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 49 genes and 10 molecular subtypes across 510 patients, 105 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • CDKN2A mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CASP8 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • NSD1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • HLA-B mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MLL2 mutation correlated to 'CN_CNMF'.

  • TGFBR2 mutation correlated to 'CN_CNMF'.

  • FAT1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • NOTCH1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • JUB mutation correlated to 'MRNASEQ_CNMF'.

  • NFE2L2 mutation correlated to 'METHLYATION_CNMF'.

  • ZNF750 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RAC1 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CNMF'.

  • EPHA2 mutation correlated to 'METHLYATION_CNMF'.

  • HLA-A mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

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

  • PIK3CA mutation correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • EP300 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • RB1 mutation correlated to 'MRNASEQ_CNMF'.

  • KEAP1 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_CHIERARCHICAL'.

  • KDM6A mutation correlated to 'CN_CNMF'.

  • CREBBP mutation correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • NUDT11 mutation correlated to 'RPPA_CNMF'.

  • SMAD4 mutation correlated to 'MIRSEQ_CNMF'.

  • CUL3 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • MYH9 mutation correlated to 'CN_CNMF'.

  • HUWE1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MRNASEQ_CHIERARCHICAL'.

  • SLC9A6 mutation correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MLL4 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF', and 'MIRSEQ_CNMF'.

  • CTCF mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

  • PTPN14 mutation correlated to 'CN_CNMF' and 'MIRSEQ_CNMF'.

  • ITGB1 mutation correlated to 'MRNASEQ_CNMF'.

  • IRS4 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • GAGE2A mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 49 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, 105 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
NSD1 63 (12%) 447 0.00421
(0.0413) 		1e-05
(0.000233) 		0.174
(0.461) 		0.0149
(0.113) 		3e-05
(0.000612) 		1e-05
(0.000233) 		0.00278
(0.0303) 		4e-05
(0.000754) 		1e-05
(0.000233) 		1e-05
(0.000233)
TP53 359 (70%) 151 1e-05
(0.000233) 		1e-05
(0.000233) 		0.618
(0.837) 		0.566
(0.816) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.00482
(0.0454) 		1e-05
(0.000233) 		3e-05
(0.000612) 		1e-05
(0.000233)
CDKN2A 112 (22%) 398 0.0231
(0.149) 		1e-05
(0.000233) 		0.0419
(0.203) 		0.717
(0.892) 		0.0254
(0.157) 		3e-05
(0.000612) 		0.214
(0.515) 		0.0584
(0.249) 		0.00226
(0.0258) 		0.0392
(0.2)
CASP8 55 (11%) 455 1e-05
(0.000233) 		1e-05
(0.000233) 		0.00039
(0.00637) 		0.352
(0.679) 		1e-05
(0.000233) 		1e-05
(0.000233) 		0.00922
(0.0766) 		0.566
(0.816) 		0.00024
(0.00406) 		0.137
(0.395)
NOTCH1 87 (17%) 423 0.0155
(0.113) 		4e-05
(0.000754) 		0.902
(0.965) 		0.0574
(0.247) 		1e-05
(0.000233) 		0.00114
(0.0147) 		1e-05
(0.000233) 		0.0677
(0.274) 		0.00864
(0.0732) 		0.0371
(0.195)
HRAS 29 (6%) 481 1e-05
(0.000233) 		1e-05
(0.000233) 		0.0138
(0.106) 		0.654
(0.857) 		0.00066
(0.00951) 		0.0021
(0.0245) 		0.00066
(0.00951) 		0.122
(0.379) 		0.023
(0.149) 		0.171
(0.457)
ZNF750 19 (4%) 491 0.214
(0.515) 		0.0108
(0.0883) 		0.278
(0.58) 		0.286
(0.591) 		0.00777
(0.068) 		0.0162
(0.113) 		0.0162
(0.113) 		0.131
(0.386) 		0.0491
(0.231) 		0.0229
(0.149)
HLA-A 22 (4%) 488 0.0032
(0.0334) 		0.0032
(0.0334) 		0.232
(0.521) 		0.639
(0.846) 		0.00465
(0.0447) 		0.00253
(0.0282) 		0.0368
(0.195) 		0.119
(0.375) 		0.551
(0.816) 		0.473
(0.767)
CUL3 14 (3%) 496 0.0205
(0.138) 		0.00407
(0.0407) 		0.277
(0.58) 		0.732
(0.897) 		0.335
(0.662) 		0.0275
(0.166) 		0.211
(0.513) 		0.84
(0.942) 		0.00144
(0.0181) 		0.38
(0.713)
HUWE1 45 (9%) 465 0.001
(0.0136) 		0.00055
(0.00842) 		0.886
(0.965) 		0.638
(0.846) 		0.0174
(0.118) 		0.0434
(0.209) 		0.174
(0.461) 		0.666
(0.869) 		0.134
(0.39) 		0.158
(0.444)
MLL4 20 (4%) 490 0.012
(0.0948) 		0.00019
(0.00332) 		0.164
(0.45) 		0.38
(0.713) 		0.00708
(0.0642) 		0.0969
(0.339) 		0.00082
(0.0115) 		0.712
(0.892) 		0.0612
(0.259) 		0.0574
(0.247)
HLA-B 24 (5%) 486 0.158
(0.444) 		0.00151
(0.0185) 		0.799
(0.931) 		0.225
(0.517) 		0.0364
(0.195) 		0.0647
(0.264) 		0.0569
(0.247) 		0.207
(0.512) 		0.0845
(0.314) 		0.0363
(0.195)
FAT1 114 (22%) 396 0.26
(0.561) 		1e-05
(0.000233) 		0.798
(0.931) 		0.487
(0.77) 		0.145
(0.414) 		0.00042
(0.00664) 		0.874
(0.962) 		0.596
(0.831) 		0.00369
(0.0377) 		0.0986
(0.343)
PIK3CA 94 (18%) 416 0.26
(0.561) 		0.209
(0.512) 		0.616
(0.837) 		0.0624
(0.261) 		0.0413
(0.203) 		0.344
(0.669) 		0.00683
(0.0631) 		0.0238
(0.151) 		0.445
(0.754) 		0.0934
(0.334)
EP300 39 (8%) 471 0.447
(0.754) 		0.0343
(0.194) 		0.344
(0.669) 		0.0859
(0.317) 		0.00746
(0.0665) 		0.0913
(0.329) 		0.559
(0.816) 		0.236
(0.528) 		0.0397
(0.201) 		1
(1.00)
RAC1 15 (3%) 495 0.112
(0.362) 		0.0363
(0.195) 		0.689
(0.881) 		0.833
(0.94) 		0.0345
(0.194) 		0.0704
(0.278) 		0.449
(0.754) 		0.407
(0.724) 		0.183
(0.479) 		0.322
(0.642)
KEAP1 22 (4%) 488 0.124
(0.381) 		0.0637
(0.262) 		0.914
(0.971) 		0.826
(0.94) 		0.0953
(0.336) 		0.00111
(0.0147) 		0.27
(0.573) 		0.0369
(0.195) 		0.41
(0.724) 		0.0699
(0.278)
CREBBP 35 (7%) 475 0.0257
(0.157) 		0.568
(0.816) 		1
(1.00) 		0.932
(0.983) 		0.129
(0.386) 		0.13
(0.386) 		0.488
(0.77) 		0.0343
(0.194) 		0.0573
(0.247) 		0.131
(0.386)
SLC9A6 5 (1%) 505 0.00867
(0.0732) 		0.0944
(0.335) 		0.776
(0.923) 		0.115
(0.364) 		0.114
(0.363) 		0.367
(0.703) 		0.0511
(0.236) 		0.229
(0.521) 		0.566
(0.816) 		0.0287
(0.172)
CTCF 16 (3%) 494 0.0497
(0.232) 		0.00161
(0.0192) 		0.16
(0.444) 		0.528
(0.802) 		0.482
(0.77) 		0.277
(0.58) 		0.692
(0.881) 		0.899
(0.965) 		0.738
(0.897) 		0.765
(0.917)
PTPN14 15 (3%) 495 0.0168
(0.116) 		0.12
(0.376) 		1
(1.00) 		0.579
(0.819) 		0.222
(0.517) 		0.717
(0.892) 		0.0463
(0.22) 		0.641
(0.846) 		0.264
(0.568) 		0.453
(0.754)
MLL2 78 (15%) 432 0.034
(0.194) 		0.124
(0.381) 		0.47
(0.765) 		0.326
(0.647) 		0.415
(0.729) 		0.399
(0.719) 		0.453
(0.754) 		0.135
(0.391) 		0.818
(0.94) 		0.185
(0.482)
TGFBR2 23 (5%) 487 0.012
(0.0948) 		0.0574
(0.247) 		0.82
(0.94) 		0.901
(0.965) 		0.102
(0.35) 		0.959
(1.00) 		0.638
(0.846) 		0.573
(0.817) 		0.729
(0.897) 		0.519
(0.795)
JUB 33 (6%) 477 0.201
(0.5) 		0.0564
(0.247) 		0.186
(0.482) 		0.815
(0.94) 		0.0417
(0.203) 		0.626
(0.842) 		0.0545
(0.247) 		0.423
(0.737) 		0.668
(0.869) 		0.511
(0.784)
NFE2L2 26 (5%) 484 0.496
(0.77) 		1e-05
(0.000233) 		0.21
(0.513) 		0.875
(0.962) 		0.846
(0.946) 		0.47
(0.765) 		0.23
(0.521) 		0.494
(0.77) 		0.597
(0.831) 		0.359
(0.689)
EPHA2 24 (5%) 486 0.496
(0.77) 		9e-05
(0.00163) 		0.933
(0.983) 		0.932
(0.983) 		0.306
(0.616) 		0.291
(0.597) 		0.894
(0.965) 		0.164
(0.45) 		0.107
(0.358) 		0.648
(0.854)
RB1 18 (4%) 492 0.602
(0.831) 		0.374
(0.712) 		0.387
(0.719) 		0.275
(0.58) 		0.0374
(0.195) 		0.378
(0.713) 		0.154
(0.437) 		0.496
(0.77) 		0.386
(0.719) 		0.62
(0.837)
KDM6A 17 (3%) 493 0.0308
(0.182) 		0.765
(0.917) 		0.523
(0.798) 		1
(1.00) 		0.901
(0.965) 		0.391
(0.719) 		0.907
(0.969) 		0.862
(0.956) 		0.566
(0.816) 		0.58
(0.819)
NUDT11 8 (2%) 502 0.798
(0.931) 		0.548
(0.816) 		0.0401
(0.201) 		0.732
(0.897) 		0.909
(0.969) 		0.631
(0.844) 		0.449
(0.754) 		0.681
(0.88) 		0.218
(0.517) 		0.744
(0.9)
SMAD4 13 (3%) 497 0.411
(0.724) 		0.782
(0.928) 		0.288
(0.593) 		0.875
(0.962) 		0.267
(0.569) 		0.559
(0.816) 		0.0257
(0.157) 		0.46
(0.757) 		0.7
(0.884) 		0.188
(0.483)
MYH9 22 (4%) 488 0.0159
(0.113) 		0.24
(0.535) 		0.218
(0.517) 		0.469
(0.765) 		0.556
(0.816) 		0.715
(0.892) 		0.705
(0.888) 		0.452
(0.754) 		0.847
(0.946) 		0.456
(0.755)
ITGB1 13 (3%) 497 0.765
(0.917) 		0.0531
(0.243) 		0.342
(0.669) 		0.61
(0.833) 		0.0128
(0.0998) 		0.0823
(0.308) 		0.56
(0.816) 		0.194
(0.491) 		0.178
(0.469) 		0.697
(0.882)
IRS4 17 (3%) 493 0.19
(0.485) 		0.57
(0.817) 		0.798
(0.931) 		0.791
(0.931) 		0.127
(0.383) 		0.0731
(0.282) 		0.216
(0.517) 		0.0635
(0.262) 		0.0158
(0.113) 		0.222
(0.517)
GAGE2A 5 (1%) 505 0.0378
(0.195) 		0.0753
(0.288) 		1
(1.00) 		0.794
(0.931) 		0.187
(0.483) 		0.248
(0.545) 		0.74
(0.897) 		0.32
(0.64) 		0.297
(0.603) 		1
(1.00)
FBXW7 33 (6%) 477 0.454
(0.754) 		0.149
(0.425) 		0.13
(0.386) 		0.232
(0.521) 		0.126
(0.383) 		0.459
(0.757) 		0.297
(0.603) 		0.485
(0.77) 		0.209
(0.512) 		0.113
(0.362)
PTEN 14 (3%) 496 0.677
(0.878) 		0.445
(0.754) 		0.198
(0.496) 		0.834
(0.94) 		0.0818
(0.308) 		0.244
(0.539) 		0.376
(0.713) 		0.224
(0.517) 		0.113
(0.362) 		0.109
(0.361)
RASA1 17 (3%) 493 0.167
(0.454) 		0.0703
(0.278) 		0.549
(0.816) 		0.714
(0.892) 		0.424
(0.737) 		0.492
(0.77) 		0.552
(0.816) 		0.406
(0.724) 		0.406
(0.724) 		0.162
(0.449)
MAPK1 9 (2%) 501 0.105
(0.354) 		0.532
(0.805) 		0.83
(0.94) 		0.832
(0.94) 		0.446
(0.754) 		0.918
(0.974) 		0.485
(0.77) 		0.836
(0.94) 		1
(1.00) 		0.738
(0.897)
NAP1L2 7 (1%) 503 0.393
(0.719) 		0.581
(0.819) 		0.883
(0.965) 		0.478
(0.77) 		0.81
(0.939) 		0.898
(0.965) 		0.898
(0.965) 		0.603
(0.831)
RHOA 10 (2%) 500 0.106
(0.355) 		0.573
(0.817) 		0.111
(0.362) 		0.242
(0.537) 		1
(1.00) 		1
(1.00) 		0.724
(0.897) 		0.563
(0.816) 		0.685
(0.881) 		0.69
(0.881)
EMG1 4 (1%) 506 0.878
(0.962) 		0.267
(0.569) 		0.197
(0.496) 		0.61
(0.833) 		0.104
(0.354) 		0.815
(0.94) 		0.695
(0.882) 		1
(1.00) 		0.252
(0.552) 		0.437
(0.754)
TIGD4 7 (1%) 503 0.498
(0.77) 		0.772
(0.921) 		1
(1.00) 		0.835
(0.94) 		0.725
(0.897) 		0.395
(0.719) 		0.653
(0.857) 		0.398
(0.719) 		0.957
(1.00) 		0.688
(0.881)
C3ORF59 11 (2%) 499 0.609
(0.833) 		0.22
(0.517) 		0.862
(0.956) 		0.399
(0.719) 		0.8
(0.931) 		0.64
(0.846) 		0.686
(0.881) 		0.302
(0.612)
ZNF623 11 (2%) 499 0.224
(0.517) 		0.786
(0.93) 		0.193
(0.491) 		0.445
(0.754) 		0.343
(0.669) 		0.17
(0.457) 		0.548
(0.816) 		0.1
(0.346) 		0.417
(0.729) 		0.228
(0.521)
NCOR1 18 (4%) 492 0.877
(0.962) 		0.0895
(0.325) 		0.282
(0.586) 		0.497
(0.77) 		0.62
(0.837) 		0.169
(0.457) 		0.539
(0.812) 		0.111
(0.362) 		0.529
(0.802) 		0.853
(0.95)
SRPX 7 (1%) 503 0.627
(0.842) 		0.985
(1.00) 		0.388
(0.719) 		1
(1.00) 		1
(1.00) 		0.604
(0.831) 		0.729
(0.897) 		1
(1.00) 		0.587
(0.825) 		0.411
(0.724)
KIAA1949 6 (1%) 504 0.808
(0.938) 		0.484
(0.77) 		0.772
(0.921) 		0.834
(0.94) 		0.669
(0.869) 		1
(1.00) 		0.578
(0.819) 		0.563
(0.816)
NOTCH2 20 (4%) 490 0.451
(0.754) 		0.397
(0.719) 		0.0786
(0.299) 		0.347
(0.671) 		0.595
(0.831) 		0.307
(0.616) 		0.504
(0.777) 		0.485
(0.77) 		0.902
(0.965) 		0.601
(0.831)
LCP1 15 (3%) 495 0.0724
(0.282) 		0.0887
(0.324) 		0.394
(0.719) 		0.826
(0.94) 		0.756
(0.912) 		0.0719
(0.282) 		0.947
(0.996) 		0.894
(0.965) 		0.738
(0.897) 		0.258
(0.561)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
TP53 MUTATED 131 117 80 27
TP53 WILD-TYPE 16 13 105 15

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
TP53 MUTATED 62 64 84 82 8 44 15
TP53 WILD-TYPE 22 11 10 6 68 30 4

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
TP53 MUTATED 50 49 65
TP53 WILD-TYPE 17 14 15
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
TP53 MUTATED 62 68 34
TP53 WILD-TYPE 16 17 13
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
TP53 MUTATED 119 126 109
TP53 WILD-TYPE 20 79 49

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
TP53 MUTATED 144 84 117 9
TP53 WILD-TYPE 32 15 48 53

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00482 (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
ALL 209 151 145
TP53 MUTATED 138 101 117
TP53 WILD-TYPE 71 50 28

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
TP53 MUTATED 155 113 88
TP53 WILD-TYPE 33 24 92

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
TP53 MUTATED 54 100 62 92 18
TP53 WILD-TYPE 14 39 31 22 28

Figure S7.  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 = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
TP53 MUTATED 115 144 67
TP53 WILD-TYPE 23 94 17

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.15

Table S11.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CDKN2A MUTATED 38 28 30 15
CDKN2A WILD-TYPE 109 102 155 27

Figure S9.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S12.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
CDKN2A MUTATED 20 12 30 23 1 22 4
CDKN2A WILD-TYPE 64 63 64 65 75 52 15

Figure S10.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0419 (Fisher's exact test), Q value = 0.2

Table S13.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
CDKN2A MUTATED 13 24 19
CDKN2A WILD-TYPE 54 39 61

Figure S11.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.717 (Fisher's exact test), Q value = 0.89

Table S14.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
CDKN2A MUTATED 23 20 13
CDKN2A WILD-TYPE 55 65 34
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.16

Table S15.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CDKN2A MUTATED 30 35 46
CDKN2A WILD-TYPE 109 170 112

Figure S12.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S16.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CDKN2A MUTATED 46 24 40 1
CDKN2A WILD-TYPE 130 75 125 61

Figure S13.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.51

Table S17.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CDKN2A MUTATED 38 37 36
CDKN2A WILD-TYPE 171 114 109
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0584 (Fisher's exact test), Q value = 0.25

Table S18.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CDKN2A MUTATED 52 27 32
CDKN2A WILD-TYPE 136 110 148
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.026

Table S19.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
CDKN2A MUTATED 11 39 14 35 4
CDKN2A WILD-TYPE 57 100 79 79 42

Figure S14.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0392 (Fisher's exact test), Q value = 0.2

Table S20.  Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
CDKN2A MUTATED 38 42 23
CDKN2A WILD-TYPE 100 196 61

Figure S15.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S21.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CASP8 MUTATED 7 0 41 6
CASP8 WILD-TYPE 140 130 144 36

Figure S16.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CASP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S22.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
CASP8 MUTATED 8 2 5 1 0 36 3
CASP8 WILD-TYPE 76 73 89 87 76 38 16

Figure S17.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.0064

Table S23.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
CASP8 MUTATED 1 14 7
CASP8 WILD-TYPE 66 49 73

Figure S18.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 0.68

Table S24.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
CASP8 MUTATED 11 6 5
CASP8 WILD-TYPE 67 79 42
'CASP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S25.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CASP8 MUTATED 10 7 38
CASP8 WILD-TYPE 129 198 120

Figure S19.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S26.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CASP8 MUTATED 16 4 35 0
CASP8 WILD-TYPE 160 95 130 62

Figure S20.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00922 (Fisher's exact test), Q value = 0.077

Table S27.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CASP8 MUTATED 15 26 13
CASP8 WILD-TYPE 194 125 132

Figure S21.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.82

Table S28.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CASP8 MUTATED 18 18 18
CASP8 WILD-TYPE 170 119 162
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00024 (Fisher's exact test), Q value = 0.0041

Table S29.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
CASP8 MUTATED 4 27 2 15 3
CASP8 WILD-TYPE 64 112 91 99 43

Figure S22.  Get High-res Image Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.39

Table S30.  Gene #3: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
CASP8 MUTATED 16 21 14
CASP8 WILD-TYPE 122 217 70
'NSD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00421 (Fisher's exact test), Q value = 0.041

Table S31.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
NSD1 MUTATED 20 26 14 2
NSD1 WILD-TYPE 127 104 171 40

Figure S23.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NSD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S32.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
NSD1 MUTATED 4 49 1 1 5 3 0
NSD1 WILD-TYPE 80 26 93 87 71 71 19

Figure S24.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.46

Table S33.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
NSD1 MUTATED 6 10 5
NSD1 WILD-TYPE 61 53 75
'NSD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.11

Table S34.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NSD1 MUTATED 7 4 10
NSD1 WILD-TYPE 71 81 37

Figure S25.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00061

Table S35.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
NSD1 MUTATED 9 43 10
NSD1 WILD-TYPE 130 162 148

Figure S26.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S36.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
NSD1 MUTATED 10 40 6 6
NSD1 WILD-TYPE 166 59 159 56

Figure S27.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00278 (Fisher's exact test), Q value = 0.03

Table S37.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
NSD1 MUTATED 38 16 9
NSD1 WILD-TYPE 171 135 136

Figure S28.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S38.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
NSD1 MUTATED 12 32 19
NSD1 WILD-TYPE 176 105 161

Figure S29.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S39.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
NSD1 MUTATED 6 10 29 9 5
NSD1 WILD-TYPE 62 129 64 105 41

Figure S30.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S40.  Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
NSD1 MUTATED 12 46 1
NSD1 WILD-TYPE 126 192 83

Figure S31.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.44

Table S41.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
HLA-B MUTATED 5 3 13 3
HLA-B WILD-TYPE 142 127 172 39
'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00151 (Fisher's exact test), Q value = 0.018

Table S42.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
HLA-B MUTATED 1 1 3 4 3 12 0
HLA-B WILD-TYPE 83 74 91 84 73 62 19

Figure S32.  Get High-res Image Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 0.93

Table S43.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
HLA-B MUTATED 2 3 2
HLA-B WILD-TYPE 65 60 78
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 0.52

Table S44.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
HLA-B MUTATED 3 1 3
HLA-B WILD-TYPE 75 84 44
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.19

Table S45.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
HLA-B MUTATED 3 7 13
HLA-B WILD-TYPE 136 198 145

Figure S33.  Get High-res Image Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0647 (Fisher's exact test), Q value = 0.26

Table S46.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
HLA-B MUTATED 4 5 13 1
HLA-B WILD-TYPE 172 94 152 61
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0569 (Fisher's exact test), Q value = 0.25

Table S47.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
HLA-B MUTATED 13 9 2
HLA-B WILD-TYPE 196 142 143
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.51

Table S48.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
HLA-B MUTATED 5 8 11
HLA-B WILD-TYPE 183 129 169
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0845 (Fisher's exact test), Q value = 0.31

Table S49.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
HLA-B MUTATED 0 12 4 5 2
HLA-B WILD-TYPE 68 127 89 109 44
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0363 (Fisher's exact test), Q value = 0.19

Table S50.  Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
HLA-B MUTATED 2 14 7
HLA-B WILD-TYPE 136 224 77

Figure S34.  Get High-res Image Gene #5: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.034 (Fisher's exact test), Q value = 0.19

Table S51.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
MLL2 MUTATED 19 30 21 7
MLL2 WILD-TYPE 128 100 164 35

Figure S35.  Get High-res Image Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.38

Table S52.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
MLL2 MUTATED 8 15 12 21 11 10 1
MLL2 WILD-TYPE 76 60 82 67 65 64 18
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.77

Table S53.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
MLL2 MUTATED 15 10 12
MLL2 WILD-TYPE 52 53 68
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.65

Table S54.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
MLL2 MUTATED 14 18 5
MLL2 WILD-TYPE 64 67 42
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 0.73

Table S55.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
MLL2 MUTATED 17 36 23
MLL2 WILD-TYPE 122 169 135
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 0.72

Table S56.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
MLL2 MUTATED 21 19 27 9
MLL2 WILD-TYPE 155 80 138 53
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.75

Table S57.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
MLL2 MUTATED 37 21 19
MLL2 WILD-TYPE 172 130 126
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.39

Table S58.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
MLL2 MUTATED 22 27 28
MLL2 WILD-TYPE 166 110 152
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 0.94

Table S59.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
MLL2 MUTATED 10 17 16 19 7
MLL2 WILD-TYPE 58 122 77 95 39
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.48

Table S60.  Gene #6: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
MLL2 MUTATED 19 42 8
MLL2 WILD-TYPE 119 196 76
'TGFBR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.095

Table S61.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
TGFBR2 MUTATED 5 1 15 2
TGFBR2 WILD-TYPE 142 129 170 40

Figure S36.  Get High-res Image Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0574 (Fisher's exact test), Q value = 0.25

Table S62.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
TGFBR2 MUTATED 4 5 3 1 1 8 1
TGFBR2 WILD-TYPE 80 70 91 87 75 66 18
'TGFBR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 0.94

Table S63.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
TGFBR2 MUTATED 2 2 4
TGFBR2 WILD-TYPE 65 61 76
'TGFBR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.901 (Fisher's exact test), Q value = 0.96

Table S64.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
TGFBR2 MUTATED 3 4 1
TGFBR2 WILD-TYPE 75 81 46
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.35

Table S65.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
TGFBR2 MUTATED 5 6 12
TGFBR2 WILD-TYPE 134 199 146
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S66.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
TGFBR2 MUTATED 9 4 8 2
TGFBR2 WILD-TYPE 167 95 157 60
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 0.85

Table S67.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
TGFBR2 MUTATED 8 9 6
TGFBR2 WILD-TYPE 201 142 139
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.82

Table S68.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
TGFBR2 MUTATED 9 8 6
TGFBR2 WILD-TYPE 179 129 174
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 0.9

Table S69.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
TGFBR2 MUTATED 3 9 3 4 3
TGFBR2 WILD-TYPE 65 130 90 110 43
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.519 (Fisher's exact test), Q value = 0.8

Table S70.  Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
TGFBR2 MUTATED 6 10 6
TGFBR2 WILD-TYPE 132 228 78
'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.56

Table S71.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
FAT1 MUTATED 26 34 41 12
FAT1 WILD-TYPE 121 96 144 30
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S72.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
FAT1 MUTATED 16 15 20 23 3 34 3
FAT1 WILD-TYPE 68 60 74 65 73 40 16

Figure S37.  Get High-res Image Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 0.93

Table S73.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
FAT1 MUTATED 15 12 19
FAT1 WILD-TYPE 52 51 61
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.77

Table S74.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
FAT1 MUTATED 16 22 8
FAT1 WILD-TYPE 62 63 39
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.41

Table S75.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
FAT1 MUTATED 31 38 43
FAT1 WILD-TYPE 108 167 115
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0066

Table S76.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
FAT1 MUTATED 41 20 48 3
FAT1 WILD-TYPE 135 79 117 59

Figure S38.  Get High-res Image Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 0.96

Table S77.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
FAT1 MUTATED 44 35 33
FAT1 WILD-TYPE 165 116 112
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.83

Table S78.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
FAT1 MUTATED 46 30 36
FAT1 WILD-TYPE 142 107 144
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00369 (Fisher's exact test), Q value = 0.038

Table S79.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
FAT1 MUTATED 16 44 16 26 3
FAT1 WILD-TYPE 52 95 77 88 43

Figure S39.  Get High-res Image Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0986 (Fisher's exact test), Q value = 0.34

Table S80.  Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
FAT1 MUTATED 36 45 24
FAT1 WILD-TYPE 102 193 60
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0155 (Fisher's exact test), Q value = 0.11

Table S81.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
NOTCH1 MUTATED 31 11 34 9
NOTCH1 WILD-TYPE 116 119 151 33

Figure S40.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.00075

Table S82.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
NOTCH1 MUTATED 19 5 19 14 3 23 4
NOTCH1 WILD-TYPE 65 70 75 74 73 51 15

Figure S41.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 0.96

Table S83.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
NOTCH1 MUTATED 12 13 14
NOTCH1 WILD-TYPE 55 50 66
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0574 (Fisher's exact test), Q value = 0.25

Table S84.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NOTCH1 MUTATED 21 11 7
NOTCH1 WILD-TYPE 57 74 40
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S85.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
NOTCH1 MUTATED 30 15 41
NOTCH1 WILD-TYPE 109 190 117

Figure S42.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00114 (Fisher's exact test), Q value = 0.015

Table S86.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
NOTCH1 MUTATED 37 10 36 3
NOTCH1 WILD-TYPE 139 89 129 59

Figure S43.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S87.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
NOTCH1 MUTATED 16 39 31
NOTCH1 WILD-TYPE 193 112 114

Figure S44.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0677 (Fisher's exact test), Q value = 0.27

Table S88.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
NOTCH1 MUTATED 41 22 23
NOTCH1 WILD-TYPE 147 115 157
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00864 (Fisher's exact test), Q value = 0.073

Table S89.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
NOTCH1 MUTATED 13 30 6 22 4
NOTCH1 WILD-TYPE 55 109 87 92 42

Figure S45.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.19

Table S90.  Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
NOTCH1 MUTATED 32 31 12
NOTCH1 WILD-TYPE 106 207 72

Figure S46.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'JUB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
JUB MUTATED 7 14 10 2
JUB WILD-TYPE 140 116 175 40
'JUB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0564 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
JUB MUTATED 1 5 6 9 2 8 2
JUB WILD-TYPE 83 70 88 79 74 66 17
'JUB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
JUB MUTATED 5 6 2
JUB WILD-TYPE 62 57 78
'JUB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.815 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
JUB MUTATED 6 5 2
JUB WILD-TYPE 72 80 45
'JUB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0417 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
JUB MUTATED 4 13 16
JUB WILD-TYPE 135 192 142

Figure S47.  Get High-res Image Gene #10: 'JUB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'JUB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
JUB MUTATED 9 8 13 3
JUB WILD-TYPE 167 91 152 59
'JUB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0545 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
JUB MUTATED 19 10 4
JUB WILD-TYPE 190 141 141
'JUB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
JUB MUTATED 9 11 13
JUB WILD-TYPE 179 126 167
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
JUB MUTATED 2 11 8 9 3
JUB WILD-TYPE 66 128 85 105 43
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
JUB MUTATED 7 20 6
JUB WILD-TYPE 131 218 78
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.77

Table S101.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
NFE2L2 MUTATED 5 9 9 3
NFE2L2 WILD-TYPE 142 121 176 39
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

Table S102.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
NFE2L2 MUTATED 1 3 0 14 1 7 0
NFE2L2 WILD-TYPE 83 72 94 74 75 67 19

Figure S48.  Get High-res Image Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.51

Table S103.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
NFE2L2 MUTATED 6 5 2
NFE2L2 WILD-TYPE 61 58 78
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 0.96

Table S104.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NFE2L2 MUTATED 5 6 2
NFE2L2 WILD-TYPE 73 79 45
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 0.95

Table S105.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
NFE2L2 MUTATED 7 12 7
NFE2L2 WILD-TYPE 132 193 151
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.47 (Fisher's exact test), Q value = 0.77

Table S106.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
NFE2L2 MUTATED 7 8 9 2
NFE2L2 WILD-TYPE 169 91 156 60
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.52

Table S107.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
NFE2L2 MUTATED 13 4 9
NFE2L2 WILD-TYPE 196 147 136
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.77

Table S108.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
NFE2L2 MUTATED 9 5 12
NFE2L2 WILD-TYPE 179 132 168
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 0.83

Table S109.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
NFE2L2 MUTATED 3 6 4 10 2
NFE2L2 WILD-TYPE 65 133 89 104 44
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.69

Table S110.  Gene #11: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
NFE2L2 MUTATED 7 16 2
NFE2L2 WILD-TYPE 131 222 82
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.75

Table S111.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
FBXW7 MUTATED 9 11 9 4
FBXW7 WILD-TYPE 138 119 176 38
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.42

Table S112.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
FBXW7 MUTATED 1 6 6 8 3 8 1
FBXW7 WILD-TYPE 83 69 88 80 73 66 18
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.39

Table S113.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
FBXW7 MUTATED 2 1 7
FBXW7 WILD-TYPE 65 62 73
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.52

Table S114.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
FBXW7 MUTATED 2 7 1
FBXW7 WILD-TYPE 76 78 46
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.38

Table S115.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
FBXW7 MUTATED 4 16 12
FBXW7 WILD-TYPE 135 189 146
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.76

Table S116.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
FBXW7 MUTATED 8 9 12 3
FBXW7 WILD-TYPE 168 90 153 59
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.6

Table S117.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
FBXW7 MUTATED 14 13 6
FBXW7 WILD-TYPE 195 138 139
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.485 (Fisher's exact test), Q value = 0.77

Table S118.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
FBXW7 MUTATED 11 12 10
FBXW7 WILD-TYPE 177 125 170
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.51

Table S119.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
FBXW7 MUTATED 3 13 8 4 1
FBXW7 WILD-TYPE 65 126 85 110 45
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.36

Table S120.  Gene #12: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
FBXW7 MUTATED 5 15 9
FBXW7 WILD-TYPE 133 223 75
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.51

Table S121.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
ZNF750 MUTATED 2 7 9 1
ZNF750 WILD-TYPE 145 123 176 41
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0108 (Fisher's exact test), Q value = 0.088

Table S122.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
ZNF750 MUTATED 1 3 0 5 8 2 0
ZNF750 WILD-TYPE 83 72 94 83 68 72 19

Figure S49.  Get High-res Image Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.58

Table S123.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
ZNF750 MUTATED 3 0 2
ZNF750 WILD-TYPE 64 63 78
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.59

Table S124.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ZNF750 MUTATED 1 4 0
ZNF750 WILD-TYPE 77 81 47
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00777 (Fisher's exact test), Q value = 0.068

Table S125.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
ZNF750 MUTATED 3 13 1
ZNF750 WILD-TYPE 136 192 157

Figure S50.  Get High-res Image Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.11

Table S126.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
ZNF750 MUTATED 3 5 3 6
ZNF750 WILD-TYPE 173 94 162 56

Figure S51.  Get High-res Image Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.11

Table S127.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
ZNF750 MUTATED 14 2 3
ZNF750 WILD-TYPE 195 149 142

Figure S52.  Get High-res Image Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.39

Table S128.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
ZNF750 MUTATED 4 4 11
ZNF750 WILD-TYPE 184 133 169
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0491 (Fisher's exact test), Q value = 0.23

Table S129.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
ZNF750 MUTATED 3 3 6 2 5
ZNF750 WILD-TYPE 65 136 87 112 41

Figure S53.  Get High-res Image Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.15

Table S130.  Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
ZNF750 MUTATED 4 15 0
ZNF750 WILD-TYPE 134 223 84

Figure S54.  Get High-res Image Gene #13: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.36

Table S131.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
RAC1 MUTATED 3 1 9 2
RAC1 WILD-TYPE 144 129 176 40
'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0363 (Fisher's exact test), Q value = 0.19

Table S132.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
RAC1 MUTATED 4 0 2 1 1 5 2
RAC1 WILD-TYPE 80 75 92 87 75 69 17

Figure S55.  Get High-res Image Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 0.88

Table S133.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
RAC1 MUTATED 1 2 1
RAC1 WILD-TYPE 66 61 79
'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 0.94

Table S134.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
RAC1 MUTATED 2 1 1
RAC1 WILD-TYPE 76 84 46
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0345 (Fisher's exact test), Q value = 0.19

Table S135.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
RAC1 MUTATED 1 4 9
RAC1 WILD-TYPE 138 201 149

Figure S56.  Get High-res Image Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0704 (Fisher's exact test), Q value = 0.28

Table S136.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
RAC1 MUTATED 2 1 9 2
RAC1 WILD-TYPE 174 98 156 60
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.75

Table S137.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
RAC1 MUTATED 8 5 2
RAC1 WILD-TYPE 201 146 143
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.407 (Fisher's exact test), Q value = 0.72

Table S138.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
RAC1 MUTATED 4 3 8
RAC1 WILD-TYPE 184 134 172
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.48

Table S139.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
RAC1 MUTATED 0 8 2 2 1
RAC1 WILD-TYPE 68 131 91 112 45
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 0.64

Table S140.  Gene #14: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
RAC1 MUTATED 2 7 4
RAC1 WILD-TYPE 136 231 80
'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.77

Table S141.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
EPHA2 MUTATED 7 3 11 2
EPHA2 WILD-TYPE 140 127 174 40
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S142.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
EPHA2 MUTATED 0 5 4 0 2 11 2
EPHA2 WILD-TYPE 84 70 90 88 74 63 17

Figure S57.  Get High-res Image Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 0.98

Table S143.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
EPHA2 MUTATED 4 4 4
EPHA2 WILD-TYPE 63 59 76
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 0.98

Table S144.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
EPHA2 MUTATED 5 5 2
EPHA2 WILD-TYPE 73 80 45
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.62

Table S145.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
EPHA2 MUTATED 6 7 11
EPHA2 WILD-TYPE 133 198 147
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 0.6

Table S146.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
EPHA2 MUTATED 8 3 12 1
EPHA2 WILD-TYPE 168 96 153 61
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 0.96

Table S147.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
EPHA2 MUTATED 9 8 6
EPHA2 WILD-TYPE 200 143 139
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.45

Table S148.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
EPHA2 MUTATED 8 10 5
EPHA2 WILD-TYPE 180 127 175
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.36

Table S149.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
EPHA2 MUTATED 1 9 2 8 0
EPHA2 WILD-TYPE 67 130 91 106 46
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 0.85

Table S150.  Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
EPHA2 MUTATED 6 9 5
EPHA2 WILD-TYPE 132 229 79
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.033

Table S151.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
HLA-A MUTATED 3 1 15 3
HLA-A WILD-TYPE 144 129 170 39

Figure S58.  Get High-res Image Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0032 (Fisher's exact test), Q value = 0.033

Table S152.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
HLA-A MUTATED 2 1 2 2 4 11 0
HLA-A WILD-TYPE 82 74 92 86 72 63 19

Figure S59.  Get High-res Image Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.52

Table S153.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
HLA-A MUTATED 0 3 2
HLA-A WILD-TYPE 67 60 78
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 0.85

Table S154.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
HLA-A MUTATED 1 2 2
HLA-A WILD-TYPE 77 83 45
'HLA-A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00465 (Fisher's exact test), Q value = 0.045

Table S155.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
HLA-A MUTATED 1 8 13
HLA-A WILD-TYPE 138 197 145

Figure S60.  Get High-res Image Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00253 (Fisher's exact test), Q value = 0.028

Table S156.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
HLA-A MUTATED 3 1 15 3
HLA-A WILD-TYPE 173 98 150 59

Figure S61.  Get High-res Image Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.19

Table S157.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
HLA-A MUTATED 7 12 3
HLA-A WILD-TYPE 202 139 142

Figure S62.  Get High-res Image Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.37

Table S158.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
HLA-A MUTATED 4 9 9
HLA-A WILD-TYPE 184 128 171
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 0.82

Table S159.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
HLA-A MUTATED 3 10 2 5 2
HLA-A WILD-TYPE 65 129 91 109 44
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.77

Table S160.  Gene #16: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
HLA-A MUTATED 5 11 6
HLA-A WILD-TYPE 133 227 78
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
HRAS MUTATED 3 0 22 3
HRAS WILD-TYPE 144 130 163 39

Figure S63.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00023

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
HRAS MUTATED 4 2 2 1 0 19 1
HRAS WILD-TYPE 80 73 92 87 76 55 18

Figure S64.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
HRAS MUTATED 0 6 2
HRAS WILD-TYPE 67 57 78

Figure S65.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
HRAS MUTATED 4 2 2
HRAS WILD-TYPE 74 83 45
'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0095

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
HRAS MUTATED 7 4 18
HRAS WILD-TYPE 132 201 140

Figure S66.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0021 (Fisher's exact test), Q value = 0.024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
HRAS MUTATED 9 2 18 0
HRAS WILD-TYPE 167 97 147 62

Figure S67.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00066 (Fisher's exact test), Q value = 0.0095

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
HRAS MUTATED 5 18 6
HRAS WILD-TYPE 204 133 139

Figure S68.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.38

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
HRAS MUTATED 10 4 15
HRAS WILD-TYPE 178 133 165
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.023 (Fisher's exact test), Q value = 0.15

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
HRAS MUTATED 3 15 1 8 1
HRAS WILD-TYPE 65 124 92 106 45

Figure S69.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
HRAS MUTATED 7 12 9
HRAS WILD-TYPE 131 226 75
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.56

Table S171.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
PIK3CA MUTATED 20 25 40 6
PIK3CA WILD-TYPE 127 105 145 36
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.51

Table S172.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
PIK3CA MUTATED 15 11 12 20 21 13 2
PIK3CA WILD-TYPE 69 64 82 68 55 61 17
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.84

Table S173.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
PIK3CA MUTATED 11 11 18
PIK3CA WILD-TYPE 56 52 62
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0624 (Fisher's exact test), Q value = 0.26

Table S174.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
PIK3CA MUTATED 15 11 14
PIK3CA WILD-TYPE 63 74 33
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.2

Table S175.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
PIK3CA MUTATED 17 47 29
PIK3CA WILD-TYPE 122 158 129

Figure S70.  Get High-res Image Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.67

Table S176.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
PIK3CA MUTATED 26 19 33 15
PIK3CA WILD-TYPE 150 80 132 47
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.063

Table S177.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
PIK3CA MUTATED 47 32 15
PIK3CA WILD-TYPE 162 119 130

Figure S71.  Get High-res Image Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0238 (Fisher's exact test), Q value = 0.15

Table S178.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
PIK3CA MUTATED 30 19 45
PIK3CA WILD-TYPE 158 118 135

Figure S72.  Get High-res Image Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.75

Table S179.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
PIK3CA MUTATED 13 20 22 23 7
PIK3CA WILD-TYPE 55 119 71 91 39
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0934 (Fisher's exact test), Q value = 0.33

Table S180.  Gene #18: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
PIK3CA MUTATED 21 53 11
PIK3CA WILD-TYPE 117 185 73
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.75

Table S181.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
EP300 MUTATED 9 8 17 5
EP300 WILD-TYPE 138 122 168 37
'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.19

Table S182.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
EP300 MUTATED 5 3 2 9 8 11 1
EP300 WILD-TYPE 79 72 92 79 68 63 18

Figure S73.  Get High-res Image Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.67

Table S183.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
EP300 MUTATED 4 6 3
EP300 WILD-TYPE 63 57 77
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0859 (Fisher's exact test), Q value = 0.32

Table S184.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
EP300 MUTATED 7 6 0
EP300 WILD-TYPE 71 79 47
'EP300 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00746 (Fisher's exact test), Q value = 0.066

Table S185.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
EP300 MUTATED 9 9 21
EP300 WILD-TYPE 130 196 137

Figure S74.  Get High-res Image Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0913 (Fisher's exact test), Q value = 0.33

Table S186.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
EP300 MUTATED 13 3 19 4
EP300 WILD-TYPE 163 96 146 58
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 0.82

Table S187.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
EP300 MUTATED 14 14 9
EP300 WILD-TYPE 195 137 136
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.236 (Fisher's exact test), Q value = 0.53

Table S188.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
EP300 MUTATED 12 7 18
EP300 WILD-TYPE 176 130 162
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0397 (Fisher's exact test), Q value = 0.2

Table S189.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
EP300 MUTATED 1 14 3 11 5
EP300 WILD-TYPE 67 125 90 103 41

Figure S75.  Get High-res Image Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S190.  Gene #19: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
EP300 MUTATED 10 18 6
EP300 WILD-TYPE 128 220 78
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 0.83

Table S191.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
RB1 MUTATED 3 5 9 1
RB1 WILD-TYPE 144 125 176 41
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.71

Table S192.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
RB1 MUTATED 1 3 2 3 6 2 1
RB1 WILD-TYPE 83 72 92 85 70 72 18
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.72

Table S193.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
RB1 MUTATED 1 0 3
RB1 WILD-TYPE 66 63 77
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.58

Table S194.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
RB1 MUTATED 0 3 1
RB1 WILD-TYPE 78 82 46
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.19

Table S195.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
RB1 MUTATED 1 12 5
RB1 WILD-TYPE 138 193 153

Figure S76.  Get High-res Image Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 0.71

Table S196.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
RB1 MUTATED 5 6 4 3
RB1 WILD-TYPE 171 93 161 59
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.44

Table S197.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
RB1 MUTATED 11 3 3
RB1 WILD-TYPE 198 148 142
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 0.77

Table S198.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
RB1 MUTATED 4 6 7
RB1 WILD-TYPE 184 131 173
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 0.72

Table S199.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
RB1 MUTATED 1 4 3 4 4
RB1 WILD-TYPE 67 135 90 110 42
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 0.84

Table S200.  Gene #20: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
RB1 MUTATED 3 10 3
RB1 WILD-TYPE 135 228 81
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
PTEN MUTATED 5 3 4 2
PTEN WILD-TYPE 142 127 181 40
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.75

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
PTEN MUTATED 1 3 1 3 4 1 1
PTEN WILD-TYPE 83 72 93 85 72 73 18
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
PTEN MUTATED 3 0 1
PTEN WILD-TYPE 64 63 79
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
PTEN MUTATED 2 1 1
PTEN WILD-TYPE 76 84 46
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0818 (Fisher's exact test), Q value = 0.31

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
PTEN MUTATED 2 10 2
PTEN WILD-TYPE 137 195 156
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
PTEN MUTATED 2 4 5 3
PTEN WILD-TYPE 174 95 160 59
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
PTEN MUTATED 8 3 2
PTEN WILD-TYPE 201 148 143
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
PTEN MUTATED 2 5 6
PTEN WILD-TYPE 186 132 174
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
PTEN MUTATED 1 2 6 1 1
PTEN WILD-TYPE 67 137 87 113 45
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
PTEN MUTATED 2 9 0
PTEN WILD-TYPE 136 229 84
'RASA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.45

Table S211.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
RASA1 MUTATED 8 5 3 0
RASA1 WILD-TYPE 139 125 182 42
'RASA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0703 (Fisher's exact test), Q value = 0.28

Table S212.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
RASA1 MUTATED 4 0 6 5 0 2 0
RASA1 WILD-TYPE 80 75 88 83 76 72 19
'RASA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.82

Table S213.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
RASA1 MUTATED 5 2 3
RASA1 WILD-TYPE 62 61 77
'RASA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 0.89

Table S214.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
RASA1 MUTATED 5 3 2
RASA1 WILD-TYPE 73 82 45
'RASA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.74

Table S215.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
RASA1 MUTATED 7 5 5
RASA1 WILD-TYPE 132 200 153
'RASA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.492 (Fisher's exact test), Q value = 0.77

Table S216.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
RASA1 MUTATED 7 4 6 0
RASA1 WILD-TYPE 169 95 159 62
'RASA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 0.82

Table S217.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
RASA1 MUTATED 6 4 7
RASA1 WILD-TYPE 203 147 138
'RASA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.406 (Fisher's exact test), Q value = 0.72

Table S218.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
RASA1 MUTATED 9 4 4
RASA1 WILD-TYPE 179 133 176
'RASA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.72

Table S219.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
RASA1 MUTATED 4 3 4 3 0
RASA1 WILD-TYPE 64 136 89 111 46
'RASA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.162 (Fisher's exact test), Q value = 0.45

Table S220.  Gene #22: 'RASA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
RASA1 MUTATED 7 4 3
RASA1 WILD-TYPE 131 234 81
'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.35

Table S221.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
MAPK1 MUTATED 0 2 6 1
MAPK1 WILD-TYPE 147 128 179 41
'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 0.8

Table S222.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
MAPK1 MUTATED 2 1 0 1 3 2 0
MAPK1 WILD-TYPE 82 74 94 87 73 72 19
'MAPK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 0.94

Table S223.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
MAPK1 MUTATED 2 1 1
MAPK1 WILD-TYPE 65 62 79
'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.832 (Fisher's exact test), Q value = 0.94

Table S224.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
MAPK1 MUTATED 2 1 1
MAPK1 WILD-TYPE 76 84 46
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.75

Table S225.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
MAPK1 MUTATED 1 3 4
MAPK1 WILD-TYPE 138 202 154
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.918 (Fisher's exact test), Q value = 0.97

Table S226.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
MAPK1 MUTATED 2 2 3 1
MAPK1 WILD-TYPE 174 97 162 61
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.77

Table S227.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
MAPK1 MUTATED 4 4 1
MAPK1 WILD-TYPE 205 147 144
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 0.94

Table S228.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
MAPK1 MUTATED 3 2 4
MAPK1 WILD-TYPE 185 135 176
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S229.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
MAPK1 MUTATED 1 3 2 2 1
MAPK1 WILD-TYPE 67 136 91 112 45
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.738 (Fisher's exact test), Q value = 0.9

Table S230.  Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
MAPK1 MUTATED 2 6 1
MAPK1 WILD-TYPE 136 232 83
'NAP1L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.72

Table S231.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
NAP1L2 MUTATED 4 2 1 0
NAP1L2 WILD-TYPE 143 128 184 42
'NAP1L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 0.82

Table S232.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
NAP1L2 MUTATED 0 1 3 2 0 1 0
NAP1L2 WILD-TYPE 84 74 91 86 76 73 19
'NAP1L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 0.96

Table S233.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
NAP1L2 MUTATED 1 3 2
NAP1L2 WILD-TYPE 138 202 156
'NAP1L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.478 (Fisher's exact test), Q value = 0.77

Table S234.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
NAP1L2 MUTATED 1 2 3 0
NAP1L2 WILD-TYPE 175 97 162 62
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.81 (Fisher's exact test), Q value = 0.94

Table S235.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
NAP1L2 MUTATED 4 2 1
NAP1L2 WILD-TYPE 205 149 144
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.898 (Fisher's exact test), Q value = 0.96

Table S236.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
NAP1L2 MUTATED 2 2 3
NAP1L2 WILD-TYPE 186 135 177
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 0.96

Table S237.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
NAP1L2 MUTATED 1 3 2 1 0
NAP1L2 WILD-TYPE 67 136 91 113 46
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.603 (Fisher's exact test), Q value = 0.83

Table S238.  Gene #24: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
NAP1L2 MUTATED 1 4 2
NAP1L2 WILD-TYPE 137 234 82
'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.38

Table S239.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
KEAP1 MUTATED 4 10 8 0
KEAP1 WILD-TYPE 143 120 177 42
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0637 (Fisher's exact test), Q value = 0.26

Table S240.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
KEAP1 MUTATED 3 5 2 8 0 4 0
KEAP1 WILD-TYPE 81 70 92 80 76 70 19
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 0.97

Table S241.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
KEAP1 MUTATED 3 2 4
KEAP1 WILD-TYPE 64 61 76
'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 0.94

Table S242.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
KEAP1 MUTATED 4 4 1
KEAP1 WILD-TYPE 74 81 46
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0953 (Fisher's exact test), Q value = 0.34

Table S243.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
KEAP1 MUTATED 3 14 5
KEAP1 WILD-TYPE 136 191 153
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.015

Table S244.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
KEAP1 MUTATED 3 11 8 0
KEAP1 WILD-TYPE 173 88 157 62

Figure S77.  Get High-res Image Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.57

Table S245.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
KEAP1 MUTATED 13 5 4
KEAP1 WILD-TYPE 196 146 141
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.19

Table S246.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
KEAP1 MUTATED 4 11 7
KEAP1 WILD-TYPE 184 126 173

Figure S78.  Get High-res Image Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 0.72

Table S247.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
KEAP1 MUTATED 4 6 6 2 1
KEAP1 WILD-TYPE 64 133 87 112 45
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0699 (Fisher's exact test), Q value = 0.28

Table S248.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
KEAP1 MUTATED 3 15 1
KEAP1 WILD-TYPE 135 223 83
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.18

Table S249.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
KDM6A MUTATED 4 8 2 3
KDM6A WILD-TYPE 143 122 183 39

Figure S79.  Get High-res Image Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.765 (Fisher's exact test), Q value = 0.92

Table S250.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
KDM6A MUTATED 1 4 3 3 2 3 1
KDM6A WILD-TYPE 83 71 91 85 74 71 18
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.8

Table S251.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
KDM6A MUTATED 3 1 1
KDM6A WILD-TYPE 64 62 79
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S252.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
KDM6A MUTATED 2 2 1
KDM6A WILD-TYPE 76 83 46
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 0.96

Table S253.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
KDM6A MUTATED 4 6 6
KDM6A WILD-TYPE 135 199 152
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.72

Table S254.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
KDM6A MUTATED 5 6 4 1
KDM6A WILD-TYPE 171 93 161 61
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 0.97

Table S255.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
KDM6A MUTATED 7 6 4
KDM6A WILD-TYPE 202 145 141
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.862 (Fisher's exact test), Q value = 0.96

Table S256.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
KDM6A MUTATED 7 5 5
KDM6A WILD-TYPE 181 132 175
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.82

Table S257.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
KDM6A MUTATED 2 7 1 5 1
KDM6A WILD-TYPE 66 132 92 109 45
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.58 (Fisher's exact test), Q value = 0.82

Table S258.  Gene #26: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
KDM6A MUTATED 3 9 4
KDM6A WILD-TYPE 135 229 80
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.36

Table S259.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
RHOA MUTATED 2 1 4 3
RHOA WILD-TYPE 145 129 181 39
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.82

Table S260.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
RHOA MUTATED 2 3 3 0 1 1 0
RHOA WILD-TYPE 82 72 91 88 75 73 19
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
RHOA MUTATED 0 0 3
RHOA WILD-TYPE 67 63 77
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.54

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
RHOA MUTATED 0 3 0
RHOA WILD-TYPE 78 82 47
'RHOA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S263.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
RHOA MUTATED 3 4 3
RHOA WILD-TYPE 136 201 155
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S264.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
RHOA MUTATED 4 2 3 1
RHOA WILD-TYPE 172 97 162 61
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.9

Table S265.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
RHOA MUTATED 3 4 3
RHOA WILD-TYPE 206 147 142
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 0.82

Table S266.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
RHOA MUTATED 4 4 2
RHOA WILD-TYPE 184 133 178
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 0.88

Table S267.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
RHOA MUTATED 3 2 2 2 1
RHOA WILD-TYPE 65 137 91 112 45
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 0.88

Table S268.  Gene #27: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
RHOA MUTATED 4 4 2
RHOA WILD-TYPE 134 234 82
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.16

Table S269.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CREBBP MUTATED 3 12 15 4
CREBBP WILD-TYPE 144 118 170 38

Figure S80.  Get High-res Image Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 0.82

Table S270.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
CREBBP MUTATED 5 8 4 7 3 7 1
CREBBP WILD-TYPE 79 67 90 81 73 67 18
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
CREBBP MUTATED 4 3 5
CREBBP WILD-TYPE 63 60 75
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
CREBBP MUTATED 5 5 2
CREBBP WILD-TYPE 73 80 45
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.39

Table S273.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CREBBP MUTATED 6 20 9
CREBBP WILD-TYPE 133 185 149
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 0.39

Table S274.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CREBBP MUTATED 7 10 15 3
CREBBP WILD-TYPE 169 89 150 59
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 0.77

Table S275.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CREBBP MUTATED 17 11 7
CREBBP WILD-TYPE 192 140 138
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0343 (Fisher's exact test), Q value = 0.19

Table S276.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CREBBP MUTATED 8 16 11
CREBBP WILD-TYPE 180 121 169

Figure S81.  Get High-res Image Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.25

Table S277.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
CREBBP MUTATED 6 10 10 2 4
CREBBP WILD-TYPE 62 129 83 112 42
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.39

Table S278.  Gene #28: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
CREBBP MUTATED 5 19 8
CREBBP WILD-TYPE 133 219 76
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 0.93

Table S279.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
NUDT11 MUTATED 3 3 2 0
NUDT11 WILD-TYPE 144 127 183 42
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.82

Table S280.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
NUDT11 MUTATED 0 3 1 1 1 2 0
NUDT11 WILD-TYPE 84 72 93 87 75 72 19
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0401 (Fisher's exact test), Q value = 0.2

Table S281.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
NUDT11 MUTATED 0 4 1
NUDT11 WILD-TYPE 67 59 79

Figure S82.  Get High-res Image Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 0.9

Table S282.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NUDT11 MUTATED 3 1 1
NUDT11 WILD-TYPE 75 84 46
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 0.97

Table S283.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
NUDT11 MUTATED 2 4 2
NUDT11 WILD-TYPE 137 201 156
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.631 (Fisher's exact test), Q value = 0.84

Table S284.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
NUDT11 MUTATED 2 3 2 1
NUDT11 WILD-TYPE 174 96 163 61
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.75

Table S285.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
NUDT11 MUTATED 2 4 2
NUDT11 WILD-TYPE 207 147 143
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.681 (Fisher's exact test), Q value = 0.88

Table S286.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
NUDT11 MUTATED 2 2 4
NUDT11 WILD-TYPE 186 135 176
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.52

Table S287.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
NUDT11 MUTATED 2 0 2 2 0
NUDT11 WILD-TYPE 66 139 91 112 46
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.744 (Fisher's exact test), Q value = 0.9

Table S288.  Gene #29: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
NUDT11 MUTATED 2 4 0
NUDT11 WILD-TYPE 136 234 84
'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 0.96

Table S289.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
EMG1 MUTATED 2 1 1 0
EMG1 WILD-TYPE 145 129 184 42
'EMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.57

Table S290.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
EMG1 MUTATED 1 0 1 1 0 0 1
EMG1 WILD-TYPE 83 75 93 87 76 74 18
'EMG1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.5

Table S291.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
EMG1 MUTATED 1 2 0
EMG1 WILD-TYPE 66 61 80
'EMG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 0.83

Table S292.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
EMG1 MUTATED 2 1 0
EMG1 WILD-TYPE 76 84 47
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.35

Table S293.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
EMG1 MUTATED 1 0 3
EMG1 WILD-TYPE 138 205 155
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.815 (Fisher's exact test), Q value = 0.94

Table S294.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
EMG1 MUTATED 2 0 2 0
EMG1 WILD-TYPE 174 99 163 62
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 0.88

Table S295.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
EMG1 MUTATED 1 1 2
EMG1 WILD-TYPE 208 150 143
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S296.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
EMG1 MUTATED 2 1 1
EMG1 WILD-TYPE 186 136 179
'EMG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.55

Table S297.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
EMG1 MUTATED 1 0 0 2 0
EMG1 WILD-TYPE 67 139 93 112 46
'EMG1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.437 (Fisher's exact test), Q value = 0.75

Table S298.  Gene #30: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
EMG1 MUTATED 2 1 0
EMG1 WILD-TYPE 136 237 84
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.72

Table S299.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
SMAD4 MUTATED 6 2 3 1
SMAD4 WILD-TYPE 141 128 182 41
'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.782 (Fisher's exact test), Q value = 0.93

Table S300.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
SMAD4 MUTATED 1 1 3 2 2 3 1
SMAD4 WILD-TYPE 83 74 91 86 74 71 18
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.59

Table S301.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
SMAD4 MUTATED 4 1 1
SMAD4 WILD-TYPE 63 62 79
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 0.96

Table S302.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
SMAD4 MUTATED 3 2 1
SMAD4 WILD-TYPE 75 83 46
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.57

Table S303.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
SMAD4 MUTATED 6 3 4
SMAD4 WILD-TYPE 133 202 154
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.82

Table S304.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
SMAD4 MUTATED 7 1 4 1
SMAD4 WILD-TYPE 169 98 161 61
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.16

Table S305.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
SMAD4 MUTATED 7 0 6
SMAD4 WILD-TYPE 202 151 139

Figure S83.  Get High-res Image Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 0.76

Table S306.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
SMAD4 MUTATED 7 3 3
SMAD4 WILD-TYPE 181 134 177
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 0.88

Table S307.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
SMAD4 MUTATED 3 4 1 2 1
SMAD4 WILD-TYPE 65 135 92 112 45
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 0.48

Table S308.  Gene #31: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
SMAD4 MUTATED 5 3 3
SMAD4 WILD-TYPE 133 235 81
'CUL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0205 (Fisher's exact test), Q value = 0.14

Table S309.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CUL3 MUTATED 3 9 2 0
CUL3 WILD-TYPE 144 121 183 42

Figure S84.  Get High-res Image Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.041

Table S310.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
CUL3 MUTATED 1 5 1 7 0 0 0
CUL3 WILD-TYPE 83 70 93 81 76 74 19

Figure S85.  Get High-res Image Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CUL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.58

Table S311.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
CUL3 MUTATED 4 3 1
CUL3 WILD-TYPE 63 60 79
'CUL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 0.9

Table S312.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
CUL3 MUTATED 2 4 2
CUL3 WILD-TYPE 76 81 45
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.66

Table S313.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CUL3 MUTATED 4 8 2
CUL3 WILD-TYPE 135 197 156
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.17

Table S314.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CUL3 MUTATED 5 7 2 0
CUL3 WILD-TYPE 171 92 163 62

Figure S86.  Get High-res Image Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.51

Table S315.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CUL3 MUTATED 9 2 3
CUL3 WILD-TYPE 200 149 142
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.84 (Fisher's exact test), Q value = 0.94

Table S316.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CUL3 MUTATED 6 4 4
CUL3 WILD-TYPE 182 133 176
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00144 (Fisher's exact test), Q value = 0.018

Table S317.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
CUL3 MUTATED 1 2 8 0 0
CUL3 WILD-TYPE 67 137 85 114 46

Figure S87.  Get High-res Image Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 0.71

Table S318.  Gene #32: 'CUL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
CUL3 MUTATED 4 7 0
CUL3 WILD-TYPE 134 231 84
'TIGD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 0.77

Table S319.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
TIGD4 MUTATED 1 3 2 1
TIGD4 WILD-TYPE 146 127 183 41
'TIGD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 0.92

Table S320.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
TIGD4 MUTATED 1 1 0 2 1 2 0
TIGD4 WILD-TYPE 83 74 94 86 75 72 19
'TIGD4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S321.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
TIGD4 MUTATED 1 1 2
TIGD4 WILD-TYPE 66 62 78
'TIGD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 0.94

Table S322.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
TIGD4 MUTATED 2 1 1
TIGD4 WILD-TYPE 76 84 46
'TIGD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 0.9

Table S323.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
TIGD4 MUTATED 1 4 2
TIGD4 WILD-TYPE 138 201 156
'TIGD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.72

Table S324.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
TIGD4 MUTATED 1 2 4 0
TIGD4 WILD-TYPE 175 97 161 62
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 0.86

Table S325.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
TIGD4 MUTATED 3 3 1
TIGD4 WILD-TYPE 206 148 144
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.72

Table S326.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
TIGD4 MUTATED 1 3 3
TIGD4 WILD-TYPE 187 134 177
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.957 (Fisher's exact test), Q value = 1

Table S327.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
TIGD4 MUTATED 1 3 1 2 0
TIGD4 WILD-TYPE 67 136 92 112 46
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.688 (Fisher's exact test), Q value = 0.88

Table S328.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
TIGD4 MUTATED 1 5 1
TIGD4 WILD-TYPE 137 233 83
'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0159 (Fisher's exact test), Q value = 0.11

Table S329.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
MYH9 MUTATED 8 1 13 0
MYH9 WILD-TYPE 139 129 172 42

Figure S88.  Get High-res Image Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.53

Table S330.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
MYH9 MUTATED 3 2 2 2 5 7 1
MYH9 WILD-TYPE 81 73 92 86 71 67 18
'MYH9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.52

Table S331.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
MYH9 MUTATED 5 1 2
MYH9 WILD-TYPE 62 62 78
'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.77

Table S332.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
MYH9 MUTATED 3 2 3
MYH9 WILD-TYPE 75 83 44
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 0.82

Table S333.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
MYH9 MUTATED 8 7 7
MYH9 WILD-TYPE 131 198 151
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.715 (Fisher's exact test), Q value = 0.89

Table S334.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
MYH9 MUTATED 10 3 6 3
MYH9 WILD-TYPE 166 96 159 59
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 0.89

Table S335.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
MYH9 MUTATED 8 6 8
MYH9 WILD-TYPE 201 145 137
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.75

Table S336.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
MYH9 MUTATED 11 4 7
MYH9 WILD-TYPE 177 133 173
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 0.95

Table S337.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
MYH9 MUTATED 4 8 3 4 2
MYH9 WILD-TYPE 64 131 90 110 44
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.76

Table S338.  Gene #34: 'MYH9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
MYH9 MUTATED 5 10 6
MYH9 WILD-TYPE 133 228 78
'C3ORF59 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.609 (Fisher's exact test), Q value = 0.83

Table S339.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
C3ORF59 MUTATED 2 2 6 1
C3ORF59 WILD-TYPE 145 128 179 41
'C3ORF59 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.52

Table S340.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
C3ORF59 MUTATED 0 1 1 2 2 4 1
C3ORF59 WILD-TYPE 84 74 93 86 74 70 18
'C3ORF59 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.862 (Fisher's exact test), Q value = 0.96

Table S341.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
C3ORF59 MUTATED 2 5 4
C3ORF59 WILD-TYPE 137 200 154
'C3ORF59 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 0.72

Table S342.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
C3ORF59 MUTATED 4 1 6 0
C3ORF59 WILD-TYPE 172 98 159 62
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.8 (Fisher's exact test), Q value = 0.93

Table S343.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
C3ORF59 MUTATED 5 4 2
C3ORF59 WILD-TYPE 204 147 143
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 0.85

Table S344.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
C3ORF59 MUTATED 3 4 4
C3ORF59 WILD-TYPE 185 133 176
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.88

Table S345.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
C3ORF59 MUTATED 2 5 1 3 0
C3ORF59 WILD-TYPE 66 134 92 111 46
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.61

Table S346.  Gene #35: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
C3ORF59 MUTATED 3 4 4
C3ORF59 WILD-TYPE 135 234 80
'HUWE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.014

Table S347.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
HUWE1 MUTATED 13 2 24 5
HUWE1 WILD-TYPE 134 128 161 37

Figure S89.  Get High-res Image Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HUWE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00055 (Fisher's exact test), Q value = 0.0084

Table S348.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
HUWE1 MUTATED 8 1 7 5 7 17 0
HUWE1 WILD-TYPE 76 74 87 83 69 57 19

Figure S90.  Get High-res Image Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HUWE1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 0.96

Table S349.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
HUWE1 MUTATED 4 5 5
HUWE1 WILD-TYPE 63 58 75
'HUWE1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 0.85

Table S350.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
HUWE1 MUTATED 7 5 2
HUWE1 WILD-TYPE 71 80 45
'HUWE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0174 (Fisher's exact test), Q value = 0.12

Table S351.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
HUWE1 MUTATED 11 11 22
HUWE1 WILD-TYPE 128 194 136

Figure S91.  Get High-res Image Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HUWE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0434 (Fisher's exact test), Q value = 0.21

Table S352.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
HUWE1 MUTATED 13 5 23 3
HUWE1 WILD-TYPE 163 94 142 59

Figure S92.  Get High-res Image Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HUWE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.46

Table S353.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
HUWE1 MUTATED 16 19 10
HUWE1 WILD-TYPE 193 132 135
'HUWE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.666 (Fisher's exact test), Q value = 0.87

Table S354.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
HUWE1 MUTATED 15 11 19
HUWE1 WILD-TYPE 173 126 161
'HUWE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.39

Table S355.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
HUWE1 MUTATED 5 20 4 12 4
HUWE1 WILD-TYPE 63 119 89 102 42
'HUWE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.44

Table S356.  Gene #36: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
HUWE1 MUTATED 9 24 12
HUWE1 WILD-TYPE 129 214 72
'SLC9A6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00867 (Fisher's exact test), Q value = 0.073

Table S357.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
SLC9A6 MUTATED 3 0 0 2
SLC9A6 WILD-TYPE 144 130 185 40

Figure S93.  Get High-res Image Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SLC9A6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0944 (Fisher's exact test), Q value = 0.34

Table S358.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
SLC9A6 MUTATED 0 0 3 0 0 2 0
SLC9A6 WILD-TYPE 84 75 91 88 76 72 19
'SLC9A6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.776 (Fisher's exact test), Q value = 0.92

Table S359.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
SLC9A6 MUTATED 1 0 2
SLC9A6 WILD-TYPE 66 63 78
'SLC9A6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.36

Table S360.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
SLC9A6 MUTATED 1 0 2
SLC9A6 WILD-TYPE 77 85 45
'SLC9A6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.36

Table S361.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
SLC9A6 MUTATED 2 0 3
SLC9A6 WILD-TYPE 137 205 155
'SLC9A6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.7

Table S362.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
SLC9A6 MUTATED 4 0 1 0
SLC9A6 WILD-TYPE 172 99 164 62
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0511 (Fisher's exact test), Q value = 0.24

Table S363.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
SLC9A6 MUTATED 1 0 4
SLC9A6 WILD-TYPE 208 151 141
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.52

Table S364.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
SLC9A6 MUTATED 4 0 1
SLC9A6 WILD-TYPE 184 137 179
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 0.82

Table S365.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
SLC9A6 MUTATED 0 3 0 2 0
SLC9A6 WILD-TYPE 68 136 93 112 46
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0287 (Fisher's exact test), Q value = 0.17

Table S366.  Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
SLC9A6 MUTATED 3 0 2
SLC9A6 WILD-TYPE 135 238 82

Figure S94.  Get High-res Image Gene #37: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF623 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.52

Table S367.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
ZNF623 MUTATED 1 2 7 1
ZNF623 WILD-TYPE 146 128 178 41
'ZNF623 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 0.93

Table S368.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
ZNF623 MUTATED 1 2 3 1 2 1 1
ZNF623 WILD-TYPE 83 73 91 87 74 73 18
'ZNF623 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.49

Table S369.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
ZNF623 MUTATED 1 4 1
ZNF623 WILD-TYPE 66 59 79
'ZNF623 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 0.75

Table S370.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ZNF623 MUTATED 3 1 2
ZNF623 WILD-TYPE 75 84 45
'ZNF623 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.67

Table S371.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
ZNF623 MUTATED 1 5 5
ZNF623 WILD-TYPE 138 200 153
'ZNF623 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.46

Table S372.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
ZNF623 MUTATED 1 2 6 2
ZNF623 WILD-TYPE 175 97 159 60
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.82

Table S373.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
ZNF623 MUTATED 4 5 2
ZNF623 WILD-TYPE 205 146 143
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.35

Table S374.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
ZNF623 MUTATED 1 5 5
ZNF623 WILD-TYPE 187 132 175
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.73

Table S375.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
ZNF623 MUTATED 0 3 0 3 0
ZNF623 WILD-TYPE 68 136 93 111 46
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.52

Table S376.  Gene #38: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
ZNF623 MUTATED 0 4 2
ZNF623 WILD-TYPE 138 234 82
'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.012 (Fisher's exact test), Q value = 0.095

Table S377.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
MLL4 MUTATED 1 4 11 4
MLL4 WILD-TYPE 146 126 174 38

Figure S95.  Get High-res Image Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0033

Table S378.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
MLL4 MUTATED 2 2 1 2 1 12 0
MLL4 WILD-TYPE 82 73 93 86 75 62 19

Figure S96.  Get High-res Image Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.45

Table S379.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
MLL4 MUTATED 0 2 4
MLL4 WILD-TYPE 67 61 76
'MLL4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 0.71

Table S380.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
MLL4 MUTATED 2 4 0
MLL4 WILD-TYPE 76 81 47
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00708 (Fisher's exact test), Q value = 0.064

Table S381.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
MLL4 MUTATED 1 6 12
MLL4 WILD-TYPE 138 199 146

Figure S97.  Get High-res Image Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MLL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0969 (Fisher's exact test), Q value = 0.34

Table S382.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
MLL4 MUTATED 5 3 11 0
MLL4 WILD-TYPE 171 96 154 62
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.011

Table S383.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
MLL4 MUTATED 4 14 2
MLL4 WILD-TYPE 205 137 143

Figure S98.  Get High-res Image Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MLL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.712 (Fisher's exact test), Q value = 0.89

Table S384.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
MLL4 MUTATED 7 7 6
MLL4 WILD-TYPE 181 130 174
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0612 (Fisher's exact test), Q value = 0.26

Table S385.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
MLL4 MUTATED 1 10 1 3 0
MLL4 WILD-TYPE 67 129 92 111 46
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0574 (Fisher's exact test), Q value = 0.25

Table S386.  Gene #39: 'MLL4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
MLL4 MUTATED 1 9 5
MLL4 WILD-TYPE 137 229 79
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0497 (Fisher's exact test), Q value = 0.23

Table S387.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CTCF MUTATED 4 1 11 0
CTCF WILD-TYPE 143 129 174 42

Figure S99.  Get High-res Image Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.019

Table S388.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
CTCF MUTATED 1 3 2 0 1 9 0
CTCF WILD-TYPE 83 72 92 88 75 65 19

Figure S100.  Get High-res Image Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
CTCF MUTATED 1 1 6
CTCF WILD-TYPE 66 62 74
'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
CTCF MUTATED 2 5 1
CTCF WILD-TYPE 76 80 46
'CTCF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.77

Table S391.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CTCF MUTATED 3 5 7
CTCF WILD-TYPE 136 200 151
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.58

Table S392.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CTCF MUTATED 4 3 8 0
CTCF WILD-TYPE 172 96 157 62
'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.88

Table S393.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CTCF MUTATED 5 6 5
CTCF WILD-TYPE 204 145 140
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.899 (Fisher's exact test), Q value = 0.96

Table S394.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CTCF MUTATED 7 4 5
CTCF WILD-TYPE 181 133 175
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 0.9

Table S395.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
CTCF MUTATED 3 5 2 4 0
CTCF WILD-TYPE 65 134 91 110 46
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 0.92

Table S396.  Gene #40: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
CTCF MUTATED 5 6 3
CTCF WILD-TYPE 133 232 81
'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 0.96

Table S397.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
NCOR1 MUTATED 4 6 6 1
NCOR1 WILD-TYPE 143 124 179 41
'NCOR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0895 (Fisher's exact test), Q value = 0.32

Table S398.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
NCOR1 MUTATED 2 3 0 5 2 6 0
NCOR1 WILD-TYPE 82 72 94 83 74 68 19
'NCOR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.59

Table S399.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
NCOR1 MUTATED 1 4 5
NCOR1 WILD-TYPE 66 59 75
'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 0.77

Table S400.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NCOR1 MUTATED 3 6 1
NCOR1 WILD-TYPE 75 79 46
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 0.84

Table S401.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
NCOR1 MUTATED 3 9 6
NCOR1 WILD-TYPE 136 196 152
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.46

Table S402.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
NCOR1 MUTATED 3 6 8 1
NCOR1 WILD-TYPE 173 93 157 61
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.81

Table S403.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
NCOR1 MUTATED 10 4 4
NCOR1 WILD-TYPE 199 147 141
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.36

Table S404.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
NCOR1 MUTATED 5 9 4
NCOR1 WILD-TYPE 183 128 176
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.529 (Fisher's exact test), Q value = 0.8

Table S405.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
NCOR1 MUTATED 4 6 5 2 1
NCOR1 WILD-TYPE 64 133 88 112 45
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.853 (Fisher's exact test), Q value = 0.95

Table S406.  Gene #41: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
NCOR1 MUTATED 6 10 2
NCOR1 WILD-TYPE 132 228 82
'PTPN14 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0168 (Fisher's exact test), Q value = 0.12

Table S407.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
PTPN14 MUTATED 3 4 3 5
PTPN14 WILD-TYPE 144 126 182 37

Figure S101.  Get High-res Image Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTPN14 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.38

Table S408.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
PTPN14 MUTATED 1 3 3 2 0 6 0
PTPN14 WILD-TYPE 83 72 91 86 76 68 19
'PTPN14 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S409.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
PTPN14 MUTATED 2 2 2
PTPN14 WILD-TYPE 65 61 78
'PTPN14 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.579 (Fisher's exact test), Q value = 0.82

Table S410.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
PTPN14 MUTATED 3 3 0
PTPN14 WILD-TYPE 75 82 47
'PTPN14 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 0.52

Table S411.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
PTPN14 MUTATED 3 4 8
PTPN14 WILD-TYPE 136 201 150
'PTPN14 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.717 (Fisher's exact test), Q value = 0.89

Table S412.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
PTPN14 MUTATED 4 3 7 1
PTPN14 WILD-TYPE 172 96 158 61
'PTPN14 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.22

Table S413.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
PTPN14 MUTATED 3 9 3
PTPN14 WILD-TYPE 206 142 142

Figure S102.  Get High-res Image Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PTPN14 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.85

Table S414.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
PTPN14 MUTATED 4 5 6
PTPN14 WILD-TYPE 184 132 174
'PTPN14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.57

Table S415.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
PTPN14 MUTATED 0 7 3 3 0
PTPN14 WILD-TYPE 68 132 90 111 46
'PTPN14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.75

Table S416.  Gene #42: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
PTPN14 MUTATED 2 9 2
PTPN14 WILD-TYPE 136 229 82
'ITGB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.765 (Fisher's exact test), Q value = 0.92

Table S417.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
ITGB1 MUTATED 5 4 4 0
ITGB1 WILD-TYPE 142 126 181 42
'ITGB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0531 (Fisher's exact test), Q value = 0.24

Table S418.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
ITGB1 MUTATED 0 1 1 5 1 5 0
ITGB1 WILD-TYPE 84 74 93 83 75 69 19
'ITGB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.67

Table S419.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
ITGB1 MUTATED 1 4 2
ITGB1 WILD-TYPE 66 59 78
'ITGB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 0.83

Table S420.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ITGB1 MUTATED 4 2 1
ITGB1 WILD-TYPE 74 83 46
'ITGB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.1

Table S421.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
ITGB1 MUTATED 0 5 8
ITGB1 WILD-TYPE 139 200 150

Figure S103.  Get High-res Image Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ITGB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0823 (Fisher's exact test), Q value = 0.31

Table S422.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
ITGB1 MUTATED 1 4 7 1
ITGB1 WILD-TYPE 175 95 158 61
'ITGB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.82

Table S423.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
ITGB1 MUTATED 7 4 2
ITGB1 WILD-TYPE 202 147 143
'ITGB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.49

Table S424.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
ITGB1 MUTATED 2 4 7
ITGB1 WILD-TYPE 186 133 173
'ITGB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.47

Table S425.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
ITGB1 MUTATED 1 2 3 7 0
ITGB1 WILD-TYPE 67 137 90 107 46
'ITGB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.697 (Fisher's exact test), Q value = 0.88

Table S426.  Gene #43: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
ITGB1 MUTATED 4 8 1
ITGB1 WILD-TYPE 134 230 83
'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.49

Table S427.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
IRS4 MUTATED 4 2 10 0
IRS4 WILD-TYPE 143 128 175 42
'IRS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.82

Table S428.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
IRS4 MUTATED 4 2 1 3 5 2 0
IRS4 WILD-TYPE 80 73 93 85 71 72 19
'IRS4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 0.93

Table S429.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
IRS4 MUTATED 2 3 2
IRS4 WILD-TYPE 65 60 78
'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 0.93

Table S430.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
IRS4 MUTATED 3 2 2
IRS4 WILD-TYPE 75 83 45
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.38

Table S431.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
IRS4 MUTATED 2 11 4
IRS4 WILD-TYPE 137 194 154
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0731 (Fisher's exact test), Q value = 0.28

Table S432.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
IRS4 MUTATED 3 5 4 5
IRS4 WILD-TYPE 173 94 161 57
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.52

Table S433.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
IRS4 MUTATED 10 5 2
IRS4 WILD-TYPE 199 146 143
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0635 (Fisher's exact test), Q value = 0.26

Table S434.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
IRS4 MUTATED 2 6 9
IRS4 WILD-TYPE 186 131 171
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0158 (Fisher's exact test), Q value = 0.11

Table S435.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
IRS4 MUTATED 2 2 2 3 6
IRS4 WILD-TYPE 66 137 91 111 40

Figure S104.  Get High-res Image Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.52

Table S436.  Gene #44: 'IRS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
IRS4 MUTATED 2 11 2
IRS4 WILD-TYPE 136 227 82
'SRPX MUTATION STATUS' versus 'CN_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 0.84

Table S437.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
SRPX MUTATED 1 2 2 1
SRPX WILD-TYPE 146 128 183 41
'SRPX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.985 (Fisher's exact test), Q value = 1

Table S438.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
SRPX MUTATED 2 1 1 1 1 1 0
SRPX WILD-TYPE 82 74 93 87 75 73 19
'SRPX MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.72

Table S439.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
SRPX MUTATED 1 0 3
SRPX WILD-TYPE 66 63 77
'SRPX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S440.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
SRPX MUTATED 1 2 1
SRPX WILD-TYPE 77 83 46
'SRPX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S441.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
SRPX MUTATED 2 2 2
SRPX WILD-TYPE 137 203 156
'SRPX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.604 (Fisher's exact test), Q value = 0.83

Table S442.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
SRPX MUTATED 3 2 1 0
SRPX WILD-TYPE 173 97 164 62
'SRPX MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 0.9

Table S443.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
SRPX MUTATED 2 2 3
SRPX WILD-TYPE 207 149 142
'SRPX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S444.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
SRPX MUTATED 3 2 2
SRPX WILD-TYPE 185 135 178
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.82

Table S445.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
SRPX MUTATED 1 3 0 1 1
SRPX WILD-TYPE 67 136 93 113 45
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 0.72

Table S446.  Gene #45: 'SRPX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
SRPX MUTATED 2 2 2
SRPX WILD-TYPE 136 236 82
'KIAA1949 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 0.94

Table S447.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
KIAA1949 MUTATED 3 1 2 0
KIAA1949 WILD-TYPE 144 129 183 42
'KIAA1949 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.77

Table S448.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
KIAA1949 MUTATED 1 2 0 1 0 2 0
KIAA1949 WILD-TYPE 83 73 94 87 76 72 19
'KIAA1949 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 0.92

Table S449.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
KIAA1949 MUTATED 2 3 1
KIAA1949 WILD-TYPE 137 202 157
'KIAA1949 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 0.94

Table S450.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
KIAA1949 MUTATED 2 2 2 0
KIAA1949 WILD-TYPE 174 97 163 62
'KIAA1949 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.669 (Fisher's exact test), Q value = 0.87

Table S451.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
KIAA1949 MUTATED 2 3 1
KIAA1949 WILD-TYPE 207 148 144
'KIAA1949 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S452.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
KIAA1949 MUTATED 2 2 2
KIAA1949 WILD-TYPE 186 135 178
'KIAA1949 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 0.82

Table S453.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
KIAA1949 MUTATED 2 1 2 1 0
KIAA1949 WILD-TYPE 66 138 91 113 46
'KIAA1949 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 0.82

Table S454.  Gene #46: 'KIAA1949 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
KIAA1949 MUTATED 3 2 1
KIAA1949 WILD-TYPE 135 236 83
'NOTCH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 0.75

Table S455.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
NOTCH2 MUTATED 5 8 5 1
NOTCH2 WILD-TYPE 142 122 180 41
'NOTCH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.72

Table S456.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
NOTCH2 MUTATED 3 2 4 3 2 3 3
NOTCH2 WILD-TYPE 81 73 90 85 74 71 16
'NOTCH2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0786 (Fisher's exact test), Q value = 0.3

Table S457.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
NOTCH2 MUTATED 3 6 1
NOTCH2 WILD-TYPE 64 57 79
'NOTCH2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 0.67

Table S458.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NOTCH2 MUTATED 6 3 1
NOTCH2 WILD-TYPE 72 82 46
'NOTCH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.595 (Fisher's exact test), Q value = 0.83

Table S459.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
NOTCH2 MUTATED 7 6 7
NOTCH2 WILD-TYPE 132 199 151
'NOTCH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.62

Table S460.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
NOTCH2 MUTATED 11 2 6 1
NOTCH2 WILD-TYPE 165 97 159 61
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 0.78

Table S461.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
NOTCH2 MUTATED 6 8 6
NOTCH2 WILD-TYPE 203 143 139
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.485 (Fisher's exact test), Q value = 0.77

Table S462.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
NOTCH2 MUTATED 10 5 5
NOTCH2 WILD-TYPE 178 132 175
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 0.96

Table S463.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
NOTCH2 MUTATED 4 5 3 4 1
NOTCH2 WILD-TYPE 64 134 90 110 45
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 0.83

Table S464.  Gene #47: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
NOTCH2 MUTATED 7 8 2
NOTCH2 WILD-TYPE 131 230 82
'GAGE2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.19

Table S465.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
GAGE2A MUTATED 1 4 0 0
GAGE2A WILD-TYPE 146 126 185 42

Figure S105.  Get High-res Image Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'GAGE2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0753 (Fisher's exact test), Q value = 0.29

Table S466.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
GAGE2A MUTATED 0 2 0 3 0 0 0
GAGE2A WILD-TYPE 84 73 94 85 76 74 19
'GAGE2A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S467.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
GAGE2A MUTATED 1 1 1
GAGE2A WILD-TYPE 66 62 79
'GAGE2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.794 (Fisher's exact test), Q value = 0.93

Table S468.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
GAGE2A MUTATED 1 2 0
GAGE2A WILD-TYPE 77 83 47
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.48

Table S469.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
GAGE2A MUTATED 1 4 0
GAGE2A WILD-TYPE 138 201 158
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.54

Table S470.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
GAGE2A MUTATED 1 3 1 0
GAGE2A WILD-TYPE 175 96 164 62
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 0.9

Table S471.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
GAGE2A MUTATED 3 1 1
GAGE2A WILD-TYPE 206 150 144
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.64

Table S472.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
GAGE2A MUTATED 1 3 1
GAGE2A WILD-TYPE 187 134 179
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.6

Table S473.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
GAGE2A MUTATED 1 0 2 1 1
GAGE2A WILD-TYPE 67 139 91 113 45
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S474.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
GAGE2A MUTATED 1 3 1
GAGE2A WILD-TYPE 137 235 83
'LCP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0724 (Fisher's exact test), Q value = 0.28

Table S475.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
LCP1 MUTATED 6 7 2 0
LCP1 WILD-TYPE 141 123 183 42
'LCP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0887 (Fisher's exact test), Q value = 0.32

Table S476.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 84 75 94 88 76 74 19
LCP1 MUTATED 1 6 3 4 0 1 0
LCP1 WILD-TYPE 83 69 91 84 76 73 19
'LCP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.72

Table S477.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 63 80
LCP1 MUTATED 1 3 5
LCP1 WILD-TYPE 66 60 75
'LCP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 0.94

Table S478.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
LCP1 MUTATED 4 4 1
LCP1 WILD-TYPE 74 81 46
'LCP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 0.91

Table S479.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
LCP1 MUTATED 4 5 6
LCP1 WILD-TYPE 135 200 152
'LCP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0719 (Fisher's exact test), Q value = 0.28

Table S480.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
LCP1 MUTATED 4 7 4 0
LCP1 WILD-TYPE 172 92 161 62
'LCP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S481.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
LCP1 MUTATED 7 4 4
LCP1 WILD-TYPE 202 147 141
'LCP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.894 (Fisher's exact test), Q value = 0.96

Table S482.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
LCP1 MUTATED 5 5 5
LCP1 WILD-TYPE 183 132 175
'LCP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 0.9

Table S483.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 139 93 114 46
LCP1 MUTATED 2 3 4 3 0
LCP1 WILD-TYPE 66 136 89 111 46
'LCP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 0.56

Table S484.  Gene #49: 'LCP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
LCP1 MUTATED 4 8 0
LCP1 WILD-TYPE 134 230 84
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/HNSC-TP/20203267/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/20125733/HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 510

  • Number of significantly mutated genes = 49

  • 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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