), Q value = 0.93

Table S323.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FBXW7 MUTATED 7 9 7
FBXW7 WILD-TYPE 113 97 96
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.441 (Fisher's exact test), Q value = 0.82

Table S324.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FBXW7 MUTATED 6 5 10 2
FBXW7 WILD-TYPE 81 109 88 28
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.85

Table S325.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
FBXW7 MUTATED 4 9 1 9 7
FBXW7 WILD-TYPE 67 121 34 90 49
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.64

Table S326.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FBXW7 MUTATED 6 6 18
FBXW7 WILD-TYPE 110 100 151
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.78

Table S327.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
FBXW7 MUTATED 10 6 8 3 3
FBXW7 WILD-TYPE 90 68 97 22 85
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 0.67

Table S328.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
FBXW7 MUTATED 22 7 1
FBXW7 WILD-TYPE 232 76 54
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.67

Table S329.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
FBXW7 MUTATED 6 6 8 10
FBXW7 WILD-TYPE 117 46 112 77
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0469 (Fisher's exact test), Q value = 0.4

Table S330.  Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
FBXW7 MUTATED 2 7 2 9 10
FBXW7 WILD-TYPE 85 54 39 113 61

Figure S65.  Get High-res Image Gene #33: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.73

Table S331.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RBM10 MUTATED 4 12 4 1 0
RBM10 WILD-TYPE 70 130 110 59 2
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.83

Table S332.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RBM10 MUTATED 8 9 1 4
RBM10 WILD-TYPE 127 113 61 72
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.85

Table S333.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RBM10 MUTATED 5 6 8
RBM10 WILD-TYPE 115 100 95
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.905 (Fisher's exact test), Q value = 0.99

Table S334.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RBM10 MUTATED 5 6 7 1
RBM10 WILD-TYPE 82 108 91 29
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.73

Table S335.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RBM10 MUTATED 1 7 2 9 3
RBM10 WILD-TYPE 70 123 33 90 53
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.886 (Fisher's exact test), Q value = 0.98

Table S336.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RBM10 MUTATED 6 7 9
RBM10 WILD-TYPE 110 99 160
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.67

Table S337.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RBM10 MUTATED 3 7 5 3 4
RBM10 WILD-TYPE 97 67 100 22 84
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.67

Table S338.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RBM10 MUTATED 12 8 2
RBM10 WILD-TYPE 242 75 53
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.73

Table S339.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RBM10 MUTATED 9 5 4 4
RBM10 WILD-TYPE 114 47 116 83
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.72

Table S340.  Gene #34: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
RBM10 MUTATED 4 7 3 6 2
RBM10 WILD-TYPE 83 54 38 116 69
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0594 (Fisher's exact test), Q value = 0.44

Table S341.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
NFE2L2 MUTATED 5 4 13 2 0
NFE2L2 WILD-TYPE 69 138 101 58 2
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.23

Table S342.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
NFE2L2 MUTATED 11 3 1 9
NFE2L2 WILD-TYPE 124 119 61 67

Figure S66.  Get High-res Image Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.56

Table S343.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
NFE2L2 MUTATED 11 3 7
NFE2L2 WILD-TYPE 109 103 96
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0687 (Fisher's exact test), Q value = 0.46

Table S344.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
NFE2L2 MUTATED 5 3 9 4
NFE2L2 WILD-TYPE 82 111 89 26
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00844 (Fisher's exact test), Q value = 0.16

Table S345.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
NFE2L2 MUTATED 4 2 6 8 3
NFE2L2 WILD-TYPE 67 128 29 91 53

Figure S67.  Get High-res Image Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0083 (Fisher's exact test), Q value = 0.16

Table S346.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NFE2L2 MUTATED 6 1 16
NFE2L2 WILD-TYPE 110 105 153

Figure S68.  Get High-res Image Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.089 (Fisher's exact test), Q value = 0.5

Table S347.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
NFE2L2 MUTATED 10 2 3 3 5
NFE2L2 WILD-TYPE 90 72 102 22 83
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 0.91

Table S348.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
NFE2L2 MUTATED 17 3 3
NFE2L2 WILD-TYPE 237 80 52
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 0.87

Table S349.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
NFE2L2 MUTATED 9 1 6 6
NFE2L2 WILD-TYPE 114 51 114 81
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0446 (Fisher's exact test), Q value = 0.4

Table S350.  Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
NFE2L2 MUTATED 5 1 6 4 6
NFE2L2 WILD-TYPE 82 60 35 118 65

Figure S69.  Get High-res Image Gene #35: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CUL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 0.97

Table S351.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
CUL1 MUTATED 3 5 5 4 0
CUL1 WILD-TYPE 71 137 109 56 2
'CUL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 0.89

Table S352.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
CUL1 MUTATED 6 5 2 6
CUL1 WILD-TYPE 129 117 60 70
'CUL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.54

Table S353.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CUL1 MUTATED 9 2 3
CUL1 WILD-TYPE 111 104 100
'CUL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.73

Table S354.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CUL1 MUTATED 5 2 5 2
CUL1 WILD-TYPE 82 112 93 28
'CUL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 0.96

Table S355.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
CUL1 MUTATED 3 5 3 5 3
CUL1 WILD-TYPE 68 125 32 94 53
'CUL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.83

Table S356.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CUL1 MUTATED 4 4 11
CUL1 WILD-TYPE 112 102 158
'CUL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 0.98

Table S357.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
CUL1 MUTATED 5 3 4 2 5
CUL1 WILD-TYPE 95 71 101 23 83
'CUL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.831 (Fisher's exact test), Q value = 0.97

Table S358.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
CUL1 MUTATED 14 3 2
CUL1 WILD-TYPE 240 80 53
'CUL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.806 (Fisher's exact test), Q value = 0.97

Table S359.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
CUL1 MUTATED 7 2 4 5
CUL1 WILD-TYPE 116 50 116 82
'CUL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.73

Table S360.  Gene #36: 'CUL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
CUL1 MUTATED 7 2 1 3 5
CUL1 WILD-TYPE 80 59 40 119 66
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.85

Table S361.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
HLA-A MUTATED 0 2 3 0 0
HLA-A WILD-TYPE 74 140 111 60 2
'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S362.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
HLA-A MUTATED 2 1 1 1
HLA-A WILD-TYPE 133 121 61 75
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.73

Table S363.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
HLA-A MUTATED 0 1 1 3 0
HLA-A WILD-TYPE 71 129 34 96 56
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S364.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
HLA-A MUTATED 2 1 2
HLA-A WILD-TYPE 114 105 167
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 0.99

Table S365.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
HLA-A MUTATED 1 1 1 0 2
HLA-A WILD-TYPE 99 73 104 25 86
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 0.73

Table S366.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
HLA-A MUTATED 2 2 1
HLA-A WILD-TYPE 252 81 54
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 0.99

Table S367.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
HLA-A MUTATED 2 1 1 1
HLA-A WILD-TYPE 121 51 119 86
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.693 (Fisher's exact test), Q value = 0.93

Table S368.  Gene #37: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
HLA-A MUTATED 1 2 0 1 1
HLA-A WILD-TYPE 86 59 41 121 70
'GNA13 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 0.96

Table S369.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
GNA13 MUTATED 3 5 2 2 0
GNA13 WILD-TYPE 71 137 112 58 2
'GNA13 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.67

Table S370.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
GNA13 MUTATED 2 3 2 5
GNA13 WILD-TYPE 133 119 60 71
'GNA13 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.78

Table S371.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
GNA13 MUTATED 6 2 2
GNA13 WILD-TYPE 114 104 101
'GNA13 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 0.96

Table S372.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
GNA13 MUTATED 4 3 3 0
GNA13 WILD-TYPE 83 111 95 30
'GNA13 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 0.93

Table S373.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
GNA13 MUTATED 4 4 0 3 1
GNA13 WILD-TYPE 67 126 35 96 55
'GNA13 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.78

Table S374.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
GNA13 MUTATED 6 2 4
GNA13 WILD-TYPE 110 104 165
'GNA13 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.542 (Fisher's exact test), Q value = 0.87

Table S375.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
GNA13 MUTATED 1 3 3 0 4
GNA13 WILD-TYPE 99 71 102 25 84
'GNA13 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.67

Table S376.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
GNA13 MUTATED 5 3 3
GNA13 WILD-TYPE 249 80 52
'GNA13 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0674 (Fisher's exact test), Q value = 0.46

Table S377.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
GNA13 MUTATED 7 2 2 0
GNA13 WILD-TYPE 116 50 118 87
'GNA13 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 0.86

Table S378.  Gene #38: 'GNA13 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
GNA13 MUTATED 4 2 2 2 1
GNA13 WILD-TYPE 83 59 39 120 70
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 0.97

Table S379.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
NUDT11 MUTATED 1 3 3 0 0
NUDT11 WILD-TYPE 73 139 111 60 2
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.8

Table S380.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
NUDT11 MUTATED 2 1 1 3
NUDT11 WILD-TYPE 133 121 61 73
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.084

Table S381.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
NUDT11 MUTATED 0 1 6
NUDT11 WILD-TYPE 120 105 97

Figure S70.  Get High-res Image Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 0.97

Table S382.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
NUDT11 MUTATED 1 3 3 0
NUDT11 WILD-TYPE 86 111 95 30
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.7

Table S383.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
NUDT11 MUTATED 0 2 1 4 0
NUDT11 WILD-TYPE 71 128 34 95 56
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 0.93

Table S384.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NUDT11 MUTATED 1 2 4
NUDT11 WILD-TYPE 115 104 165
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 0.95

Table S385.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
NUDT11 MUTATED 3 2 1 0 1
NUDT11 WILD-TYPE 97 72 104 25 87
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.78

Table S386.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
NUDT11 MUTATED 4 3 0
NUDT11 WILD-TYPE 250 80 55
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.78

Table S387.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
NUDT11 MUTATED 1 2 1 2
NUDT11 WILD-TYPE 122 50 119 85
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 0.88

Table S388.  Gene #39: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
NUDT11 MUTATED 1 2 0 1 2
NUDT11 WILD-TYPE 86 59 41 121 69
'MBD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.66

Table S389.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
MBD1 MUTATED 0 5 3 4 0
MBD1 WILD-TYPE 74 137 111 56 2
'MBD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.875 (Fisher's exact test), Q value = 0.98

Table S390.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
MBD1 MUTATED 3 4 2 3
MBD1 WILD-TYPE 132 118 60 73
'MBD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.85

Table S391.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MBD1 MUTATED 4 2 5
MBD1 WILD-TYPE 116 104 98
'MBD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 0.73

Table S392.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MBD1 MUTATED 2 2 5 2
MBD1 WILD-TYPE 85 112 93 28
'MBD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.67

Table S393.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
MBD1 MUTATED 2 1 1 5 3
MBD1 WILD-TYPE 69 129 34 94 53
'MBD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 0.91

Table S394.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MBD1 MUTATED 2 4 6
MBD1 WILD-TYPE 114 102 163
'MBD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 0.96

Table S395.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
MBD1 MUTATED 4 1 4 0 2
MBD1 WILD-TYPE 96 73 101 25 86
'MBD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 0.89

Table S396.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
MBD1 MUTATED 8 1 2
MBD1 WILD-TYPE 246 82 53
'MBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.88

Table S397.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
MBD1 MUTATED 2 1 3 4
MBD1 WILD-TYPE 121 51 117 83
'MBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 0.95

Table S398.  Gene #40: 'MBD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
MBD1 MUTATED 1 1 1 4 3
MBD1 WILD-TYPE 86 60 40 118 68
'SCARF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.8

Table S399.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
SCARF2 MUTATED 2 5 1 0 0
SCARF2 WILD-TYPE 72 137 113 60 2
'SCARF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0534 (Fisher's exact test), Q value = 0.41

Table S400.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
SCARF2 MUTATED 0 3 3 2
SCARF2 WILD-TYPE 135 119 59 74
'SCARF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.75

Table S401.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SCARF2 MUTATED 1 4 1
SCARF2 WILD-TYPE 119 102 102
'SCARF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 0.67

Table S402.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SCARF2 MUTATED 0 4 1 1
SCARF2 WILD-TYPE 87 110 97 29
'SCARF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0702 (Fisher's exact test), Q value = 0.46

Table S403.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
SCARF2 MUTATED 0 6 1 0 1
SCARF2 WILD-TYPE 71 124 34 99 55
'SCARF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.64

Table S404.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SCARF2 MUTATED 3 4 1
SCARF2 WILD-TYPE 113 102 168
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 0.98

Table S405.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
SCARF2 MUTATED 1 2 3 0 2
SCARF2 WILD-TYPE 99 72 102 25 86
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 0.85

Table S406.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
SCARF2 MUTATED 4 2 2
SCARF2 WILD-TYPE 250 81 53
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.72

Table S407.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
SCARF2 MUTATED 3 0 4 0
SCARF2 WILD-TYPE 120 52 116 87
'SCARF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.555 (Fisher's exact test), Q value = 0.87

Table S408.  Gene #41: 'SCARF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
SCARF2 MUTATED 1 1 1 4 0
SCARF2 WILD-TYPE 86 60 40 118 71
'FOXQ1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.94

Table S409.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
FOXQ1 MUTATED 1 6 5 2 0
FOXQ1 WILD-TYPE 73 136 109 58 2
'FOXQ1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 0.95

Table S410.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
FOXQ1 MUTATED 5 6 1 2
FOXQ1 WILD-TYPE 130 116 61 74
'FOXQ1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 0.91

Table S411.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FOXQ1 MUTATED 3 4 5
FOXQ1 WILD-TYPE 117 102 98
'FOXQ1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.72

Table S412.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FOXQ1 MUTATED 1 6 3 2
FOXQ1 WILD-TYPE 86 108 95 28
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 0.94

Table S413.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
FOXQ1 MUTATED 1 7 1 3 2
FOXQ1 WILD-TYPE 70 123 34 96 54
'FOXQ1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 0.98

Table S414.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FOXQ1 MUTATED 5 3 6
FOXQ1 WILD-TYPE 111 103 163
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.831 (Fisher's exact test), Q value = 0.97

Table S415.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
FOXQ1 MUTATED 5 2 3 1 2
FOXQ1 WILD-TYPE 95 72 102 24 86
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.841 (Fisher's exact test), Q value = 0.97

Table S416.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
FOXQ1 MUTATED 8 3 2
FOXQ1 WILD-TYPE 246 80 53
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S417.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
FOXQ1 MUTATED 4 2 4 3
FOXQ1 WILD-TYPE 119 50 116 84
'FOXQ1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.968 (Fisher's exact test), Q value = 1

Table S418.  Gene #42: 'FOXQ1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
FOXQ1 MUTATED 3 3 1 4 2
FOXQ1 WILD-TYPE 84 58 40 118 69
'FAM47C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.8

Table S419.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
FAM47C MUTATED 6 6 4 5 0
FAM47C WILD-TYPE 68 136 110 55 2
'FAM47C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 0.97

Table S420.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
FAM47C MUTATED 8 6 2 5
FAM47C WILD-TYPE 127 116 60 71
'FAM47C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00698 (Fisher's exact test), Q value = 0.14

Table S421.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
FAM47C MUTATED 3 3 12
FAM47C WILD-TYPE 117 103 91

Figure S71.  Get High-res Image Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'FAM47C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 0.94

Table S422.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
FAM47C MUTATED 3 7 7 1
FAM47C WILD-TYPE 84 107 91 29
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.8

Table S423.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
FAM47C MUTATED 3 6 2 9 1
FAM47C WILD-TYPE 68 124 33 90 55
'FAM47C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 0.93

Table S424.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
FAM47C MUTATED 7 4 10
FAM47C WILD-TYPE 109 102 159
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.73

Table S425.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
FAM47C MUTATED 8 1 5 2 5
FAM47C WILD-TYPE 92 73 100 23 83
'FAM47C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.155 (Fisher's exact test), Q value = 0.64

Table S426.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
FAM47C MUTATED 17 1 3
FAM47C WILD-TYPE 237 82 52
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.92

Table S427.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
FAM47C MUTATED 7 1 6 6
FAM47C WILD-TYPE 116 51 114 81
'FAM47C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.408 (Fisher's exact test), Q value = 0.8

Table S428.  Gene #43: 'FAM47C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
FAM47C MUTATED 4 1 4 6 5
FAM47C WILD-TYPE 83 60 37 116 66
'METTL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 0.95

Table S429.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
METTL3 MUTATED 5 6 4 2 0
METTL3 WILD-TYPE 69 136 110 58 2
'METTL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.93

Table S430.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
METTL3 MUTATED 4 7 3 3
METTL3 WILD-TYPE 131 115 59 73
'METTL3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S431.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
METTL3 MUTATED 6 6 5
METTL3 WILD-TYPE 114 100 98
'METTL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 0.93

Table S432.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
METTL3 MUTATED 5 7 3 2
METTL3 WILD-TYPE 82 107 95 28
'METTL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.88

Table S433.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
METTL3 MUTATED 5 6 1 2 3
METTL3 WILD-TYPE 66 124 34 97 53
'METTL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.67

Table S434.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
METTL3 MUTATED 7 6 4
METTL3 WILD-TYPE 109 100 165
'METTL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.8

Table S435.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
METTL3 MUTATED 3 1 7 1 5
METTL3 WILD-TYPE 97 73 98 24 83
'METTL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.73

Table S436.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
METTL3 MUTATED 13 1 3
METTL3 WILD-TYPE 241 82 52
'METTL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 0.88

Table S437.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
METTL3 MUTATED 6 1 7 2
METTL3 WILD-TYPE 117 51 113 85
'METTL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.54

Table S438.  Gene #44: 'METTL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
METTL3 MUTATED 5 1 3 7 0
METTL3 WILD-TYPE 82 60 38 115 71
'ZNF185 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 0.98

Table S439.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ZNF185 MUTATED 1 1 2 1 0
ZNF185 WILD-TYPE 73 141 112 59 2
'ZNF185 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.708 (Fisher's exact test), Q value = 0.93

Table S440.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ZNF185 MUTATED 2 1 0 2
ZNF185 WILD-TYPE 133 121 62 74
'ZNF185 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0763 (Fisher's exact test), Q value = 0.47

Table S441.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ZNF185 MUTATED 0 1 3
ZNF185 WILD-TYPE 120 105 100
'ZNF185 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.78

Table S442.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ZNF185 MUTATED 0 1 3 0
ZNF185 WILD-TYPE 87 113 95 30
'ZNF185 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.79

Table S443.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ZNF185 MUTATED 0 1 0 2 2
ZNF185 WILD-TYPE 71 129 35 97 54
'ZNF185 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.864 (Fisher's exact test), Q value = 0.98

Table S444.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ZNF185 MUTATED 1 1 3
ZNF185 WILD-TYPE 115 105 166
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 0.91

Table S445.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ZNF185 MUTATED 3 0 1 0 1
ZNF185 WILD-TYPE 97 74 104 25 87
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 0.91

Table S446.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ZNF185 MUTATED 4 0 1
ZNF185 WILD-TYPE 250 83 54
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 0.94

Table S447.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ZNF185 MUTATED 1 0 1 2
ZNF185 WILD-TYPE 122 52 119 85
'ZNF185 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 0.71

Table S448.  Gene #45: 'ZNF185 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ZNF185 MUTATED 0 0 1 1 2
ZNF185 WILD-TYPE 87 61 40 121 69
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 0.95

Table S449.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ERBB2 MUTATED 9 17 12 10 0
ERBB2 WILD-TYPE 65 125 102 50 2
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.67

Table S450.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ERBB2 MUTATED 19 9 8 12
ERBB2 WILD-TYPE 116 113 54 64
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.53 (Fisher's exact test), Q value = 0.85

Table S451.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ERBB2 MUTATED 16 9 11
ERBB2 WILD-TYPE 104 97 92
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.92

Table S452.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ERBB2 MUTATED 8 11 14 3
ERBB2 WILD-TYPE 79 103 84 27
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S453.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ERBB2 MUTATED 8 14 2 17 6
ERBB2 WILD-TYPE 63 116 33 82 50
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.67

Table S454.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ERBB2 MUTATED 10 11 26
ERBB2 WILD-TYPE 106 95 143
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0701 (Fisher's exact test), Q value = 0.46

Table S455.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ERBB2 MUTATED 12 11 8 0 15
ERBB2 WILD-TYPE 88 63 97 25 73
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.68

Table S456.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ERBB2 MUTATED 26 10 10
ERBB2 WILD-TYPE 228 73 45
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 0.78

Table S457.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ERBB2 MUTATED 17 6 9 12
ERBB2 WILD-TYPE 106 46 111 75
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 0.8

Table S458.  Gene #46: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ERBB2 MUTATED 11 8 7 9 9
ERBB2 WILD-TYPE 76 53 34 113 62
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.85

Table S459.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ATM MUTATED 9 17 18 8 1
ATM WILD-TYPE 65 125 96 52 1
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.65

Table S460.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ATM MUTATED 22 19 7 5
ATM WILD-TYPE 113 103 55 71
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.64

Table S461.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ATM MUTATED 13 19 10
ATM WILD-TYPE 107 87 93
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0183 (Fisher's exact test), Q value = 0.26

Table S462.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ATM MUTATED 4 20 12 6
ATM WILD-TYPE 83 94 86 24

Figure S72.  Get High-res Image Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.91

Table S463.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ATM MUTATED 7 22 3 13 8
ATM WILD-TYPE 64 108 32 86 48
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 0.91

Table S464.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ATM MUTATED 17 16 20
ATM WILD-TYPE 99 90 149
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.72

Table S465.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ATM MUTATED 15 14 12 4 7
ATM WILD-TYPE 85 60 93 21 81
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.67

Table S466.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ATM MUTATED 33 15 4
ATM WILD-TYPE 221 68 51
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 0.72

Table S467.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ATM MUTATED 11 9 18 14
ATM WILD-TYPE 112 43 102 73
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0976 (Fisher's exact test), Q value = 0.53

Table S468.  Gene #47: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ATM MUTATED 8 9 2 24 9
ATM WILD-TYPE 79 52 39 98 62
'UNC93B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.88

Table S469.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
UNC93B1 MUTATED 2 2 1 2 0
UNC93B1 WILD-TYPE 72 140 113 58 2
'UNC93B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 0.91

Table S470.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
UNC93B1 MUTATED 3 3 1 0
UNC93B1 WILD-TYPE 132 119 61 76
'UNC93B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.85

Table S471.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
UNC93B1 MUTATED 4 1 2
UNC93B1 WILD-TYPE 116 105 101
'UNC93B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S472.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
UNC93B1 MUTATED 2 2 2 1
UNC93B1 WILD-TYPE 85 112 96 29
'UNC93B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 0.99

Table S473.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
UNC93B1 MUTATED 1 2 0 3 1
UNC93B1 WILD-TYPE 70 128 35 96 55
'UNC93B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S474.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
UNC93B1 MUTATED 2 1 4
UNC93B1 WILD-TYPE 114 105 165
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S475.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
UNC93B1 MUTATED 2 1 2 0 2
UNC93B1 WILD-TYPE 98 73 103 25 86
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S476.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
UNC93B1 MUTATED 5 1 1
UNC93B1 WILD-TYPE 249 82 54
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 0.92

Table S477.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
UNC93B1 MUTATED 2 0 2 3
UNC93B1 WILD-TYPE 121 52 118 84
'UNC93B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 0.91

Table S478.  Gene #48: 'UNC93B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
UNC93B1 MUTATED 1 1 0 2 3
UNC93B1 WILD-TYPE 86 60 41 120 68
'SF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.78

Table S479.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
SF1 MUTATED 1 6 1 2 0
SF1 WILD-TYPE 73 136 113 58 2
'SF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 0.91

Table S480.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
SF1 MUTATED 3 3 3 1
SF1 WILD-TYPE 132 119 59 75
'SF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.73

Table S481.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SF1 MUTATED 2 2 5
SF1 WILD-TYPE 118 104 98
'SF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0172 (Fisher's exact test), Q value = 0.25

Table S482.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SF1 MUTATED 0 2 7 0
SF1 WILD-TYPE 87 112 91 30

Figure S73.  Get High-res Image Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 0.98

Table S483.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
SF1 MUTATED 1 4 0 3 2
SF1 WILD-TYPE 70 126 35 96 54
'SF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S484.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SF1 MUTATED 3 3 4
SF1 WILD-TYPE 113 103 165
'SF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0033 (Fisher's exact test), Q value = 0.084

Table S485.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
SF1 MUTATED 0 6 3 1 0
SF1 WILD-TYPE 100 68 102 24 88

Figure S74.  Get High-res Image Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0167 (Fisher's exact test), Q value = 0.25

Table S486.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
SF1 MUTATED 4 6 0
SF1 WILD-TYPE 250 77 55

Figure S75.  Get High-res Image Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0927 (Fisher's exact test), Q value = 0.51

Table S487.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
SF1 MUTATED 1 4 3 2
SF1 WILD-TYPE 122 48 117 85
'SF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 0.85

Table S488.  Gene #49: 'SF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
SF1 MUTATED 1 3 1 2 3
SF1 WILD-TYPE 86 58 40 120 68
'BCL2L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0662 (Fisher's exact test), Q value = 0.46

Table S489.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
BCL2L1 MUTATED 3 1 0 0 0
BCL2L1 WILD-TYPE 71 141 114 60 2
'BCL2L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0326 (Fisher's exact test), Q value = 0.35

Table S490.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
BCL2L1 MUTATED 0 1 0 3
BCL2L1 WILD-TYPE 135 121 62 73

Figure S76.  Get High-res Image Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BCL2L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0769 (Fisher's exact test), Q value = 0.47

Table S491.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
BCL2L1 MUTATED 0 1 3
BCL2L1 WILD-TYPE 120 105 100
'BCL2L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.525 (Fisher's exact test), Q value = 0.85

Table S492.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
BCL2L1 MUTATED 0 3 1 0
BCL2L1 WILD-TYPE 87 111 97 30
'BCL2L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 0.93

Table S493.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
BCL2L1 MUTATED 0 1 0 2 1
BCL2L1 WILD-TYPE 71 129 35 97 55
'BCL2L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.692 (Fisher's exact test), Q value = 0.93

Table S494.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
BCL2L1 MUTATED 1 2 1
BCL2L1 WILD-TYPE 115 104 168
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.749 (Fisher's exact test), Q value = 0.94

Table S495.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
BCL2L1 MUTATED 2 1 1 0 0
BCL2L1 WILD-TYPE 98 73 104 25 88
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S496.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
BCL2L1 MUTATED 3 1 0
BCL2L1 WILD-TYPE 251 82 55
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.8

Table S497.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
BCL2L1 MUTATED 0 1 2 1
BCL2L1 WILD-TYPE 123 51 118 86
'BCL2L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.816 (Fisher's exact test), Q value = 0.97

Table S498.  Gene #50: 'BCL2L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
BCL2L1 MUTATED 0 1 0 2 1
BCL2L1 WILD-TYPE 87 60 41 120 70
'DNAH6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 0.94

Table S499.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
DNAH6 MUTATED 4 7 4 1 0
DNAH6 WILD-TYPE 70 135 110 59 2
'DNAH6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.6

Table S500.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
DNAH6 MUTATED 3 8 4 1
DNAH6 WILD-TYPE 132 114 58 75
'DNAH6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.83

Table S501.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
DNAH6 MUTATED 6 7 3
DNAH6 WILD-TYPE 114 99 100
'DNAH6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.66

Table S502.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
DNAH6 MUTATED 3 9 2 2
DNAH6 WILD-TYPE 84 105 96 28
'DNAH6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.29

Table S503.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
DNAH6 MUTATED 4 10 1 0 1
DNAH6 WILD-TYPE 67 120 34 99 55

Figure S77.  Get High-res Image Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'DNAH6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.2

Table S504.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
DNAH6 MUTATED 5 9 2
DNAH6 WILD-TYPE 111 97 167

Figure S78.  Get High-res Image Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DNAH6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 0.76

Table S505.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
DNAH6 MUTATED 1 3 6 1 5
DNAH6 WILD-TYPE 99 71 99 24 83
'DNAH6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.6

Table S506.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
DNAH6 MUTATED 7 5 4
DNAH6 WILD-TYPE 247 78 51
'DNAH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0685 (Fisher's exact test), Q value = 0.46

Table S507.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
DNAH6 MUTATED 5 2 8 0
DNAH6 WILD-TYPE 118 50 112 87
'DNAH6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0861 (Fisher's exact test), Q value = 0.5

Table S508.  Gene #51: 'DNAH6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
DNAH6 MUTATED 5 2 0 8 0
DNAH6 WILD-TYPE 82 59 41 114 71
'HES1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S509.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
HES1 MUTATED 2 4 3 2 0
HES1 WILD-TYPE 72 138 111 58 2
'HES1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S510.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
HES1 MUTATED 3 4 2 2
HES1 WILD-TYPE 132 118 60 74
'HES1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 0.88

Table S511.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
HES1 MUTATED 2 3 4
HES1 WILD-TYPE 118 103 99
'HES1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.58

Table S512.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
HES1 MUTATED 0 4 3 2
HES1 WILD-TYPE 87 110 95 28
'HES1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.92 (Fisher's exact test), Q value = 0.99

Table S513.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
HES1 MUTATED 1 5 1 3 1
HES1 WILD-TYPE 70 125 34 96 55
'HES1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 0.91

Table S514.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
HES1 MUTATED 2 4 5
HES1 WILD-TYPE 114 102 164
'HES1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.78

Table S515.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
HES1 MUTATED 2 4 1 1 3
HES1 WILD-TYPE 98 70 104 24 85
'HES1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.308 (Fisher's exact test), Q value = 0.73

Table S516.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
HES1 MUTATED 5 4 2
HES1 WILD-TYPE 249 79 53
'HES1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 0.98

Table S517.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
HES1 MUTATED 3 2 3 3
HES1 WILD-TYPE 120 50 117 84
'HES1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 0.85

Table S518.  Gene #52: 'HES1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
HES1 MUTATED 1 3 2 4 1
HES1 WILD-TYPE 86 58 39 118 70
'ERBB3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.85

Table S519.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ERBB3 MUTATED 11 15 8 7 0
ERBB3 WILD-TYPE 63 127 106 53 2
'ERBB3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 0.78

Table S520.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ERBB3 MUTATED 10 16 5 10
ERBB3 WILD-TYPE 125 106 57 66
'ERBB3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 0.99

Table S521.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ERBB3 MUTATED 14 11 10
ERBB3 WILD-TYPE 106 95 93
'ERBB3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.268 (Fisher's exact test), Q value = 0.72

Table S522.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ERBB3 MUTATED 13 13 6 3
ERBB3 WILD-TYPE 74 101 92 27
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 0.85

Table S523.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ERBB3 MUTATED 5 12 6 12 5
ERBB3 WILD-TYPE 66 118 29 87 51
'ERBB3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.67

Table S524.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ERBB3 MUTATED 8 15 17
ERBB3 WILD-TYPE 108 91 152
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.858 (Fisher's exact test), Q value = 0.98

Table S525.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ERBB3 MUTATED 13 7 9 3 9
ERBB3 WILD-TYPE 87 67 96 22 79
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.856 (Fisher's exact test), Q value = 0.98

Table S526.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ERBB3 MUTATED 28 7 6
ERBB3 WILD-TYPE 226 76 49
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.944 (Fisher's exact test), Q value = 0.99

Table S527.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ERBB3 MUTATED 14 4 13 9
ERBB3 WILD-TYPE 109 48 107 78
'ERBB3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.73

Table S528.  Gene #53: 'ERBB3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ERBB3 MUTATED 10 3 2 15 10
ERBB3 WILD-TYPE 77 58 39 107 61
'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 0.93

Table S529.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
TXNIP MUTATED 2 6 4 4 0
TXNIP WILD-TYPE 72 136 110 56 2
'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.85

Table S530.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
TXNIP MUTATED 4 7 4 2
TXNIP WILD-TYPE 131 115 58 74
'TXNIP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.58

Table S531.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
TXNIP MUTATED 4 2 8
TXNIP WILD-TYPE 116 104 95
'TXNIP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.746 (Fisher's exact test), Q value = 0.94

Table S532.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
TXNIP MUTATED 3 7 3 1
TXNIP WILD-TYPE 84 107 95 29
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.73

Table S533.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
TXNIP MUTATED 4 7 2 1 3
TXNIP WILD-TYPE 67 123 33 98 53
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00862 (Fisher's exact test), Q value = 0.16

Table S534.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TXNIP MUTATED 11 3 3
TXNIP WILD-TYPE 105 103 166

Figure S79.  Get High-res Image Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.719 (Fisher's exact test), Q value = 0.93

Table S535.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
TXNIP MUTATED 4 2 4 2 5
TXNIP WILD-TYPE 96 72 101 23 83
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.81

Table S536.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
TXNIP MUTATED 14 2 1
TXNIP WILD-TYPE 240 81 54
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 0.99

Table S537.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
TXNIP MUTATED 7 2 5 3
TXNIP WILD-TYPE 116 50 115 84
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 0.96

Table S538.  Gene #54: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
TXNIP MUTATED 6 2 1 6 2
TXNIP WILD-TYPE 81 59 40 116 69
'THRAP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 0.97

Table S539.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
THRAP3 MUTATED 3 5 3 3 0
THRAP3 WILD-TYPE 71 137 111 57 2
'THRAP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 0.91

Table S540.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
THRAP3 MUTATED 3 5 2 4
THRAP3 WILD-TYPE 132 117 60 72
'THRAP3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S541.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
THRAP3 MUTATED 3 3 3
THRAP3 WILD-TYPE 117 103 100
'THRAP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S542.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
THRAP3 MUTATED 2 3 3 1
THRAP3 WILD-TYPE 85 111 95 29
'THRAP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S543.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
THRAP3 MUTATED 2 5 1 4 2
THRAP3 WILD-TYPE 69 125 34 95 54
'THRAP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.784 (Fisher's exact test), Q value = 0.96

Table S544.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
THRAP3 MUTATED 5 4 5
THRAP3 WILD-TYPE 111 102 164
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.77

Table S545.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
THRAP3 MUTATED 6 3 1 1 3
THRAP3 WILD-TYPE 94 71 104 24 85
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 0.99

Table S546.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
THRAP3 MUTATED 10 2 2
THRAP3 WILD-TYPE 244 81 53
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S547.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
THRAP3 MUTATED 5 1 5 3
THRAP3 WILD-TYPE 118 51 115 84
'THRAP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 0.97

Table S548.  Gene #55: 'THRAP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
THRAP3 MUTATED 3 1 1 5 4
THRAP3 WILD-TYPE 84 60 40 117 67
'SPTAN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.91

Table S549.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
SPTAN1 MUTATED 7 15 17 5 0
SPTAN1 WILD-TYPE 67 127 97 55 2
'SPTAN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.64

Table S550.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
SPTAN1 MUTATED 10 20 6 9
SPTAN1 WILD-TYPE 125 102 56 67
'SPTAN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.71

Table S551.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SPTAN1 MUTATED 13 17 9
SPTAN1 WILD-TYPE 107 89 94
'SPTAN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.56

Table S552.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SPTAN1 MUTATED 11 19 6 3
SPTAN1 WILD-TYPE 76 95 92 27
'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.72

Table S553.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
SPTAN1 MUTATED 8 21 4 9 3
SPTAN1 WILD-TYPE 63 109 31 90 53
'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.67

Table S554.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SPTAN1 MUTATED 16 15 14
SPTAN1 WILD-TYPE 100 91 155
'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.67

Table S555.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
SPTAN1 MUTATED 7 10 15 5 8
SPTAN1 WILD-TYPE 93 64 90 20 80
'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S556.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
SPTAN1 MUTATED 28 12 5
SPTAN1 WILD-TYPE 226 71 50
'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.73

Table S557.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
SPTAN1 MUTATED 16 5 18 6
SPTAN1 WILD-TYPE 107 47 102 81
'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.64

Table S558.  Gene #56: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
SPTAN1 MUTATED 9 9 2 20 5
SPTAN1 WILD-TYPE 78 52 39 102 66
'ARID1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.529 (Fisher's exact test), Q value = 0.85

Table S559.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ARID1B MUTATED 4 12 5 2 0
ARID1B WILD-TYPE 70 130 109 58 2
'ARID1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0895 (Fisher's exact test), Q value = 0.5

Table S560.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ARID1B MUTATED 5 12 1 5
ARID1B WILD-TYPE 130 110 61 71
'ARID1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.66

Table S561.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ARID1B MUTATED 4 4 9
ARID1B WILD-TYPE 116 102 94
'ARID1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 0.88

Table S562.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ARID1B MUTATED 4 8 5 0
ARID1B WILD-TYPE 83 106 93 30
'ARID1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0992 (Fisher's exact test), Q value = 0.54

Table S563.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ARID1B MUTATED 5 13 0 3 2
ARID1B WILD-TYPE 66 117 35 96 54
'ARID1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0579 (Fisher's exact test), Q value = 0.43

Table S564.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ARID1B MUTATED 12 5 6
ARID1B WILD-TYPE 104 101 163
'ARID1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.67

Table S565.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ARID1B MUTATED 4 7 8 2 2
ARID1B WILD-TYPE 96 67 97 23 86
'ARID1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.64

Table S566.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ARID1B MUTATED 14 8 1
ARID1B WILD-TYPE 240 75 54
'ARID1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.64

Table S567.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ARID1B MUTATED 7 6 7 2
ARID1B WILD-TYPE 116 46 113 85
'ARID1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.54

Table S568.  Gene #57: 'ARID1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ARID1B MUTATED 3 7 2 9 1
ARID1B WILD-TYPE 84 54 39 113 70
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.73

Table S569.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
NRAS MUTATED 0 5 1 1 0
NRAS WILD-TYPE 74 137 113 59 2
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.82

Table S570.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
NRAS MUTATED 2 3 2 0
NRAS WILD-TYPE 133 119 60 76
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S571.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
NRAS MUTATED 2 1 1
NRAS WILD-TYPE 118 105 102
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 0.91

Table S572.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
NRAS MUTATED 1 1 1 1
NRAS WILD-TYPE 86 113 97 29
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 0.91

Table S573.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
NRAS MUTATED 0 4 0 2 1
NRAS WILD-TYPE 71 126 35 97 55
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 0.91

Table S574.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
NRAS MUTATED 3 2 2
NRAS WILD-TYPE 113 104 167
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.81

Table S575.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
NRAS MUTATED 2 3 2 0 0
NRAS WILD-TYPE 98 71 103 25 88
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.78

Table S576.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
NRAS MUTATED 4 3 0
NRAS WILD-TYPE 250 80 55
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0434 (Fisher's exact test), Q value = 0.4

Table S577.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
NRAS MUTATED 0 3 2 2
NRAS WILD-TYPE 123 49 118 85

Figure S80.  Get High-res Image Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 0.67

Table S578.  Gene #58: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
NRAS MUTATED 0 3 0 3 1
NRAS WILD-TYPE 87 58 41 119 70
'RPTN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.938 (Fisher's exact test), Q value = 0.99

Table S579.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RPTN MUTATED 2 7 4 2 0
RPTN WILD-TYPE 72 135 110 58 2
'RPTN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.78

Table S580.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RPTN MUTATED 6 6 0 3
RPTN WILD-TYPE 129 116 62 73
'RPTN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 0.98

Table S581.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RPTN MUTATED 5 3 4
RPTN WILD-TYPE 115 103 99
'RPTN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 0.95

Table S582.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RPTN MUTATED 3 4 3 2
RPTN WILD-TYPE 84 110 95 28
'RPTN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.85

Table S583.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RPTN MUTATED 3 6 2 4 0
RPTN WILD-TYPE 68 124 33 95 56
'RPTN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S584.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RPTN MUTATED 4 4 7
RPTN WILD-TYPE 112 102 162
'RPTN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.67

Table S585.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RPTN MUTATED 5 6 2 0 2
RPTN WILD-TYPE 95 68 103 25 86
'RPTN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.67

Table S586.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RPTN MUTATED 8 6 1
RPTN WILD-TYPE 246 77 54
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 0.96

Table S587.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RPTN MUTATED 4 2 4 5
RPTN WILD-TYPE 119 50 116 82
'RPTN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.782 (Fisher's exact test), Q value = 0.96

Table S588.  Gene #59: 'RPTN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
RPTN MUTATED 4 3 0 5 3
RPTN WILD-TYPE 83 58 41 117 68
'RAI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 0.91

Table S589.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RAI1 MUTATED 2 7 8 4 0
RAI1 WILD-TYPE 72 135 106 56 2
'RAI1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.6

Table S590.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RAI1 MUTATED 4 10 5 2
RAI1 WILD-TYPE 131 112 57 74
'RAI1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.56

Table S591.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RAI1 MUTATED 3 9 7
RAI1 WILD-TYPE 117 97 96
'RAI1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0772 (Fisher's exact test), Q value = 0.47

Table S592.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RAI1 MUTATED 2 12 4 1
RAI1 WILD-TYPE 85 102 94 29
'RAI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.34

Table S593.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RAI1 MUTATED 0 13 1 4 3
RAI1 WILD-TYPE 71 117 34 95 53

Figure S81.  Get High-res Image Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.35

Table S594.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RAI1 MUTATED 5 11 5
RAI1 WILD-TYPE 111 95 164

Figure S82.  Get High-res Image Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RAI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.64

Table S595.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RAI1 MUTATED 4 2 6 4 4
RAI1 WILD-TYPE 96 72 99 21 84
'RAI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.43 (Fisher's exact test), Q value = 0.81

Table S596.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RAI1 MUTATED 16 2 2
RAI1 WILD-TYPE 238 81 53
'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.8

Table S597.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RAI1 MUTATED 5 2 10 3
RAI1 WILD-TYPE 118 50 110 84
'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 0.88

Table S598.  Gene #60: 'RAI1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
RAI1 MUTATED 4 2 2 10 2
RAI1 WILD-TYPE 83 59 39 112 69
'TMCO4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.753 (Fisher's exact test), Q value = 0.94

Table S599.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
TMCO4 MUTATED 2 6 2 2 0
TMCO4 WILD-TYPE 72 136 112 58 2
'TMCO4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0532 (Fisher's exact test), Q value = 0.41

Table S600.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
TMCO4 MUTATED 1 6 4 1
TMCO4 WILD-TYPE 134 116 58 75
'TMCO4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.87

Table S601.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
TMCO4 MUTATED 4 5 2
TMCO4 WILD-TYPE 116 101 101
'TMCO4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.73

Table S602.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
TMCO4 MUTATED 3 5 1 2
TMCO4 WILD-TYPE 84 109 97 28
'TMCO4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0479 (Fisher's exact test), Q value = 0.4

Table S603.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
TMCO4 MUTATED 2 4 3 0 3
TMCO4 WILD-TYPE 69 126 32 99 53

Figure S83.  Get High-res Image Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TMCO4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0753 (Fisher's exact test), Q value = 0.47

Table S604.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
TMCO4 MUTATED 2 7 3
TMCO4 WILD-TYPE 114 99 166
'TMCO4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.67

Table S605.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
TMCO4 MUTATED 1 2 7 0 2
TMCO4 WILD-TYPE 99 72 98 25 86
'TMCO4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S606.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
TMCO4 MUTATED 9 2 1
TMCO4 WILD-TYPE 245 81 54
'TMCO4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.4

Table S607.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
TMCO4 MUTATED 2 0 8 1
TMCO4 WILD-TYPE 121 52 112 86

Figure S84.  Get High-res Image Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TMCO4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.67

Table S608.  Gene #61: 'TMCO4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
TMCO4 MUTATED 1 0 1 7 2
TMCO4 WILD-TYPE 86 61 40 115 69
'CNOT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.82

Table S609.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
CNOT1 MUTATED 6 9 5 1 0
CNOT1 WILD-TYPE 68 133 109 59 2
'CNOT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.64

Table S610.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
CNOT1 MUTATED 3 9 3 6
CNOT1 WILD-TYPE 132 113 59 70
'CNOT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.78

Table S611.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CNOT1 MUTATED 4 6 8
CNOT1 WILD-TYPE 116 100 95
'CNOT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.8

Table S612.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CNOT1 MUTATED 2 8 7 1
CNOT1 WILD-TYPE 85 106 91 29
'CNOT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 0.89

Table S613.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
CNOT1 MUTATED 2 10 2 4 2
CNOT1 WILD-TYPE 69 120 33 95 54
'CNOT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.83

Table S614.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CNOT1 MUTATED 5 8 7
CNOT1 WILD-TYPE 111 98 162
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.87

Table S615.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
CNOT1 MUTATED 6 4 7 2 2
CNOT1 WILD-TYPE 94 70 98 23 86
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.895 (Fisher's exact test), Q value = 0.98

Table S616.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
CNOT1 MUTATED 15 4 2
CNOT1 WILD-TYPE 239 79 53
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 0.99

Table S617.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
CNOT1 MUTATED 6 2 8 4
CNOT1 WILD-TYPE 117 50 112 83
'CNOT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.881 (Fisher's exact test), Q value = 0.98

Table S618.  Gene #62: 'CNOT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
CNOT1 MUTATED 3 3 3 7 4
CNOT1 WILD-TYPE 84 58 38 115 67
'PARD3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.54

Table S619.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
PARD3 MUTATED 3 7 5 6 1
PARD3 WILD-TYPE 71 135 109 54 1
'PARD3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 0.91

Table S620.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
PARD3 MUTATED 8 8 4 2
PARD3 WILD-TYPE 127 114 58 74
'PARD3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 0.81

Table S621.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
PARD3 MUTATED 4 7 7
PARD3 WILD-TYPE 116 99 96
'PARD3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.78

Table S622.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
PARD3 MUTATED 3 8 7 0
PARD3 WILD-TYPE 84 106 91 30
'PARD3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0885 (Fisher's exact test), Q value = 0.5

Table S623.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
PARD3 MUTATED 3 9 1 2 7
PARD3 WILD-TYPE 68 121 34 97 49
'PARD3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 0.98

Table S624.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
PARD3 MUTATED 6 5 11
PARD3 WILD-TYPE 110 101 158
'PARD3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.971 (Fisher's exact test), Q value = 1

Table S625.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
PARD3 MUTATED 5 5 5 1 4
PARD3 WILD-TYPE 95 69 100 24 84
'PARD3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S626.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
PARD3 MUTATED 10 7 3
PARD3 WILD-TYPE 244 76 52
'PARD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 0.98

Table S627.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
PARD3 MUTATED 5 3 5 5
PARD3 WILD-TYPE 118 49 115 82
'PARD3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S628.  Gene #63: 'PARD3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
PARD3 MUTATED 4 6 0 5 3
PARD3 WILD-TYPE 83 55 41 117 68
'EZR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.82

Table S629.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
EZR MUTATED 2 3 3 4 0
EZR WILD-TYPE 72 139 111 56 2
'EZR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.85

Table S630.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
EZR MUTATED 5 5 0 2
EZR WILD-TYPE 130 117 62 74
'EZR MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S631.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

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

P value = 0.384 (Fisher's exact test), Q value = 0.8

Table S632.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EZR MUTATED 2 2 4 2
EZR WILD-TYPE 85 112 94 28
'EZR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 0.8

Table S633.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
EZR MUTATED 4 3 0 2 3
EZR WILD-TYPE 67 127 35 97 53
'EZR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.871 (Fisher's exact test), Q value = 0.98

Table S634.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EZR MUTATED 3 4 5
EZR WILD-TYPE 113 102 164
'EZR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.936 (Fisher's exact test), Q value = 0.99

Table S635.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
EZR MUTATED 3 2 3 0 4
EZR WILD-TYPE 97 72 102 25 84
'EZR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.65

Table S636.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
EZR MUTATED 6 2 4
EZR WILD-TYPE 248 81 51
'EZR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.892 (Fisher's exact test), Q value = 0.98

Table S637.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
EZR MUTATED 4 1 5 2
EZR WILD-TYPE 119 51 115 85
'EZR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 0.94

Table S638.  Gene #64: 'EZR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
EZR MUTATED 4 1 0 5 2
EZR WILD-TYPE 83 60 41 117 69
'MOAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 0.97

Table S639.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
MOAP1 MUTATED 1 3 3 0 0
MOAP1 WILD-TYPE 73 139 111 60 2
'MOAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 0.73

Table S640.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
MOAP1 MUTATED 1 4 0 2
MOAP1 WILD-TYPE 134 118 62 74
'MOAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.85

Table S641.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MOAP1 MUTATED 1 3 2
MOAP1 WILD-TYPE 119 103 101
'MOAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 0.89

Table S642.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MOAP1 MUTATED 1 3 1 1
MOAP1 WILD-TYPE 86 111 97 29
'MOAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.67

Table S643.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
MOAP1 MUTATED 0 5 1 1 0
MOAP1 WILD-TYPE 71 125 34 98 56
'MOAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.91

Table S644.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MOAP1 MUTATED 3 2 2
MOAP1 WILD-TYPE 113 104 167
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.72

Table S645.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
MOAP1 MUTATED 0 2 4 0 1
MOAP1 WILD-TYPE 100 72 101 25 87
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 0.98

Table S646.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
MOAP1 MUTATED 4 2 1
MOAP1 WILD-TYPE 250 81 54
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 0.99

Table S647.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
MOAP1 MUTATED 2 1 3 1
MOAP1 WILD-TYPE 121 51 117 86
'MOAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 0.94

Table S648.  Gene #65: 'MOAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
MOAP1 MUTATED 2 1 1 3 0
MOAP1 WILD-TYPE 85 60 40 119 71
'SF3B1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.78

Table S649.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
SF3B1 MUTATED 6 11 3 4 0
SF3B1 WILD-TYPE 68 131 111 56 2
'SF3B1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 0.98

Table S650.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
SF3B1 MUTATED 7 9 3 5
SF3B1 WILD-TYPE 128 113 59 71
'SF3B1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.85

Table S651.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SF3B1 MUTATED 4 5 7
SF3B1 WILD-TYPE 116 101 96
'SF3B1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.457 (Fisher's exact test), Q value = 0.83

Table S652.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SF3B1 MUTATED 3 8 3 2
SF3B1 WILD-TYPE 84 106 95 28
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 0.93

Table S653.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
SF3B1 MUTATED 2 8 3 7 4
SF3B1 WILD-TYPE 69 122 32 92 52
'SF3B1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.616 (Fisher's exact test), Q value = 0.9

Table S654.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SF3B1 MUTATED 5 8 11
SF3B1 WILD-TYPE 111 98 158
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 0.99

Table S655.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
SF3B1 MUTATED 5 5 6 2 5
SF3B1 WILD-TYPE 95 69 99 23 83
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.88

Table S656.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
SF3B1 MUTATED 13 6 4
SF3B1 WILD-TYPE 241 77 51
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.8

Table S657.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
SF3B1 MUTATED 9 4 7 2
SF3B1 WILD-TYPE 114 48 113 85
'SF3B1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.147 (Fisher's exact test), Q value = 0.62

Table S658.  Gene #66: 'SF3B1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
SF3B1 MUTATED 4 5 5 7 1
SF3B1 WILD-TYPE 83 56 36 115 70
'RUNX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.91

Table S659.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
RUNX1 MUTATED 3 5 2 3 0
RUNX1 WILD-TYPE 71 137 112 57 2
'RUNX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 0.92

Table S660.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
RUNX1 MUTATED 5 4 3 1
RUNX1 WILD-TYPE 130 118 59 75
'RUNX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S661.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
RUNX1 MUTATED 4 1 5
RUNX1 WILD-TYPE 116 105 98
'RUNX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.85

Table S662.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
RUNX1 MUTATED 2 2 5 1
RUNX1 WILD-TYPE 85 112 93 29
'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00225 (Fisher's exact test), Q value = 0.061

Table S663.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
RUNX1 MUTATED 0 2 0 4 7
RUNX1 WILD-TYPE 71 128 35 95 49

Figure S85.  Get High-res Image Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RUNX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0465 (Fisher's exact test), Q value = 0.4

Table S664.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
RUNX1 MUTATED 5 0 8
RUNX1 WILD-TYPE 111 106 161

Figure S86.  Get High-res Image Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.66

Table S665.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
RUNX1 MUTATED 3 2 2 3 2
RUNX1 WILD-TYPE 97 72 103 22 86
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.917 (Fisher's exact test), Q value = 0.99

Table S666.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
RUNX1 MUTATED 8 2 2
RUNX1 WILD-TYPE 246 81 53
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 0.97

Table S667.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
RUNX1 MUTATED 4 1 3 4
RUNX1 WILD-TYPE 119 51 117 83
'RUNX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00109 (Fisher's exact test), Q value = 0.035

Table S668.  Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
RUNX1 MUTATED 1 1 6 1 3
RUNX1 WILD-TYPE 86 60 35 121 68

Figure S87.  Get High-res Image Gene #67: 'RUNX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MEGF8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 0.91

Table S669.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
MEGF8 MUTATED 5 9 4 2 0
MEGF8 WILD-TYPE 69 133 110 58 2
'MEGF8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.82

Table S670.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
MEGF8 MUTATED 4 9 3 4
MEGF8 WILD-TYPE 131 113 59 72
'MEGF8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 0.93

Table S671.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
MEGF8 MUTATED 5 7 4
MEGF8 WILD-TYPE 115 99 99
'MEGF8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S672.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
MEGF8 MUTATED 4 6 5 1
MEGF8 WILD-TYPE 83 108 93 29
'MEGF8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.6

Table S673.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
MEGF8 MUTATED 0 7 2 7 4
MEGF8 WILD-TYPE 71 123 33 92 52
'MEGF8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 0.87

Table S674.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
MEGF8 MUTATED 4 7 9
MEGF8 WILD-TYPE 112 99 160
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.67

Table S675.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
MEGF8 MUTATED 5 4 8 2 1
MEGF8 WILD-TYPE 95 70 97 23 87
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 0.88

Table S676.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
MEGF8 MUTATED 15 4 1
MEGF8 WILD-TYPE 239 79 54
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 0.99

Table S677.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
MEGF8 MUTATED 6 2 8 4
MEGF8 WILD-TYPE 117 50 112 83
'MEGF8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 0.98

Table S678.  Gene #68: 'MEGF8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
MEGF8 MUTATED 4 2 3 7 4
MEGF8 WILD-TYPE 83 59 38 115 67
'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.85

Table S679.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
CASP8 MUTATED 2 4 7 1 0
CASP8 WILD-TYPE 72 138 107 59 2
'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 0.85

Table S680.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
CASP8 MUTATED 7 5 1 1
CASP8 WILD-TYPE 128 117 61 75
'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0822 (Fisher's exact test), Q value = 0.49

Table S681.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CASP8 MUTATED 1 5 6
CASP8 WILD-TYPE 119 101 97
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.54

Table S682.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CASP8 MUTATED 0 6 5 1
CASP8 WILD-TYPE 87 108 93 29
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 0.98

Table S683.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
CASP8 MUTATED 2 6 0 4 2
CASP8 WILD-TYPE 69 124 35 95 54
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.577 (Fisher's exact test), Q value = 0.88

Table S684.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CASP8 MUTATED 5 2 7
CASP8 WILD-TYPE 111 104 162
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.64

Table S685.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
CASP8 MUTATED 5 0 3 2 4
CASP8 WILD-TYPE 95 74 102 23 84
'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.8

Table S686.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
CASP8 MUTATED 10 1 3
CASP8 WILD-TYPE 244 82 52
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 0.87

Table S687.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
CASP8 MUTATED 5 0 4 4
CASP8 WILD-TYPE 118 52 116 83
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 0.73

Table S688.  Gene #69: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
CASP8 MUTATED 3 0 1 4 5
CASP8 WILD-TYPE 84 61 40 118 66
'DAZAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.78

Table S689.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
DAZAP1 MUTATED 2 1 1 2 0
DAZAP1 WILD-TYPE 72 141 113 58 2
'DAZAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0875 (Fisher's exact test), Q value = 0.5

Table S690.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
DAZAP1 MUTATED 1 5 0 0
DAZAP1 WILD-TYPE 134 117 62 76
'DAZAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.87

Table S691.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
DAZAP1 MUTATED 2 2 0
DAZAP1 WILD-TYPE 118 104 103
'DAZAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.75

Table S692.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
DAZAP1 MUTATED 1 2 0 1
DAZAP1 WILD-TYPE 86 112 98 29
'DAZAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.83

Table S693.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
DAZAP1 MUTATED 1 3 1 0 1
DAZAP1 WILD-TYPE 70 127 34 99 55
'DAZAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0105 (Fisher's exact test), Q value = 0.18

Table S694.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
DAZAP1 MUTATED 0 5 1
DAZAP1 WILD-TYPE 116 101 168

Figure S88.  Get High-res Image Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.66

Table S695.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
DAZAP1 MUTATED 2 0 4 0 0
DAZAP1 WILD-TYPE 98 74 101 25 88
'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 0.79

Table S696.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
DAZAP1 MUTATED 6 0 0
DAZAP1 WILD-TYPE 248 83 55
'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.85

Table S697.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
DAZAP1 MUTATED 1 0 3 0
DAZAP1 WILD-TYPE 122 52 117 87
'DAZAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S698.  Gene #70: 'DAZAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
DAZAP1 MUTATED 1 0 0 3 0
DAZAP1 WILD-TYPE 86 61 41 119 71
'USP28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.8

Table S699.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
USP28 MUTATED 5 3 3 2 0
USP28 WILD-TYPE 69 139 111 58 2
'USP28 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S700.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
USP28 MUTATED 5 3 2 3
USP28 WILD-TYPE 130 119 60 73
'USP28 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S701.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
USP28 MUTATED 2 3 4
USP28 WILD-TYPE 118 103 99
'USP28 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.8

Table S702.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
USP28 MUTATED 1 3 5 0
USP28 WILD-TYPE 86 111 93 30
'USP28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 0.97

Table S703.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
USP28 MUTATED 2 3 1 4 3
USP28 WILD-TYPE 69 127 34 95 53
'USP28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S704.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
USP28 MUTATED 4 3 6
USP28 WILD-TYPE 112 103 163
'USP28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 0.94

Table S705.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
USP28 MUTATED 3 1 5 1 3
USP28 WILD-TYPE 97 73 100 24 85
'USP28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S706.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
USP28 MUTATED 9 3 1
USP28 WILD-TYPE 245 80 54
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.613 (Fisher's exact test), Q value = 0.9

Table S707.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
USP28 MUTATED 5 1 5 1
USP28 WILD-TYPE 118 51 115 86
'USP28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 0.8

Table S708.  Gene #71: 'USP28 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
USP28 MUTATED 3 2 1 6 0
USP28 WILD-TYPE 84 59 40 116 71
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 0.93

Table S709.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
SETD2 MUTATED 4 13 6 4 0
SETD2 WILD-TYPE 70 129 108 56 2
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 0.93

Table S710.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
SETD2 MUTATED 10 10 4 3
SETD2 WILD-TYPE 125 112 58 73
'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 0.85

Table S711.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SETD2 MUTATED 6 9 5
SETD2 WILD-TYPE 114 97 98
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 0.97

Table S712.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SETD2 MUTATED 5 9 5 1
SETD2 WILD-TYPE 82 105 93 29
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S713.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
SETD2 MUTATED 5 9 2 7 4
SETD2 WILD-TYPE 66 121 33 92 52
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.819 (Fisher's exact test), Q value = 0.97

Table S714.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SETD2 MUTATED 9 6 12
SETD2 WILD-TYPE 107 100 157
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.263 (Fisher's exact test), Q value = 0.71

Table S715.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
SETD2 MUTATED 6 5 4 4 7
SETD2 WILD-TYPE 94 69 101 21 81
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.43 (Fisher's exact test), Q value = 0.81

Table S716.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
SETD2 MUTATED 14 7 5
SETD2 WILD-TYPE 240 76 50
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 0.97

Table S717.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
SETD2 MUTATED 9 3 6 7
SETD2 WILD-TYPE 114 49 114 80
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 0.98

Table S718.  Gene #72: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
SETD2 MUTATED 6 5 1 8 5
SETD2 WILD-TYPE 81 56 40 114 66
'EME1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 0.91

Table S719.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
EME1 MUTATED 0 3 2 0 0
EME1 WILD-TYPE 74 139 112 60 2
'EME1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.73

Table S720.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
EME1 MUTATED 2 0 1 2
EME1 WILD-TYPE 133 122 61 74
'EME1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.93

Table S721.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EME1 MUTATED 1 1 2
EME1 WILD-TYPE 119 105 101
'EME1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.73

Table S722.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EME1 MUTATED 0 1 2 1
EME1 WILD-TYPE 87 113 96 29
'EME1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.85

Table S723.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
EME1 MUTATED 0 2 0 3 0
EME1 WILD-TYPE 71 128 35 96 56
'EME1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 0.77

Table S724.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EME1 MUTATED 1 0 4
EME1 WILD-TYPE 115 106 165
'EME1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 0.85

Table S725.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
EME1 MUTATED 2 2 0 0 1
EME1 WILD-TYPE 98 72 105 25 87
'EME1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.54

Table S726.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
EME1 MUTATED 2 3 0
EME1 WILD-TYPE 252 80 55
'EME1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.64

Table S727.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
EME1 MUTATED 3 1 0 0
EME1 WILD-TYPE 120 51 120 87
'EME1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.54

Table S728.  Gene #73: 'EME1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
EME1 MUTATED 1 2 1 0 0
EME1 WILD-TYPE 86 59 40 122 71
'ADC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0817 (Fisher's exact test), Q value = 0.49

Table S729.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
ADC MUTATED 0 5 0 0 0
ADC WILD-TYPE 74 137 114 60 2
'ADC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 0.99

Table S730.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
ADC MUTATED 2 2 0 1
ADC WILD-TYPE 133 120 62 75
'ADC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 0.93

Table S731.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
ADC MUTATED 1 1 2
ADC WILD-TYPE 119 105 101
'ADC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.7 (Fisher's exact test), Q value = 0.93

Table S732.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
ADC MUTATED 0 2 2 0
ADC WILD-TYPE 87 112 96 30
'ADC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 0.99

Table S733.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
ADC MUTATED 1 3 0 1 0
ADC WILD-TYPE 70 127 35 98 56
'ADC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S734.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
ADC MUTATED 2 1 2
ADC WILD-TYPE 114 105 167
'ADC MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S735.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
ADC MUTATED 1 1 2 0 1
ADC WILD-TYPE 99 73 103 25 87
'ADC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 0.85

Table S736.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
ADC MUTATED 3 2 0
ADC WILD-TYPE 251 81 55
'ADC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.569 (Fisher's exact test), Q value = 0.88

Table S737.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
ADC MUTATED 2 1 2 0
ADC WILD-TYPE 121 51 118 87
'ADC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 0.95

Table S738.  Gene #74: 'ADC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
ADC MUTATED 1 1 1 2 0
ADC WILD-TYPE 86 60 40 120 71
'CNOT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.54

Table S739.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
CNOT3 MUTATED 1 1 4 4 0
CNOT3 WILD-TYPE 73 141 110 56 2
'CNOT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.75

Table S740.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
CNOT3 MUTATED 6 1 1 2
CNOT3 WILD-TYPE 129 121 61 74
'CNOT3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 0.93

Table S741.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
CNOT3 MUTATED 3 2 4
CNOT3 WILD-TYPE 117 104 99
'CNOT3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.64

Table S742.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
CNOT3 MUTATED 1 2 6 0
CNOT3 WILD-TYPE 86 112 92 30
'CNOT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0483 (Fisher's exact test), Q value = 0.4

Table S743.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
CNOT3 MUTATED 1 1 0 7 1
CNOT3 WILD-TYPE 70 129 35 92 55

Figure S89.  Get High-res Image Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CNOT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.56

Table S744.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
CNOT3 MUTATED 3 0 7
CNOT3 WILD-TYPE 113 106 162
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00871 (Fisher's exact test), Q value = 0.16

Table S745.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
CNOT3 MUTATED 6 3 0 1 0
CNOT3 WILD-TYPE 94 71 105 24 88

Figure S90.  Get High-res Image Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CNOT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.446 (Fisher's exact test), Q value = 0.82

Table S746.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
CNOT3 MUTATED 7 3 0
CNOT3 WILD-TYPE 247 80 55
'CNOT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00735 (Fisher's exact test), Q value = 0.15

Table S747.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
CNOT3 MUTATED 2 2 0 6
CNOT3 WILD-TYPE 121 50 120 81

Figure S91.  Get High-res Image Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CNOT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-04 (Fisher's exact test), Q value = 0.023

Table S748.  Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
CNOT3 MUTATED 0 3 1 0 6
CNOT3 WILD-TYPE 87 58 40 122 65

Figure S92.  Get High-res Image Gene #75: 'CNOT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SSH3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.67

Table S749.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
SSH3 MUTATED 5 4 6 0 0
SSH3 WILD-TYPE 69 138 108 60 2
'SSH3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.058 (Fisher's exact test), Q value = 0.43

Table S750.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
SSH3 MUTATED 3 2 5 5
SSH3 WILD-TYPE 132 120 57 71
'SSH3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0342 (Fisher's exact test), Q value = 0.36

Table S751.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
SSH3 MUTATED 1 8 3
SSH3 WILD-TYPE 119 98 100

Figure S93.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'SSH3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0438 (Fisher's exact test), Q value = 0.4

Table S752.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
SSH3 MUTATED 2 9 1 0
SSH3 WILD-TYPE 85 105 97 30

Figure S94.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SSH3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0779 (Fisher's exact test), Q value = 0.47

Table S753.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
SSH3 MUTATED 0 8 3 3 1
SSH3 WILD-TYPE 71 122 32 96 55
'SSH3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.8

Table S754.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
SSH3 MUTATED 6 5 4
SSH3 WILD-TYPE 110 101 165
'SSH3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.58

Table S755.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
SSH3 MUTATED 2 5 7 0 1
SSH3 WILD-TYPE 98 69 98 25 87
'SSH3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.67

Table S756.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
SSH3 MUTATED 8 6 1
SSH3 WILD-TYPE 246 77 54
'SSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0369 (Fisher's exact test), Q value = 0.38

Table S757.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
SSH3 MUTATED 4 4 7 0
SSH3 WILD-TYPE 119 48 113 87

Figure S95.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SSH3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.35

Table S758.  Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
SSH3 MUTATED 1 5 3 6 0
SSH3 WILD-TYPE 86 56 38 116 71

Figure S96.  Get High-res Image Gene #76: 'SSH3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AHR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 0.91

Table S759.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
AHR MUTATED 2 10 6 4 0
AHR WILD-TYPE 72 132 108 56 2
'AHR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.54

Table S760.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
AHR MUTATED 3 9 6 4
AHR WILD-TYPE 132 113 56 72
'AHR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.64

Table S761.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
AHR MUTATED 4 10 6
AHR WILD-TYPE 116 96 97
'AHR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.778 (Fisher's exact test), Q value = 0.96

Table S762.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
AHR MUTATED 6 8 4 2
AHR WILD-TYPE 81 106 94 28
'AHR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.521 (Fisher's exact test), Q value = 0.85

Table S763.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
AHR MUTATED 2 11 2 4 3
AHR WILD-TYPE 69 119 33 95 53
'AHR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0741 (Fisher's exact test), Q value = 0.47

Table S764.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
AHR MUTATED 7 10 5
AHR WILD-TYPE 109 96 164
'AHR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 0.93

Table S765.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
AHR MUTATED 4 4 9 1 4
AHR WILD-TYPE 96 70 96 24 84
'AHR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S766.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
AHR MUTATED 14 5 3
AHR WILD-TYPE 240 78 52
'AHR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 0.85

Table S767.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
AHR MUTATED 5 2 10 4
AHR WILD-TYPE 118 50 110 83
'AHR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.67

Table S768.  Gene #77: 'AHR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
AHR MUTATED 4 4 1 11 1
AHR WILD-TYPE 83 57 40 111 70
'EIF4A2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 0.85

Table S769.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
EIF4A2 MUTATED 3 4 1 2 0
EIF4A2 WILD-TYPE 71 138 113 58 2
'EIF4A2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.93

Table S770.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
EIF4A2 MUTATED 3 3 3 2
EIF4A2 WILD-TYPE 132 119 59 74
'EIF4A2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.8

Table S771.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EIF4A2 MUTATED 2 3 5
EIF4A2 WILD-TYPE 118 103 98
'EIF4A2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.611 (Fisher's exact test), Q value = 0.9

Table S772.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EIF4A2 MUTATED 2 3 5 0
EIF4A2 WILD-TYPE 85 111 93 30
'EIF4A2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 0.94

Table S773.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
EIF4A2 MUTATED 2 3 2 2 2
EIF4A2 WILD-TYPE 69 127 33 97 54
'EIF4A2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S774.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EIF4A2 MUTATED 1 3 7
EIF4A2 WILD-TYPE 115 103 162
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.81

Table S775.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
EIF4A2 MUTATED 4 0 3 1 3
EIF4A2 WILD-TYPE 96 74 102 24 85
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 0.66

Table S776.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
EIF4A2 MUTATED 9 0 2
EIF4A2 WILD-TYPE 245 83 53
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 0.91

Table S777.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
EIF4A2 MUTATED 3 0 4 3
EIF4A2 WILD-TYPE 120 52 116 84
'EIF4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0541 (Fisher's exact test), Q value = 0.41

Table S778.  Gene #78: 'EIF4A2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
EIF4A2 MUTATED 1 0 3 2 4
EIF4A2 WILD-TYPE 86 61 38 120 67
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.942 (Fisher's exact test), Q value = 0.99

Table S779.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
EPHA2 MUTATED 3 8 6 2 0
EPHA2 WILD-TYPE 71 134 108 58 2
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0398 (Fisher's exact test), Q value = 0.4

Table S780.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
EPHA2 MUTATED 4 10 0 5
EPHA2 WILD-TYPE 131 112 62 71

Figure S97.  Get High-res Image Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 0.91

Table S781.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
EPHA2 MUTATED 6 6 3
EPHA2 WILD-TYPE 114 100 100
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.85

Table S782.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
EPHA2 MUTATED 3 5 4 3
EPHA2 WILD-TYPE 84 109 94 27
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 0.99

Table S783.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
EPHA2 MUTATED 2 6 1 6 3
EPHA2 WILD-TYPE 69 124 34 93 53
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S784.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
EPHA2 MUTATED 5 5 8
EPHA2 WILD-TYPE 111 101 161
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 0.94

Table S785.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
EPHA2 MUTATED 6 5 4 0 4
EPHA2 WILD-TYPE 94 69 101 25 84
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 0.85

Table S786.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
EPHA2 MUTATED 11 6 2
EPHA2 WILD-TYPE 243 77 53
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 0.99

Table S787.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
EPHA2 MUTATED 5 3 6 5
EPHA2 WILD-TYPE 118 49 114 82
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.73

Table S788.  Gene #79: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
EPHA2 MUTATED 1 3 3 7 5
EPHA2 WILD-TYPE 86 58 38 115 66
'OGDH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.67

Table S789.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
OGDH MUTATED 4 11 2 2 0
OGDH WILD-TYPE 70 131 112 58 2
'OGDH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.59

Table S790.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
OGDH MUTATED 11 4 3 1
OGDH WILD-TYPE 124 118 59 75
'OGDH MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S791.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
OGDH MUTATED 4 4 5
OGDH WILD-TYPE 116 102 98
'OGDH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S792.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
OGDH MUTATED 2 4 5 2
OGDH WILD-TYPE 85 110 93 28
'OGDH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 0.97

Table S793.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
OGDH MUTATED 4 4 2 5 3
OGDH WILD-TYPE 67 126 33 94 53
'OGDH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 0.98

Table S794.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
OGDH MUTATED 5 4 9
OGDH WILD-TYPE 111 102 160
'OGDH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.84

Table S795.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
OGDH MUTATED 5 6 3 0 5
OGDH WILD-TYPE 95 68 102 25 83
'OGDH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 0.68

Table S796.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
OGDH MUTATED 9 6 4
OGDH WILD-TYPE 245 77 51
'OGDH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.81

Table S797.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
OGDH MUTATED 7 3 3 6
OGDH WILD-TYPE 116 49 117 81
'OGDH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.72

Table S798.  Gene #80: 'OGDH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
OGDH MUTATED 3 5 3 3 5
OGDH WILD-TYPE 84 56 38 119 66
'POU3F1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.577 (Fisher's exact test), Q value = 0.88

Table S799.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 74 142 114 60 2
POU3F1 MUTATED 1 2 0 0 0
POU3F1 WILD-TYPE 73 140 114 60 2
'POU3F1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.66

Table S800.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 135 122 62 76
POU3F1 MUTATED 1 0 0 2
POU3F1 WILD-TYPE 134 122 62 74
'POU3F1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0305 (Fisher's exact test), Q value = 0.35

Table S801.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 120 106 103
POU3F1 MUTATED 0 0 3
POU3F1 WILD-TYPE 120 106 100

Figure S98.  Get High-res Image Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'POU3F1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 0.91

Table S802.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 87 114 98 30
POU3F1 MUTATED 0 1 2 0
POU3F1 WILD-TYPE 87 113 96 30
'POU3F1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0446 (Fisher's exact test), Q value = 0.4

Table S803.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 71 130 35 99 56
POU3F1 MUTATED 2 0 1 0 0
POU3F1 WILD-TYPE 69 130 34 99 56

Figure S99.  Get High-res Image Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'POU3F1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 0.96

Table S804.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 116 106 169
POU3F1 MUTATED 1 0 2
POU3F1 WILD-TYPE 115 106 167
'POU3F1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.73

Table S805.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 100 74 105 25 88
POU3F1 MUTATED 1 2 0 0 0
POU3F1 WILD-TYPE 99 72 105 25 88
'POU3F1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.64

Table S806.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 254 83 55
POU3F1 MUTATED 1 2 0
POU3F1 WILD-TYPE 253 81 55
'POU3F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0442 (Fisher's exact test), Q value = 0.4

Table S807.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 123 52 120 87
POU3F1 MUTATED 0 2 1 0
POU3F1 WILD-TYPE 123 50 119 87

Figure S100.  Get High-res Image Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'POU3F1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.67

Table S808.  Gene #81: 'POU3F1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 87 61 41 122 71
POU3F1 MUTATED 0 2 0 1 0
POU3F1 WILD-TYPE 87 59 41 121 71
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/22811976/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/BLCA-TP/22541056/BLCA-TP.transferedmergedcluster.txt

  • Number of patients = 395

  • Number of significantly mutated genes = 81

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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