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 64 genes and 10 molecular subtypes across 510 patients, 107 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'.

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

  • 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'.

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

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

  • EPHA2 mutation correlated to 'METHLYATION_CNMF'.

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

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

  • NFE2L2 mutation correlated to 'METHLYATION_CNMF'.

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

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

  • RB1 mutation correlated to 'MRNASEQ_CNMF'.

  • KDM6A mutation correlated to 'CN_CNMF'.

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

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

  • CTCF mutation correlated to 'METHLYATION_CNMF'.

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

  • SMAD4 mutation correlated to 'RPPA_CNMF' and 'MIRSEQ_CNMF'.

  • ASXL1 mutation correlated to 'MRNASEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • IRS4 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • ARID2 mutation correlated to 'METHLYATION_CNMF'.

  • CBWD1 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • HNRNPL mutation correlated to 'METHLYATION_CNMF'.

  • ITGB1 mutation correlated to 'MRNASEQ_CNMF'.

  • LRRC37B mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • VPS33B mutation correlated to 'METHLYATION_CNMF'.

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

  • MYH9 mutation correlated to 'CN_CNMF'.

  • TP63 mutation correlated to 'MIRSEQ_CNMF'.

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

  • PTPN14 mutation correlated to 'CN_CNMF'.

  • IRF2 mutation correlated to 'MRNASEQ_CNMF'.

  • AMPD1 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

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

  • CCNG2 mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 64 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, 107 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 0.00435
(0.058) 		1e-05
(0.000376) 		0.251
(0.636) 		0.0149
(0.152) 		2e-05
(0.000582) 		1e-05
(0.000376) 		0.0025
(0.0381) 		6e-05
(0.00142) 		1e-05
(0.000376) 		3e-05
(8e-04)
TP53 359 (70%) 151 1e-05
(0.000376) 		1e-05
(0.000376) 		0.11
(0.424) 		0.564
(0.886) 		2e-05
(0.000582) 		1e-05
(0.000376) 		0.00478
(0.0612) 		1e-05
(0.000376) 		1e-05
(0.000376) 		1e-05
(0.000376)
CDKN2A 112 (22%) 398 0.0238
(0.191) 		1e-05
(0.000376) 		0.00214
(0.0351) 		0.718
(0.962) 		0.0251
(0.199) 		2e-05
(0.000582) 		0.215
(0.592) 		0.0568
(0.307) 		0.00223
(0.0357) 		0.0394
(0.242)
CASP8 55 (11%) 455 1e-05
(0.000376) 		1e-05
(0.000376) 		0.0157
(0.155) 		0.351
(0.769) 		1e-05
(0.000376) 		1e-05
(0.000376) 		0.009
(0.103) 		0.568
(0.886) 		0.00024
(0.00549) 		0.138
(0.449)
NOTCH1 87 (17%) 423 0.0151
(0.152) 		4e-05
(0.00102) 		0.057
(0.307) 		0.0595
(0.313) 		1e-05
(0.000376) 		0.00141
(0.0244) 		2e-05
(0.000582) 		0.0664
(0.327) 		0.00849
(0.101) 		0.0375
(0.24)
HRAS 29 (6%) 481 3e-05
(8e-04) 		1e-05
(0.000376) 		0.375
(0.794) 		0.653
(0.922) 		0.00051
(0.0105) 		0.00229
(0.0357) 		0.00074
(0.0148) 		0.121
(0.435) 		0.0214
(0.178) 		0.172
(0.508)
ZNF750 19 (4%) 491 0.214
(0.592) 		0.0106
(0.119) 		0.762
(0.97) 		0.288
(0.7) 		0.00732
(0.0901) 		0.0152
(0.152) 		0.0162
(0.155) 		0.133
(0.444) 		0.0505
(0.284) 		0.022
(0.181)
HLA-A 22 (4%) 488 0.00313
(0.0452) 		0.00319
(0.0452) 		1
(1.00) 		0.639
(0.911) 		0.00473
(0.0612) 		0.00256
(0.0381) 		0.0364
(0.24) 		0.12
(0.435) 		0.552
(0.886) 		0.475
(0.861)
CUL3 14 (3%) 496 0.0203
(0.173) 		0.00375
(0.0511) 		0.365
(0.786) 		0.731
(0.962) 		0.332
(0.752) 		0.0277
(0.211) 		0.214
(0.592) 		0.84
(1.00) 		0.00145
(0.0244) 		0.379
(0.795)
PIK3CA 94 (18%) 416 0.262
(0.655) 		0.206
(0.586) 		0.778
(0.98) 		0.0632
(0.326) 		0.0411
(0.248) 		0.342
(0.757) 		0.00705
(0.0885) 		0.0232
(0.188) 		0.445
(0.852) 		0.0947
(0.389)
FAT1 114 (22%) 396 0.26
(0.652) 		1e-05
(0.000376) 		0.848
(1.00) 		0.488
(0.863) 		0.145
(0.469) 		0.00035
(0.00772) 		0.874
(1.00) 		0.595
(0.889) 		0.00325
(0.0452) 		0.1
(0.406)
HLA-B 24 (5%) 486 0.156
(0.489) 		0.00127
(0.0239) 		1
(1.00) 		0.221
(0.602) 		0.0353
(0.24) 		0.063
(0.326) 		0.057
(0.307) 		0.209
(0.586) 		0.0861
(0.373) 		0.036
(0.24)
EP300 39 (8%) 471 0.446
(0.852) 		0.0348
(0.24) 		0.563
(0.886) 		0.0848
(0.372) 		0.00763
(0.0921) 		0.091
(0.383) 		0.554
(0.886) 		0.237
(0.618) 		0.0398
(0.242) 		1
(1.00)
HUWE1 45 (9%) 465 0.00112
(0.0217) 		0.00044
(0.00939) 		0.408
(0.808) 		0.637
(0.911) 		0.0178
(0.163) 		0.0428
(0.254) 		0.175
(0.511) 		0.668
(0.935) 		0.132
(0.444) 		0.157
(0.489)
DYSF 21 (4%) 489 0.883
(1.00) 		0.0186
(0.163) 		0.135
(0.446) 		0.732
(0.962) 		0.0921
(0.385) 		0.0166
(0.156) 		0.244
(0.628) 		0.225
(0.604) 		0.0389
(0.242) 		0.0764
(0.342)
RAC1 15 (3%) 495 0.111
(0.424) 		0.0355
(0.24) 		1
(1.00) 		0.834
(1.00) 		0.0345
(0.24) 		0.0692
(0.334) 		0.45
(0.852) 		0.406
(0.808) 		0.18
(0.525) 		0.325
(0.744)
CREBBP 35 (7%) 475 0.0266
(0.208) 		0.565
(0.886) 		0.741
(0.962) 		0.932
(1.00) 		0.131
(0.444) 		0.13
(0.444) 		0.487
(0.863) 		0.0356
(0.24) 		0.0596
(0.313) 		0.131
(0.444)
KEAP1 22 (4%) 488 0.124
(0.442) 		0.0653
(0.327) 		0.61
(0.897) 		0.827
(1.00) 		0.0945
(0.389) 		0.00138
(0.0244) 		0.268
(0.664) 		0.0384
(0.241) 		0.409
(0.808) 		0.0706
(0.337)
SMAD4 14 (3%) 496 0.528
(0.878) 		0.855
(1.00) 		0.0382
(0.241) 		0.872
(1.00) 		0.402
(0.808) 		0.783
(0.98) 		0.0195
(0.169) 		0.49
(0.863) 		0.864
(1.00) 		0.414
(0.814)
ASXL1 16 (3%) 494 0.723
(0.962) 		0.295
(0.704) 		0.63
(0.91) 		0.876
(1.00) 		0.0755
(0.34) 		0.017
(0.158) 		0.0562
(0.307) 		0.0646
(0.326) 		0.833
(1.00) 		0.0113
(0.124)
SLC9A6 5 (1%) 505 0.00883
(0.103) 		0.0937
(0.389) 		0.873
(1.00) 		0.116
(0.428) 		0.113
(0.424) 		0.37
(0.791) 		0.0501
(0.284) 		0.23
(0.612) 		0.569
(0.886) 		0.0281
(0.211)
TGFBR2 23 (5%) 487 0.0124
(0.133) 		0.058
(0.309) 		0.466
(0.856) 		0.901
(1.00) 		0.103
(0.413) 		0.959
(1.00) 		0.637
(0.911) 		0.57
(0.886) 		0.727
(0.962) 		0.516
(0.875)
EPHA2 24 (5%) 486 0.498
(0.863) 		6e-05
(0.00142) 		0.756
(0.969) 		0.933
(1.00) 		0.31
(0.721) 		0.291
(0.702) 		0.895
(1.00) 		0.164
(0.498) 		0.107
(0.423) 		0.649
(0.921)
NFE2L2 26 (5%) 484 0.495
(0.863) 		2e-05
(0.000582) 		0.501
(0.863) 		0.874
(1.00) 		0.846
(1.00) 		0.468
(0.856) 		0.233
(0.614) 		0.493
(0.863) 		0.597
(0.889) 		0.357
(0.775)
RB1 18 (4%) 492 0.601
(0.89) 		0.371
(0.791) 		0.355
(0.774) 		0.273
(0.672) 		0.0372
(0.24) 		0.377
(0.794) 		0.154
(0.486) 		0.497
(0.863) 		0.385
(0.805) 		0.618
(0.899)
KDM6A 17 (3%) 493 0.0296
(0.214) 		0.766
(0.971) 		0.142
(0.463) 		1
(1.00) 		0.899
(1.00) 		0.39
(0.807) 		0.907
(1.00) 		0.863
(1.00) 		0.564
(0.886) 		0.582
(0.889)
CTCF 16 (3%) 494 0.0503
(0.284) 		0.00135
(0.0244) 		0.614
(0.898) 		0.523
(0.877) 		0.482
(0.863) 		0.272
(0.672) 		0.692
(0.947) 		0.901
(1.00) 		0.737
(0.962) 		0.765
(0.971)
IRS4 17 (3%) 493 0.192
(0.557) 		0.57
(0.886) 		0.259
(0.652) 		0.79
(0.985) 		0.127
(0.444) 		0.0731
(0.34) 		0.216
(0.593) 		0.0643
(0.326) 		0.0149
(0.152) 		0.221
(0.602)
ARID2 20 (4%) 490 0.321
(0.739) 		0.0297
(0.214) 		0.611
(0.897) 		0.795
(0.99) 		0.227
(0.606) 		0.615
(0.898) 		0.167
(0.504) 		0.681
(0.947) 		0.525
(0.877) 		0.691
(0.947)
CBWD1 5 (1%) 505 0.594
(0.889) 		0.804
(0.998) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.855
(1.00) 		0.836
(1.00) 		0.0125
(0.133)
HNRNPL 11 (2%) 499 0.475
(0.861) 		0.0209
(0.176) 		0.209
(0.586) 		0.758
(0.969) 		0.597
(0.889) 		0.353
(0.772) 		0.742
(0.962) 		0.129
(0.444) 		0.758
(0.969) 		0.465
(0.856)
ITGB1 14 (3%) 496 0.617
(0.899) 		0.0752
(0.34) 		0.278
(0.682) 		0.61
(0.897) 		0.0183
(0.163) 		0.0475
(0.274) 		0.403
(0.808) 		0.113
(0.424) 		0.147
(0.474) 		0.585
(0.889)
LRRC37B 16 (3%) 494 0.152
(0.485) 		0.326
(0.744) 		1
(1.00) 		1
(1.00) 		0.235
(0.616) 		0.156
(0.488) 		0.901
(1.00) 		0.532
(0.879) 		0.0274
(0.211) 		0.569
(0.886)
VPS33B 7 (1%) 503 0.108
(0.423) 		0.0291
(0.214) 		0.704
(0.954) 		1
(1.00) 		0.724
(0.962) 		0.334
(0.753) 		0.576
(0.889) 		0.566
(0.886) 		0.969
(1.00) 		0.336
(0.753)
MYH9 22 (4%) 488 0.016
(0.155) 		0.238
(0.618) 		0.544
(0.886) 		0.47
(0.857) 		0.557
(0.886) 		0.717
(0.962) 		0.704
(0.954) 		0.454
(0.852) 		0.846
(1.00) 		0.455
(0.852)
TP63 12 (2%) 498 0.2
(0.571) 		0.928
(1.00) 		0.821
(1.00) 		1
(1.00) 		0.5
(0.863) 		0.731
(0.962) 		0.0414
(0.248) 		0.427
(0.834) 		0.783
(0.98) 		0.549
(0.886)
PTPN14 15 (3%) 495 0.0182
(0.163) 		0.119
(0.434) 		0.848
(1.00) 		0.578
(0.889) 		0.226
(0.606) 		0.721
(0.962) 		0.0451
(0.263) 		0.638
(0.911) 		0.263
(0.656) 		0.451
(0.852)
IRF2 8 (2%) 502 0.066
(0.327) 		0.13
(0.444) 		0.0298
(0.214) 		0.0799
(0.355) 		0.807
(0.998) 		0.349
(0.768) 		0.434
(0.838) 		0.69
(0.947)
AMPD1 6 (1%) 504 0.115
(0.426) 		0.64
(0.911) 		0.339
(0.753) 		0.174
(0.511) 		0.293
(0.702) 		0.0309
(0.22) 		0.837
(1.00) 		0.119
(0.434)
CCNG2 3 (1%) 507 0.0368
(0.24) 		0.586
(0.889) 		1
(1.00) 		0.74
(0.962) 		0.482
(0.863) 		1
(1.00)
PTEN 14 (3%) 496 0.677
(0.945) 		0.449
(0.852) 		0.831
(1.00) 		0.833
(1.00) 		0.0803
(0.355) 		0.246
(0.629) 		0.377
(0.794) 		0.224
(0.604) 		0.114
(0.424) 		0.11
(0.424)
MAPK1 9 (2%) 501 0.105
(0.419) 		0.531
(0.879) 		1
(1.00) 		0.835
(1.00) 		0.451
(0.852) 		0.919
(1.00) 		0.489
(0.863) 		0.837
(1.00) 		1
(1.00) 		0.737
(0.962)
RASA1 17 (3%) 493 0.168
(0.504) 		0.0695
(0.334) 		0.388
(0.806) 		0.711
(0.962) 		0.424
(0.829) 		0.493
(0.863) 		0.552
(0.886) 		0.408
(0.808) 		0.404
(0.808) 		0.163
(0.498)
NAP1L2 7 (1%) 503 0.391
(0.808) 		0.58
(0.889) 		0.884
(1.00) 		0.483
(0.863) 		0.81
(0.999) 		0.898
(1.00) 		0.901
(1.00) 		0.602
(0.89)
RHOA 10 (2%) 500 0.103
(0.413) 		0.575
(0.889) 		0.168
(0.504) 		0.242
(0.626) 		1
(1.00) 		1
(1.00) 		0.725
(0.962) 		0.563
(0.886) 		0.687
(0.947) 		0.691
(0.947)
FBXW7 33 (6%) 477 0.453
(0.852) 		0.15
(0.479) 		0.503
(0.863) 		0.232
(0.614) 		0.125
(0.444) 		0.457
(0.852) 		0.297
(0.705) 		0.483
(0.863) 		0.21
(0.586) 		0.113
(0.424)
TIGD4 7 (1%) 503 0.497
(0.863) 		0.771
(0.975) 		0.292
(0.702) 		0.832
(1.00) 		0.72
(0.962) 		0.395
(0.808) 		0.653
(0.922) 		0.397
(0.808) 		0.956
(1.00) 		0.69
(0.947)
KRT5 11 (2%) 499 0.194
(0.558) 		0.747
(0.966) 		0.13
(0.444) 		0.223
(0.604) 		0.593
(0.889) 		0.622
(0.901) 		1
(1.00) 		0.0856
(0.373) 		0.819
(1.00) 		0.82
(1.00)
CES2 11 (2%) 499 0.369
(0.791) 		0.539
(0.881) 		0.93
(1.00) 		1
(1.00) 		0.433
(0.838) 		0.299
(0.706) 		0.466
(0.856) 		0.587
(0.889) 		0.974
(1.00) 		0.468
(0.856)
RGL4 7 (1%) 503 0.525
(0.877) 		0.978
(1.00) 		0.0551
(0.307) 		0.338
(0.753) 		0.807
(0.998) 		0.363
(0.784) 		0.43
(0.837) 		0.4
(0.808) 		0.17
(0.504) 		0.337
(0.753)
B2M 7 (1%) 503 0.194
(0.558) 		0.332
(0.752) 		0.242
(0.626) 		0.137
(0.449) 		0.0727
(0.34) 		0.159
(0.49) 		1
(1.00) 		0.127
(0.444)
PPFIA4 14 (3%) 496 0.895
(1.00) 		0.585
(0.889) 		0.286
(0.698) 		0.734
(0.962) 		0.658
(0.926) 		0.54
(0.881) 		0.0899
(0.382) 		0.316
(0.73) 		0.773
(0.975) 		0.632
(0.911)
PIK3R1 9 (2%) 501 0.518
(0.875) 		0.0678
(0.331) 		0.333
(0.752) 		0.135
(0.446) 		0.58
(0.889) 		0.25
(0.636) 		0.296
(0.704) 		0.397
(0.808)
C8ORF31 4 (1%) 506 1
(1.00) 		0.406
(0.808) 		0.387
(0.806) 		1
(1.00) 		0.692
(0.947) 		1
(1.00) 		0.842
(1.00) 		0.758
(0.969)
NCOR1 18 (4%) 492 0.877
(1.00) 		0.0901
(0.382) 		0.468
(0.856) 		0.495
(0.863) 		0.622
(0.901) 		0.17
(0.504) 		0.539
(0.881) 		0.109
(0.424) 		0.525
(0.877) 		0.853
(1.00)
SEH1L 4 (1%) 506 0.208
(0.586) 		0.0645
(0.326) 		0.309
(0.721) 		0.0451
(0.263) 		0.394
(0.808) 		0.098
(0.4) 		0.154
(0.486) 		1
(1.00)
NOTCH2 20 (4%) 490 0.453
(0.852) 		0.4
(0.808) 		0.075
(0.34) 		0.347
(0.766) 		0.594
(0.889) 		0.307
(0.721) 		0.502
(0.863) 		0.486
(0.863) 		0.901
(1.00) 		0.599
(0.89)
YTHDF1 6 (1%) 504 0.59
(0.889) 		0.839
(1.00) 		1
(1.00) 		0.834
(1.00) 		0.587
(0.889) 		0.518
(0.875) 		0.535
(0.881) 		1
(1.00)
FOSL2 10 (2%) 500 0.858
(1.00) 		0.415
(0.814) 		0.306
(0.721) 		0.511
(0.872) 		0.16
(0.491) 		0.372
(0.791) 		0.789
(0.985) 		0.78
(0.98) 		0.114
(0.424) 		0.133
(0.444)
TMEM2 17 (3%) 493 0.289
(0.701) 		0.0751
(0.34) 		0.863
(1.00) 		0.16
(0.491) 		0.315
(0.73) 		0.466
(0.856) 		0.702
(0.954) 		0.518
(0.875) 		0.72
(0.962) 		0.56
(0.886)
RBM10 4 (1%) 506 0.455
(0.852) 		0.526
(0.877) 		0.692
(0.947) 		0.667
(0.935) 		0.696
(0.949) 		0.565
(0.886) 		0.806
(0.998) 		0.654
(0.922)
ZMYM1 9 (2%) 501 0.961
(1.00) 		0.129
(0.444) 		0.506
(0.866) 		0.545
(0.886) 		0.534
(0.881) 		0.721
(0.962) 		0.761
(0.97) 		0.839
(1.00) 		0.743
(0.962) 		0.633
(0.911)
LCP1 15 (3%) 495 0.0738
(0.34) 		0.0899
(0.382) 		0.754
(0.969) 		0.827
(1.00) 		0.755
(0.969) 		0.0721
(0.34) 		0.946
(1.00) 		0.896
(1.00) 		0.736
(0.962) 		0.255
(0.644)
TACR2 4 (1%) 506 1
(1.00) 		0.862
(1.00) 		1
(1.00) 		0.904
(1.00) 		1
(1.00) 		0.684
(0.947) 		0.945
(1.00) 		1
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00038

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 = 0.00038

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 = 0.11 (Fisher's exact test), Q value = 0.42

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
TP53 MUTATED 45 34 29 56
TP53 WILD-TYPE 10 18 6 12
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.564 (Fisher's exact test), Q value = 0.89

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 = 2e-05 (Fisher's exact test), Q value = 0.00058

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 = 0.00038

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 = 0.00478 (Fisher's exact test), Q value = 0.061

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 = 0.00038

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 = 1e-05 (Fisher's exact test), Q value = 0.00038

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 = 0.00038

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 = 0.0238 (Fisher's exact test), Q value = 0.19

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 = 0.00038

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 = 0.00214 (Fisher's exact test), Q value = 0.035

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
CDKN2A MUTATED 11 7 17 21
CDKN2A WILD-TYPE 44 45 18 47

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 = 0.718 (Fisher's exact test), Q value = 0.96

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 = 0.0251 (Fisher's exact test), Q value = 0.2

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 = 2e-05 (Fisher's exact test), Q value = 0.00058

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 = 0.215 (Fisher's exact test), Q value = 0.59

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 = 0.0568 (Fisher's exact test), Q value = 0.31

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 = 0.00223 (Fisher's exact test), Q value = 0.036

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 = 0.0394 (Fisher's exact test), Q value = 0.24

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'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.66

Table S21.  Gene #3: '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 = 0.206 (Fisher's exact test), Q value = 0.59

Table S22.  Gene #3: '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 = 0.778 (Fisher's exact test), Q value = 0.98

Table S23.  Gene #3: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
PIK3CA MUTATED 12 9 8 11
PIK3CA WILD-TYPE 43 43 27 57
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0632 (Fisher's exact test), Q value = 0.33

Table S24.  Gene #3: '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 = 0.0411 (Fisher's exact test), Q value = 0.25

Table S25.  Gene #3: '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 S16.  Get High-res Image Gene #3: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 0.76

Table S26.  Gene #3: '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 = 0.00705 (Fisher's exact test), Q value = 0.088

Table S27.  Gene #3: '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 S17.  Get High-res Image Gene #3: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.19

Table S28.  Gene #3: '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 S18.  Get High-res Image Gene #3: '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 = 0.85

Table S29.  Gene #3: '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 = 0.0947 (Fisher's exact test), Q value = 0.39

Table S30.  Gene #3: '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
'NSD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00435 (Fisher's exact test), Q value = 0.058

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 S19.  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 = 0.00038

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 S20.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.64

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
NSD1 MUTATED 7 7 4 3
NSD1 WILD-TYPE 48 45 31 65
'NSD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0149 (Fisher's exact test), Q value = 0.15

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 S21.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00058

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 S22.  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 = 0.00038

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 S23.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0025 (Fisher's exact test), Q value = 0.038

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 S24.  Get High-res Image Gene #4: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0014

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 S25.  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 = 0.00038

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 S26.  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 = 3e-05 (Fisher's exact test), Q value = 8e-04

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 S27.  Get High-res Image Gene #4: 'NSD1 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 = 0.00038

Table S41.  Gene #5: '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 S28.  Get High-res Image Gene #5: '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 = 0.00038

Table S42.  Gene #5: '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 S29.  Get High-res Image Gene #5: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.15

Table S43.  Gene #5: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
CASP8 MUTATED 5 1 8 8
CASP8 WILD-TYPE 50 51 27 60

Figure S30.  Get High-res Image Gene #5: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.351 (Fisher's exact test), Q value = 0.77

Table S44.  Gene #5: '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 = 0.00038

Table S45.  Gene #5: '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 S31.  Get High-res Image Gene #5: '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 = 0.00038

Table S46.  Gene #5: '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 S32.  Get High-res Image Gene #5: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.009 (Fisher's exact test), Q value = 0.1

Table S47.  Gene #5: '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 S33.  Get High-res Image Gene #5: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.89

Table S48.  Gene #5: '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 = 0.0055

Table S49.  Gene #5: '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 S34.  Get High-res Image Gene #5: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.45

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

P value = 3e-05 (Fisher's exact test), Q value = 8e-04

Table S51.  Gene #6: '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 S35.  Get High-res Image Gene #6: '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 = 0.00038

Table S52.  Gene #6: '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 S36.  Get High-res Image Gene #6: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
HRAS MUTATED 1 1 3 3
HRAS WILD-TYPE 54 51 32 65
'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 0.92

Table S54.  Gene #6: '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 = 0.00051 (Fisher's exact test), Q value = 0.011

Table S55.  Gene #6: '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 S37.  Get High-res Image Gene #6: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00229 (Fisher's exact test), Q value = 0.036

Table S56.  Gene #6: '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 S38.  Get High-res Image Gene #6: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00074 (Fisher's exact test), Q value = 0.015

Table S57.  Gene #6: '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 S39.  Get High-res Image Gene #6: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.44

Table S58.  Gene #6: '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 = 0.0214 (Fisher's exact test), Q value = 0.18

Table S59.  Gene #6: '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 S40.  Get High-res Image Gene #6: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.51

Table S60.  Gene #6: '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
'TGFBR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0124 (Fisher's exact test), Q value = 0.13

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 S41.  Get High-res Image Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.058 (Fisher's exact test), Q value = 0.31

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 = 0.466 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
TGFBR2 MUTATED 3 1 0 4
TGFBR2 WILD-TYPE 52 51 35 64
'TGFBR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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 = 0.103 (Fisher's exact test), Q value = 0.41

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 = 0.637 (Fisher's exact test), Q value = 0.91

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 = 0.57 (Fisher's exact test), Q value = 0.89

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 = 0.727 (Fisher's exact test), Q value = 0.96

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 = 0.516 (Fisher's exact test), Q value = 0.88

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 = 0.65

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 = 0.00038

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 S42.  Get High-res Image Gene #8: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
FAT1 MUTATED 12 11 6 17
FAT1 WILD-TYPE 43 41 29 51
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 0.86

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 = 0.47

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 = 0.00035 (Fisher's exact test), Q value = 0.0077

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 S43.  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 = 1

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 = 0.595 (Fisher's exact test), Q value = 0.89

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 = 0.00325 (Fisher's exact test), Q value = 0.045

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 S44.  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 = 0.1 (Fisher's exact test), Q value = 0.41

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 = 0.0151 (Fisher's exact test), Q value = 0.15

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 S45.  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 = 0.001

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 S46.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.057 (Fisher's exact test), Q value = 0.31

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
NOTCH1 MUTATED 15 4 6 14
NOTCH1 WILD-TYPE 40 48 29 54
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0595 (Fisher's exact test), Q value = 0.31

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 = 0.00038

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 S47.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00141 (Fisher's exact test), Q value = 0.024

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 S48.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00058

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 S49.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0664 (Fisher's exact test), Q value = 0.33

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 = 0.00849 (Fisher's exact test), Q value = 0.1

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 S50.  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 = 0.0375 (Fisher's exact test), Q value = 0.24

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 S51.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 0.86

Table S91.  Gene #10: '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 = 6e-05 (Fisher's exact test), Q value = 0.0014

Table S92.  Gene #10: '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 S52.  Get High-res Image Gene #10: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 0.97

Table S93.  Gene #10: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
EPHA2 MUTATED 4 2 1 5
EPHA2 WILD-TYPE 51 50 34 63
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: '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 = 0.31 (Fisher's exact test), Q value = 0.72

Table S95.  Gene #10: '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 = 0.7

Table S96.  Gene #10: '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 = 0.895 (Fisher's exact test), Q value = 1

Table S97.  Gene #10: '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 = 0.5

Table S98.  Gene #10: '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 = 0.42

Table S99.  Gene #10: '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 = 0.649 (Fisher's exact test), Q value = 0.92

Table S100.  Gene #10: '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-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.49

Table S101.  Gene #11: '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 = 0.00127 (Fisher's exact test), Q value = 0.024

Table S102.  Gene #11: '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 S53.  Get High-res Image Gene #11: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S103.  Gene #11: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
HLA-B MUTATED 2 2 1 2
HLA-B WILD-TYPE 53 50 34 66
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.6

Table S104.  Gene #11: '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 = 0.0353 (Fisher's exact test), Q value = 0.24

Table S105.  Gene #11: '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 S54.  Get High-res Image Gene #11: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.063 (Fisher's exact test), Q value = 0.33

Table S106.  Gene #11: '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 = 0.057 (Fisher's exact test), Q value = 0.31

Table S107.  Gene #11: '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 = 0.209 (Fisher's exact test), Q value = 0.59

Table S108.  Gene #11: '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 = 0.0861 (Fisher's exact test), Q value = 0.37

Table S109.  Gene #11: '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 = 0.036 (Fisher's exact test), Q value = 0.24

Table S110.  Gene #11: '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 S55.  Get High-res Image Gene #11: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.42

Table S111.  Gene #12: '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 = 0.0355 (Fisher's exact test), Q value = 0.24

Table S112.  Gene #12: '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 S56.  Get High-res Image Gene #12: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S113.  Gene #12: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
RAC1 MUTATED 1 1 1 1
RAC1 WILD-TYPE 54 51 34 67
'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: '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 = 0.24

Table S115.  Gene #12: '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 S57.  Get High-res Image Gene #12: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0692 (Fisher's exact test), Q value = 0.33

Table S116.  Gene #12: '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 = 0.45 (Fisher's exact test), Q value = 0.85

Table S117.  Gene #12: '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 = 0.406 (Fisher's exact test), Q value = 0.81

Table S118.  Gene #12: '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 = 0.18 (Fisher's exact test), Q value = 0.52

Table S119.  Gene #12: '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 = 0.325 (Fisher's exact test), Q value = 0.74

Table S120.  Gene #12: '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
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 0.86

Table S121.  Gene #13: '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 = 2e-05 (Fisher's exact test), Q value = 0.00058

Table S122.  Gene #13: '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 S58.  Get High-res Image Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.501 (Fisher's exact test), Q value = 0.86

Table S123.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
NFE2L2 MUTATED 4 5 2 2
NFE2L2 WILD-TYPE 51 47 33 66
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: '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 = 1

Table S125.  Gene #13: '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 = 0.468 (Fisher's exact test), Q value = 0.86

Table S126.  Gene #13: '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 = 0.233 (Fisher's exact test), Q value = 0.61

Table S127.  Gene #13: '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 = 0.493 (Fisher's exact test), Q value = 0.86

Table S128.  Gene #13: '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 = 0.89

Table S129.  Gene #13: '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 = 0.357 (Fisher's exact test), Q value = 0.77

Table S130.  Gene #13: '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
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.59

Table S131.  Gene #14: '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 = 0.0106 (Fisher's exact test), Q value = 0.12

Table S132.  Gene #14: '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 S59.  Get High-res Image Gene #14: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 0.97

Table S133.  Gene #14: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
ZNF750 MUTATED 1 2 0 2
ZNF750 WILD-TYPE 54 50 35 66
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.7

Table S134.  Gene #14: '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 = 0.00732 (Fisher's exact test), Q value = 0.09

Table S135.  Gene #14: '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 S60.  Get High-res Image Gene #14: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0152 (Fisher's exact test), Q value = 0.15

Table S136.  Gene #14: '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 S61.  Get High-res Image Gene #14: '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 = 0.16

Table S137.  Gene #14: '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 S62.  Get High-res Image Gene #14: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.44

Table S138.  Gene #14: '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 = 0.0505 (Fisher's exact test), Q value = 0.28

Table S139.  Gene #14: '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
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.18

Table S140.  Gene #14: '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 S63.  Get High-res Image Gene #14: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.95

Table S141.  Gene #15: '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 = 0.449 (Fisher's exact test), Q value = 0.85

Table S142.  Gene #15: '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 = 0.831 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
PTEN MUTATED 2 1 0 1
PTEN WILD-TYPE 53 51 35 67
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: '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 = 0.0803 (Fisher's exact test), Q value = 0.35

Table S145.  Gene #15: '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 = 0.246 (Fisher's exact test), Q value = 0.63

Table S146.  Gene #15: '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 = 0.377 (Fisher's exact test), Q value = 0.79

Table S147.  Gene #15: '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 = 0.6

Table S148.  Gene #15: '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 = 0.114 (Fisher's exact test), Q value = 0.42

Table S149.  Gene #15: '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 = 0.11 (Fisher's exact test), Q value = 0.42

Table S150.  Gene #15: '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
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00313 (Fisher's exact test), Q value = 0.045

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 S64.  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 = 0.00319 (Fisher's exact test), Q value = 0.045

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 S65.  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 = 1 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
HLA-A MUTATED 1 1 1 2
HLA-A WILD-TYPE 54 51 34 66
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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 = 0.00473 (Fisher's exact test), Q value = 0.061

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 S66.  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 = 0.00256 (Fisher's exact test), Q value = 0.038

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 S67.  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 = 0.0364 (Fisher's exact test), Q value = 0.24

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 S68.  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 = 0.12 (Fisher's exact test), Q value = 0.43

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 = 0.552 (Fisher's exact test), Q value = 0.89

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 = 0.475 (Fisher's exact test), Q value = 0.86

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
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 0.89

Table S161.  Gene #17: '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 = 0.371 (Fisher's exact test), Q value = 0.79

Table S162.  Gene #17: '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 = 0.355 (Fisher's exact test), Q value = 0.77

Table S163.  Gene #17: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
RB1 MUTATED 0 1 0 3
RB1 WILD-TYPE 55 51 35 65
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.67

Table S164.  Gene #17: '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 = 0.0372 (Fisher's exact test), Q value = 0.24

Table S165.  Gene #17: '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 S69.  Get High-res Image Gene #17: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.79

Table S166.  Gene #17: '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 = 0.49

Table S167.  Gene #17: '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 = 0.497 (Fisher's exact test), Q value = 0.86

Table S168.  Gene #17: '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 = 0.385 (Fisher's exact test), Q value = 0.81

Table S169.  Gene #17: '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 = 0.618 (Fisher's exact test), Q value = 0.9

Table S170.  Gene #17: '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
'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.42

Table S171.  Gene #18: '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 = 0.531 (Fisher's exact test), Q value = 0.88

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

Table S173.  Gene #18: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
MAPK1 MUTATED 1 1 1 1
MAPK1 WILD-TYPE 54 51 34 67
'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S174.  Gene #18: '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 = 0.451 (Fisher's exact test), Q value = 0.85

Table S175.  Gene #18: '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 = 0.919 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: '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 = 0.489 (Fisher's exact test), Q value = 0.86

Table S177.  Gene #18: '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 = 0.837 (Fisher's exact test), Q value = 1

Table S178.  Gene #18: '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 S179.  Gene #18: '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 = 0.737 (Fisher's exact test), Q value = 0.96

Table S180.  Gene #18: '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
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0296 (Fisher's exact test), Q value = 0.21

Table S181.  Gene #19: '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 S70.  Get High-res Image Gene #19: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 0.97

Table S182.  Gene #19: '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 = 0.142 (Fisher's exact test), Q value = 0.46

Table S183.  Gene #19: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
KDM6A MUTATED 1 3 1 0
KDM6A WILD-TYPE 54 49 34 68
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S184.  Gene #19: '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 = 0.899 (Fisher's exact test), Q value = 1

Table S185.  Gene #19: '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 = 0.39 (Fisher's exact test), Q value = 0.81

Table S186.  Gene #19: '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 = 1

Table S187.  Gene #19: '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 = 0.863 (Fisher's exact test), Q value = 1

Table S188.  Gene #19: '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 = 0.564 (Fisher's exact test), Q value = 0.89

Table S189.  Gene #19: '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 = 0.582 (Fisher's exact test), Q value = 0.89

Table S190.  Gene #19: '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
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.85

Table S191.  Gene #20: '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 = 0.0348 (Fisher's exact test), Q value = 0.24

Table S192.  Gene #20: '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 S71.  Get High-res Image Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 0.89

Table S193.  Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
EP300 MUTATED 3 2 4 4
EP300 WILD-TYPE 52 50 31 64
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0848 (Fisher's exact test), Q value = 0.37

Table S194.  Gene #20: '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 = 0.00763 (Fisher's exact test), Q value = 0.092

Table S195.  Gene #20: '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 S72.  Get High-res Image Gene #20: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.091 (Fisher's exact test), Q value = 0.38

Table S196.  Gene #20: '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 = 0.554 (Fisher's exact test), Q value = 0.89

Table S197.  Gene #20: '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 = 0.237 (Fisher's exact test), Q value = 0.62

Table S198.  Gene #20: '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 = 0.0398 (Fisher's exact test), Q value = 0.24

Table S199.  Gene #20: '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 S73.  Get High-res Image Gene #20: '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 S200.  Gene #20: '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
'RASA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.5

Table S201.  Gene #21: '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 = 0.0695 (Fisher's exact test), Q value = 0.33

Table S202.  Gene #21: '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 = 0.388 (Fisher's exact test), Q value = 0.81

Table S203.  Gene #21: 'RASA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
RASA1 MUTATED 5 1 1 3
RASA1 WILD-TYPE 50 51 34 65
'RASA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.711 (Fisher's exact test), Q value = 0.96

Table S204.  Gene #21: '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 = 0.83

Table S205.  Gene #21: '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 = 0.493 (Fisher's exact test), Q value = 0.86

Table S206.  Gene #21: '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 = 0.89

Table S207.  Gene #21: '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 = 0.408 (Fisher's exact test), Q value = 0.81

Table S208.  Gene #21: '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 = 0.404 (Fisher's exact test), Q value = 0.81

Table S209.  Gene #21: '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 = 0.163 (Fisher's exact test), Q value = 0.5

Table S210.  Gene #21: '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
'NAP1L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.81

Table S211.  Gene #22: '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 = 0.58 (Fisher's exact test), Q value = 0.89

Table S212.  Gene #22: '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 = 0.884 (Fisher's exact test), Q value = 1

Table S213.  Gene #22: '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 = 0.483 (Fisher's exact test), Q value = 0.86

Table S214.  Gene #22: '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 = 1

Table S215.  Gene #22: '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 = 1

Table S216.  Gene #22: '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 = 0.901 (Fisher's exact test), Q value = 1

Table S217.  Gene #22: '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 = 0.602 (Fisher's exact test), Q value = 0.89

Table S218.  Gene #22: '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
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0266 (Fisher's exact test), Q value = 0.21

Table S219.  Gene #23: '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 S74.  Get High-res Image Gene #23: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 0.89

Table S220.  Gene #23: '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 = 0.741 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
CREBBP MUTATED 4 4 1 3
CREBBP WILD-TYPE 51 48 34 65
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: '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 = 0.131 (Fisher's exact test), Q value = 0.44

Table S223.  Gene #23: '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 = 0.44

Table S224.  Gene #23: '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 = 0.487 (Fisher's exact test), Q value = 0.86

Table S225.  Gene #23: '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 = 0.0356 (Fisher's exact test), Q value = 0.24

Table S226.  Gene #23: '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 S75.  Get High-res Image Gene #23: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0596 (Fisher's exact test), Q value = 0.31

Table S227.  Gene #23: '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 = 0.44

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

P value = 0.0503 (Fisher's exact test), Q value = 0.28

Table S229.  Gene #24: '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
'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.024

Table S230.  Gene #24: '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 S76.  Get High-res Image Gene #24: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
CTCF MUTATED 2 2 0 4
CTCF WILD-TYPE 53 50 35 64
'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.523 (Fisher's exact test), Q value = 0.88

Table S232.  Gene #24: '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 = 0.86

Table S233.  Gene #24: '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 = 0.272 (Fisher's exact test), Q value = 0.67

Table S234.  Gene #24: '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 = 0.95

Table S235.  Gene #24: '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 = 0.901 (Fisher's exact test), Q value = 1

Table S236.  Gene #24: '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 = 0.737 (Fisher's exact test), Q value = 0.96

Table S237.  Gene #24: '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 = 0.97

Table S238.  Gene #24: '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
'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.44

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 = 0.0653 (Fisher's exact test), Q value = 0.33

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 = 0.61 (Fisher's exact test), Q value = 0.9

Table S241.  Gene #25: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
KEAP1 MUTATED 3 3 0 3
KEAP1 WILD-TYPE 52 49 35 65
'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

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 = 0.0945 (Fisher's exact test), Q value = 0.39

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 = 0.00138 (Fisher's exact test), Q value = 0.024

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 = 0.268 (Fisher's exact test), Q value = 0.66

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 = 0.0384 (Fisher's exact test), Q value = 0.24

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 = 0.409 (Fisher's exact test), Q value = 0.81

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 = 0.0706 (Fisher's exact test), Q value = 0.34

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
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.41

Table S249.  Gene #26: '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 = 0.575 (Fisher's exact test), Q value = 0.89

Table S250.  Gene #26: '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 = 0.168 (Fisher's exact test), Q value = 0.5

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
RHOA MUTATED 0 0 0 3
RHOA WILD-TYPE 55 52 35 65
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.63

Table S252.  Gene #26: '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 S253.  Gene #26: '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 S254.  Gene #26: '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 = 0.725 (Fisher's exact test), Q value = 0.96

Table S255.  Gene #26: '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 = 0.89

Table S256.  Gene #26: '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 = 0.687 (Fisher's exact test), Q value = 0.95

Table S257.  Gene #26: '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 = 0.691 (Fisher's exact test), Q value = 0.95

Table S258.  Gene #26: '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
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.85

Table S259.  Gene #27: '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 = 0.15 (Fisher's exact test), Q value = 0.48

Table S260.  Gene #27: '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 = 0.503 (Fisher's exact test), Q value = 0.86

Table S261.  Gene #27: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
FBXW7 MUTATED 1 4 1 4
FBXW7 WILD-TYPE 54 48 34 64
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.61

Table S262.  Gene #27: '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 = 0.125 (Fisher's exact test), Q value = 0.44

Table S263.  Gene #27: '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 = 0.457 (Fisher's exact test), Q value = 0.85

Table S264.  Gene #27: '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 = 0.7

Table S265.  Gene #27: '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 = 0.483 (Fisher's exact test), Q value = 0.86

Table S266.  Gene #27: '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 = 0.21 (Fisher's exact test), Q value = 0.59

Table S267.  Gene #27: '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 = 0.42

Table S268.  Gene #27: '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
'TIGD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.86

Table S269.  Gene #28: '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 = 0.771 (Fisher's exact test), Q value = 0.98

Table S270.  Gene #28: '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 = 0.292 (Fisher's exact test), Q value = 0.7

Table S271.  Gene #28: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
TIGD4 MUTATED 1 0 2 1
TIGD4 WILD-TYPE 54 52 33 67
'TIGD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S272.  Gene #28: '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 = 0.72 (Fisher's exact test), Q value = 0.96

Table S273.  Gene #28: '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 = 0.81

Table S274.  Gene #28: '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 = 0.92

Table S275.  Gene #28: '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 = 0.397 (Fisher's exact test), Q value = 0.81

Table S276.  Gene #28: '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 = 0.956 (Fisher's exact test), Q value = 1

Table S277.  Gene #28: '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 = 0.69 (Fisher's exact test), Q value = 0.95

Table S278.  Gene #28: '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
'KRT5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.56

Table S279.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
KRT5 MUTATED 3 6 2 0
KRT5 WILD-TYPE 144 124 183 42
'KRT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 0.97

Table S280.  Gene #29: 'KRT5 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
KRT5 MUTATED 1 1 3 3 1 1 1
KRT5 WILD-TYPE 83 74 91 85 75 73 18
'KRT5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.44

Table S281.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
KRT5 MUTATED 1 0 3 3
KRT5 WILD-TYPE 54 52 32 65
'KRT5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.6

Table S282.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
KRT5 MUTATED 3 1 3
KRT5 WILD-TYPE 75 84 44
'KRT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.593 (Fisher's exact test), Q value = 0.89

Table S283.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
KRT5 MUTATED 4 3 4
KRT5 WILD-TYPE 135 202 154
'KRT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.622 (Fisher's exact test), Q value = 0.9

Table S284.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
KRT5 MUTATED 6 2 2 1
KRT5 WILD-TYPE 170 97 163 61
'KRT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S285.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
KRT5 MUTATED 5 3 3
KRT5 WILD-TYPE 204 148 142
'KRT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0856 (Fisher's exact test), Q value = 0.37

Table S286.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
KRT5 MUTATED 6 0 5
KRT5 WILD-TYPE 182 137 175
'KRT5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S287.  Gene #29: 'KRT5 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
KRT5 MUTATED 2 3 1 3 0
KRT5 WILD-TYPE 66 136 92 111 46
'KRT5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S288.  Gene #29: 'KRT5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
KRT5 MUTATED 3 4 2
KRT5 WILD-TYPE 135 234 82
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.88

Table S289.  Gene #30: '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 3 3 1
SMAD4 WILD-TYPE 141 127 182 41
'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S290.  Gene #30: '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 2 3 2 2 3 1
SMAD4 WILD-TYPE 83 73 91 86 74 71 18
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0382 (Fisher's exact test), Q value = 0.24

Table S291.  Gene #30: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
SMAD4 MUTATED 4 2 0 0
SMAD4 WILD-TYPE 51 50 35 68

Figure S79.  Get High-res Image Gene #30: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S292.  Gene #30: '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 = 0.402 (Fisher's exact test), Q value = 0.81

Table S293.  Gene #30: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
SMAD4 MUTATED 6 4 4
SMAD4 WILD-TYPE 133 201 154
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.783 (Fisher's exact test), Q value = 0.98

Table S294.  Gene #30: '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 2 4 1
SMAD4 WILD-TYPE 169 97 161 61
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0195 (Fisher's exact test), Q value = 0.17

Table S295.  Gene #30: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
SMAD4 MUTATED 8 0 6
SMAD4 WILD-TYPE 201 151 139

Figure S80.  Get High-res Image Gene #30: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 0.86

Table S296.  Gene #30: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
SMAD4 MUTATED 7 4 3
SMAD4 WILD-TYPE 181 133 177
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S297.  Gene #30: '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 2 2 1
SMAD4 WILD-TYPE 65 135 91 112 45
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 0.81

Table S298.  Gene #30: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
SMAD4 MUTATED 5 4 3
SMAD4 WILD-TYPE 133 234 81
'ASXL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 0.96

Table S299.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
ASXL1 MUTATED 4 5 7 0
ASXL1 WILD-TYPE 143 125 178 42
'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.7

Table S300.  Gene #31: 'ASXL1 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
ASXL1 MUTATED 3 0 3 4 2 2 2
ASXL1 WILD-TYPE 81 75 91 84 74 72 17
'ASXL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 0.91

Table S301.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
ASXL1 MUTATED 2 1 2 1
ASXL1 WILD-TYPE 53 51 33 67
'ASXL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S302.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ASXL1 MUTATED 3 2 1
ASXL1 WILD-TYPE 75 83 46
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 0.34

Table S303.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
ASXL1 MUTATED 1 7 8
ASXL1 WILD-TYPE 138 198 150
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.017 (Fisher's exact test), Q value = 0.16

Table S304.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
ASXL1 MUTATED 1 4 10 1
ASXL1 WILD-TYPE 175 95 155 61

Figure S81.  Get High-res Image Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 0.31

Table S305.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
ASXL1 MUTATED 7 8 1
ASXL1 WILD-TYPE 202 143 144
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0646 (Fisher's exact test), Q value = 0.33

Table S306.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
ASXL1 MUTATED 2 7 7
ASXL1 WILD-TYPE 186 130 173
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.833 (Fisher's exact test), Q value = 1

Table S307.  Gene #31: 'ASXL1 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
ASXL1 MUTATED 1 4 4 5 2
ASXL1 WILD-TYPE 67 135 89 109 44
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.12

Table S308.  Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
ASXL1 MUTATED 2 14 0
ASXL1 WILD-TYPE 136 224 84

Figure S82.  Get High-res Image Gene #31: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CES2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.369 (Fisher's exact test), Q value = 0.79

Table S309.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CES2 MUTATED 2 4 3 2
CES2 WILD-TYPE 145 126 182 40
'CES2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.88

Table S310.  Gene #32: 'CES2 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
CES2 MUTATED 1 2 3 4 0 1 0
CES2 WILD-TYPE 83 73 91 84 76 73 19
'CES2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S311.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
CES2 MUTATED 2 1 1 1
CES2 WILD-TYPE 53 51 34 67
'CES2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S312.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
CES2 MUTATED 2 2 1
CES2 WILD-TYPE 76 83 46
'CES2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.84

Table S313.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CES2 MUTATED 5 4 2
CES2 WILD-TYPE 134 201 156
'CES2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.71

Table S314.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CES2 MUTATED 5 4 2 0
CES2 WILD-TYPE 171 95 163 62
'CES2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.86

Table S315.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CES2 MUTATED 4 2 5
CES2 WILD-TYPE 205 149 140
'CES2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 0.89

Table S316.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CES2 MUTATED 6 2 3
CES2 WILD-TYPE 182 135 177
'CES2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.974 (Fisher's exact test), Q value = 1

Table S317.  Gene #32: 'CES2 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
CES2 MUTATED 2 3 2 2 1
CES2 WILD-TYPE 66 136 91 112 45
'CES2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.86

Table S318.  Gene #32: 'CES2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
CES2 MUTATED 5 4 1
CES2 WILD-TYPE 133 234 83
'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.56

Table S319.  Gene #33: '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 = 0.89

Table S320.  Gene #33: '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 = 0.259 (Fisher's exact test), Q value = 0.65

Table S321.  Gene #33: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
IRS4 MUTATED 1 2 3 1
IRS4 WILD-TYPE 54 50 32 67
'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.79 (Fisher's exact test), Q value = 0.99

Table S322.  Gene #33: '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 = 0.44

Table S323.  Gene #33: '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 = 0.34

Table S324.  Gene #33: '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 = 0.59

Table S325.  Gene #33: '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 = 0.0643 (Fisher's exact test), Q value = 0.33

Table S326.  Gene #33: '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 = 0.0149 (Fisher's exact test), Q value = 0.15

Table S327.  Gene #33: '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 S83.  Get High-res Image Gene #33: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.6

Table S328.  Gene #33: '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
'ARID2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.74

Table S329.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
ARID2 MUTATED 6 2 10 2
ARID2 WILD-TYPE 141 128 175 40
'ARID2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.21

Table S330.  Gene #34: 'ARID2 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
ARID2 MUTATED 2 1 3 3 1 9 1
ARID2 WILD-TYPE 82 74 91 85 75 65 18

Figure S84.  Get High-res Image Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ARID2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 0.9

Table S331.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
ARID2 MUTATED 3 2 0 2
ARID2 WILD-TYPE 52 50 35 66
'ARID2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 0.99

Table S332.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ARID2 MUTATED 3 2 2
ARID2 WILD-TYPE 75 83 45
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.61

Table S333.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
ARID2 MUTATED 4 6 10
ARID2 WILD-TYPE 135 199 148
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.615 (Fisher's exact test), Q value = 0.9

Table S334.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
ARID2 MUTATED 7 2 9 2
ARID2 WILD-TYPE 169 97 156 60
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.167 (Fisher's exact test), Q value = 0.5

Table S335.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
ARID2 MUTATED 6 10 4
ARID2 WILD-TYPE 203 141 141
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.681 (Fisher's exact test), Q value = 0.95

Table S336.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
ARID2 MUTATED 6 5 9
ARID2 WILD-TYPE 182 132 171
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 0.88

Table S337.  Gene #34: 'ARID2 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
ARID2 MUTATED 1 9 3 4 1
ARID2 WILD-TYPE 67 130 90 110 45
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 0.95

Table S338.  Gene #34: 'ARID2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
ARID2 MUTATED 4 10 4
ARID2 WILD-TYPE 134 228 80
'CBWD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.594 (Fisher's exact test), Q value = 0.89

Table S339.  Gene #35: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CBWD1 MUTATED 2 0 3 0
CBWD1 WILD-TYPE 145 130 182 42
'CBWD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.804 (Fisher's exact test), Q value = 1

Table S340.  Gene #35: 'CBWD1 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
CBWD1 MUTATED 1 1 2 0 0 1 0
CBWD1 WILD-TYPE 83 74 92 88 76 73 19
'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S341.  Gene #35: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CBWD1 MUTATED 1 2 2
CBWD1 WILD-TYPE 138 203 156
'CBWD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S342.  Gene #35: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CBWD1 MUTATED 2 1 2 0
CBWD1 WILD-TYPE 174 98 163 62
'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S343.  Gene #35: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CBWD1 MUTATED 2 2 1
CBWD1 WILD-TYPE 207 149 144
'CBWD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.855 (Fisher's exact test), Q value = 1

Table S344.  Gene #35: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CBWD1 MUTATED 2 2 1
CBWD1 WILD-TYPE 186 135 179
'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S345.  Gene #35: 'CBWD1 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
CBWD1 MUTATED 0 3 1 1 0
CBWD1 WILD-TYPE 68 136 92 113 46
'CBWD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0125 (Fisher's exact test), Q value = 0.13

Table S346.  Gene #35: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
CBWD1 MUTATED 2 0 3
CBWD1 WILD-TYPE 136 238 81

Figure S85.  Get High-res Image Gene #35: 'CBWD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RGL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 0.88

Table S347.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
RGL4 MUTATED 1 1 4 1
RGL4 WILD-TYPE 146 129 181 41
'RGL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S348.  Gene #36: 'RGL4 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
RGL4 MUTATED 1 1 1 1 2 1 0
RGL4 WILD-TYPE 83 74 93 87 74 73 19
'RGL4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0551 (Fisher's exact test), Q value = 0.31

Table S349.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
RGL4 MUTATED 0 1 2 0
RGL4 WILD-TYPE 55 51 33 68
'RGL4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.75

Table S350.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
RGL4 MUTATED 2 0 1
RGL4 WILD-TYPE 76 85 46
'RGL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S351.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
RGL4 MUTATED 1 3 3
RGL4 WILD-TYPE 138 202 155
'RGL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.78

Table S352.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
RGL4 MUTATED 1 1 3 2
RGL4 WILD-TYPE 175 98 162 60
'RGL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.84

Table S353.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
RGL4 MUTATED 5 1 1
RGL4 WILD-TYPE 204 150 144
'RGL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.4 (Fisher's exact test), Q value = 0.81

Table S354.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
RGL4 MUTATED 1 3 3
RGL4 WILD-TYPE 187 134 177
'RGL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.5

Table S355.  Gene #36: 'RGL4 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
RGL4 MUTATED 0 0 2 3 1
RGL4 WILD-TYPE 68 139 91 111 45
'RGL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.337 (Fisher's exact test), Q value = 0.75

Table S356.  Gene #36: 'RGL4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
RGL4 MUTATED 1 5 0
RGL4 WILD-TYPE 137 233 84
'HUWE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.022

Table S357.  Gene #37: '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 S86.  Get High-res Image Gene #37: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HUWE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00044 (Fisher's exact test), Q value = 0.0094

Table S358.  Gene #37: '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 S87.  Get High-res Image Gene #37: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HUWE1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.81

Table S359.  Gene #37: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
HUWE1 MUTATED 5 1 3 5
HUWE1 WILD-TYPE 50 51 32 63
'HUWE1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.91

Table S360.  Gene #37: '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 = 0.0178 (Fisher's exact test), Q value = 0.16

Table S361.  Gene #37: '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 S88.  Get High-res Image Gene #37: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HUWE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0428 (Fisher's exact test), Q value = 0.25

Table S362.  Gene #37: '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 S89.  Get High-res Image Gene #37: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HUWE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.51

Table S363.  Gene #37: '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 = 0.668 (Fisher's exact test), Q value = 0.93

Table S364.  Gene #37: '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 = 0.132 (Fisher's exact test), Q value = 0.44

Table S365.  Gene #37: '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 = 0.157 (Fisher's exact test), Q value = 0.49

Table S366.  Gene #37: '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
'HNRNPL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.86

Table S367.  Gene #38: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
HNRNPL MUTATED 5 1 4 1
HNRNPL WILD-TYPE 142 129 181 41
'HNRNPL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0209 (Fisher's exact test), Q value = 0.18

Table S368.  Gene #38: 'HNRNPL 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
HNRNPL MUTATED 2 1 0 2 0 4 2
HNRNPL WILD-TYPE 82 74 94 86 76 70 17

Figure S90.  Get High-res Image Gene #38: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HNRNPL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
HNRNPL MUTATED 2 2 2 0
HNRNPL WILD-TYPE 53 50 33 68
'HNRNPL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
HNRNPL MUTATED 2 2 2
HNRNPL WILD-TYPE 76 83 45
'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.597 (Fisher's exact test), Q value = 0.89

Table S371.  Gene #38: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
HNRNPL MUTATED 4 3 4
HNRNPL WILD-TYPE 135 202 154
'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.353 (Fisher's exact test), Q value = 0.77

Table S372.  Gene #38: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
HNRNPL MUTATED 6 3 2 0
HNRNPL WILD-TYPE 170 96 163 62
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 0.96

Table S373.  Gene #38: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
HNRNPL MUTATED 5 2 4
HNRNPL WILD-TYPE 204 149 141
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 0.44

Table S374.  Gene #38: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
HNRNPL MUTATED 5 5 1
HNRNPL WILD-TYPE 183 132 179
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 0.97

Table S375.  Gene #38: 'HNRNPL 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
HNRNPL MUTATED 2 2 3 3 0
HNRNPL WILD-TYPE 66 137 90 111 46
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 0.86

Table S376.  Gene #38: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
HNRNPL MUTATED 5 4 1
HNRNPL WILD-TYPE 133 234 83
'ITGB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 0.9

Table S377.  Gene #39: '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 5 4 0
ITGB1 WILD-TYPE 142 125 181 42
'ITGB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0752 (Fisher's exact test), Q value = 0.34

Table S378.  Gene #39: '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 2 1 5 1 5 0
ITGB1 WILD-TYPE 84 73 93 83 75 69 19
'ITGB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.68

Table S379.  Gene #39: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
ITGB1 MUTATED 2 1 3 1
ITGB1 WILD-TYPE 53 51 32 67
'ITGB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 0.9

Table S380.  Gene #39: '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 = 0.0183 (Fisher's exact test), Q value = 0.16

Table S381.  Gene #39: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
ITGB1 MUTATED 0 6 8
ITGB1 WILD-TYPE 139 199 150

Figure S91.  Get High-res Image Gene #39: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ITGB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0475 (Fisher's exact test), Q value = 0.27

Table S382.  Gene #39: '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 5 7 1
ITGB1 WILD-TYPE 175 94 158 61

Figure S92.  Get High-res Image Gene #39: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ITGB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.81

Table S383.  Gene #39: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
ITGB1 MUTATED 8 4 2
ITGB1 WILD-TYPE 201 147 143
'ITGB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.42

Table S384.  Gene #39: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
ITGB1 MUTATED 2 4 8
ITGB1 WILD-TYPE 186 133 172
'ITGB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.47

Table S385.  Gene #39: '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 4 7 0
ITGB1 WILD-TYPE 67 137 89 107 46
'ITGB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 0.89

Table S386.  Gene #39: 'ITGB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
ITGB1 MUTATED 4 9 1
ITGB1 WILD-TYPE 134 229 83
'B2M MUTATION STATUS' versus 'CN_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.56

Table S387.  Gene #40: 'B2M MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
B2M MUTATED 0 2 5 0
B2M WILD-TYPE 147 128 180 42
'B2M MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.75

Table S388.  Gene #40: 'B2M 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
B2M MUTATED 0 0 1 1 3 2 0
B2M WILD-TYPE 84 75 93 87 73 72 19
'B2M MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.63

Table S389.  Gene #40: 'B2M MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
B2M MUTATED 0 4 3
B2M WILD-TYPE 139 201 155
'B2M MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.137 (Fisher's exact test), Q value = 0.45

Table S390.  Gene #40: 'B2M MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
B2M MUTATED 1 1 2 3
B2M WILD-TYPE 175 98 163 59
'B2M MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0727 (Fisher's exact test), Q value = 0.34

Table S391.  Gene #40: 'B2M MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
B2M MUTATED 6 1 0
B2M WILD-TYPE 203 150 145
'B2M MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.49

Table S392.  Gene #40: 'B2M MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
B2M MUTATED 1 1 5
B2M WILD-TYPE 187 136 175
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S393.  Gene #40: 'B2M 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
B2M MUTATED 1 2 1 2 1
B2M WILD-TYPE 67 137 92 112 45
'B2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.44

Table S394.  Gene #40: 'B2M MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
B2M MUTATED 0 6 1
B2M WILD-TYPE 138 232 83
'LRRC37B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.49

Table S395.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
LRRC37B MUTATED 2 4 10 0
LRRC37B WILD-TYPE 145 126 175 42
'LRRC37B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.74

Table S396.  Gene #41: 'LRRC37B 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
LRRC37B MUTATED 5 3 2 2 4 0 0
LRRC37B WILD-TYPE 79 72 92 86 72 74 19
'LRRC37B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S397.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
LRRC37B MUTATED 1 1 0 1
LRRC37B WILD-TYPE 54 51 35 67
'LRRC37B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S398.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
LRRC37B MUTATED 1 1 1
LRRC37B WILD-TYPE 77 84 46
'LRRC37B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.62

Table S399.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
LRRC37B MUTATED 4 9 2
LRRC37B WILD-TYPE 135 196 156
'LRRC37B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 0.49

Table S400.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
LRRC37B MUTATED 5 4 2 4
LRRC37B WILD-TYPE 171 95 163 58
'LRRC37B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S401.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
LRRC37B MUTATED 7 4 5
LRRC37B WILD-TYPE 202 147 140
'LRRC37B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 0.88

Table S402.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
LRRC37B MUTATED 6 6 4
LRRC37B WILD-TYPE 182 131 176
'LRRC37B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0274 (Fisher's exact test), Q value = 0.21

Table S403.  Gene #41: 'LRRC37B 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
LRRC37B MUTATED 3 4 4 0 4
LRRC37B WILD-TYPE 65 135 89 114 42

Figure S93.  Get High-res Image Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'LRRC37B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 0.89

Table S404.  Gene #41: 'LRRC37B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
LRRC37B MUTATED 5 9 1
LRRC37B WILD-TYPE 133 229 83
'PPFIA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S405.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
PPFIA4 MUTATED 4 4 6 0
PPFIA4 WILD-TYPE 143 126 179 42
'PPFIA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.585 (Fisher's exact test), Q value = 0.89

Table S406.  Gene #42: 'PPFIA4 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
PPFIA4 MUTATED 2 4 1 3 1 2 1
PPFIA4 WILD-TYPE 82 71 93 85 75 72 18
'PPFIA4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.7

Table S407.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
PPFIA4 MUTATED 2 0 2 1
PPFIA4 WILD-TYPE 53 52 33 67
'PPFIA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.734 (Fisher's exact test), Q value = 0.96

Table S408.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
PPFIA4 MUTATED 3 1 1
PPFIA4 WILD-TYPE 75 84 46
'PPFIA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 0.93

Table S409.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
PPFIA4 MUTATED 3 5 6
PPFIA4 WILD-TYPE 136 200 152
'PPFIA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.54 (Fisher's exact test), Q value = 0.88

Table S410.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
PPFIA4 MUTATED 3 3 7 1
PPFIA4 WILD-TYPE 173 96 158 61
'PPFIA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0899 (Fisher's exact test), Q value = 0.38

Table S411.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
PPFIA4 MUTATED 3 8 3
PPFIA4 WILD-TYPE 206 143 142
'PPFIA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.73

Table S412.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
PPFIA4 MUTATED 3 6 5
PPFIA4 WILD-TYPE 185 131 175
'PPFIA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 0.98

Table S413.  Gene #42: 'PPFIA4 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
PPFIA4 MUTATED 1 5 2 2 2
PPFIA4 WILD-TYPE 67 134 91 112 44
'PPFIA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.632 (Fisher's exact test), Q value = 0.91

Table S414.  Gene #42: 'PPFIA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
PPFIA4 MUTATED 3 8 1
PPFIA4 WILD-TYPE 135 230 83
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 0.88

Table S415.  Gene #43: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
PIK3R1 MUTATED 2 1 5 1
PIK3R1 WILD-TYPE 145 129 180 41
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0678 (Fisher's exact test), Q value = 0.33

Table S416.  Gene #43: 'PIK3R1 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
PIK3R1 MUTATED 1 2 1 0 4 0 1
PIK3R1 WILD-TYPE 83 73 93 88 72 74 18
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.75

Table S417.  Gene #43: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
PIK3R1 MUTATED 1 6 2
PIK3R1 WILD-TYPE 138 199 156
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.45

Table S418.  Gene #43: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
PIK3R1 MUTATED 1 2 3 3
PIK3R1 WILD-TYPE 175 97 162 59
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.58 (Fisher's exact test), Q value = 0.89

Table S419.  Gene #43: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
PIK3R1 MUTATED 5 3 1
PIK3R1 WILD-TYPE 204 148 144
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 0.64

Table S420.  Gene #43: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
PIK3R1 MUTATED 1 3 5
PIK3R1 WILD-TYPE 187 134 175
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.7

Table S421.  Gene #43: 'PIK3R1 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
PIK3R1 MUTATED 0 2 3 1 2
PIK3R1 WILD-TYPE 68 137 90 113 44
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.81

Table S422.  Gene #43: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
PIK3R1 MUTATED 2 6 0
PIK3R1 WILD-TYPE 136 232 84
'VPS33B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.42

Table S423.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
VPS33B MUTATED 0 4 2 1
VPS33B WILD-TYPE 147 126 183 41
'VPS33B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0291 (Fisher's exact test), Q value = 0.21

Table S424.  Gene #44: 'VPS33B 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
VPS33B MUTATED 0 0 0 4 1 1 1
VPS33B WILD-TYPE 84 75 94 84 75 73 18

Figure S94.  Get High-res Image Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'VPS33B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.704 (Fisher's exact test), Q value = 0.95

Table S425.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
VPS33B MUTATED 0 1 1 1
VPS33B WILD-TYPE 55 51 34 67
'VPS33B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S426.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
VPS33B MUTATED 1 1 1
VPS33B WILD-TYPE 77 84 46
'VPS33B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.96

Table S427.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
VPS33B MUTATED 1 4 2
VPS33B WILD-TYPE 138 201 156
'VPS33B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.75

Table S428.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
VPS33B MUTATED 1 3 2 1
VPS33B WILD-TYPE 175 96 163 61
'VPS33B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 0.89

Table S429.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
VPS33B MUTATED 4 1 2
VPS33B WILD-TYPE 205 150 143
'VPS33B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.89

Table S430.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
VPS33B MUTATED 2 1 4
VPS33B WILD-TYPE 186 136 176
'VPS33B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.969 (Fisher's exact test), Q value = 1

Table S431.  Gene #44: 'VPS33B 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
VPS33B MUTATED 1 2 1 1 1
VPS33B WILD-TYPE 67 137 92 113 45
'VPS33B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.336 (Fisher's exact test), Q value = 0.75

Table S432.  Gene #44: 'VPS33B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
VPS33B MUTATED 1 5 0
VPS33B WILD-TYPE 137 233 84
'C8ORF31 MUTATION STATUS' versus 'CN_CNMF'

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

Table S433.  Gene #45: 'C8ORF31 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
C8ORF31 MUTATED 1 1 1 0
C8ORF31 WILD-TYPE 146 129 184 42
'C8ORF31 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.81

Table S434.  Gene #45: 'C8ORF31 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
C8ORF31 MUTATED 2 1 0 0 0 1 0
C8ORF31 WILD-TYPE 82 74 94 88 76 73 19
'C8ORF31 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.81

Table S435.  Gene #45: 'C8ORF31 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
C8ORF31 MUTATED 2 2 0
C8ORF31 WILD-TYPE 137 203 158
'C8ORF31 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S436.  Gene #45: 'C8ORF31 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
C8ORF31 MUTATED 2 1 1 0
C8ORF31 WILD-TYPE 174 98 164 62
'C8ORF31 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.95

Table S437.  Gene #45: 'C8ORF31 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
C8ORF31 MUTATED 1 1 2
C8ORF31 WILD-TYPE 208 150 143
'C8ORF31 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S438.  Gene #45: 'C8ORF31 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
C8ORF31 MUTATED 2 1 1
C8ORF31 WILD-TYPE 186 136 179
'C8ORF31 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S439.  Gene #45: 'C8ORF31 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
C8ORF31 MUTATED 1 1 0 1 0
C8ORF31 WILD-TYPE 67 138 93 113 46
'C8ORF31 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 0.97

Table S440.  Gene #45: 'C8ORF31 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
C8ORF31 MUTATED 1 1 1
C8ORF31 WILD-TYPE 137 237 83
'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S441.  Gene #46: '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 = 0.0901 (Fisher's exact test), Q value = 0.38

Table S442.  Gene #46: '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 = 0.468 (Fisher's exact test), Q value = 0.86

Table S443.  Gene #46: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
NCOR1 MUTATED 1 2 3 4
NCOR1 WILD-TYPE 54 50 32 64
'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.495 (Fisher's exact test), Q value = 0.86

Table S444.  Gene #46: '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 = 0.622 (Fisher's exact test), Q value = 0.9

Table S445.  Gene #46: '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 = 0.17 (Fisher's exact test), Q value = 0.5

Table S446.  Gene #46: '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 = 0.88

Table S447.  Gene #46: '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 = 0.109 (Fisher's exact test), Q value = 0.42

Table S448.  Gene #46: '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 = 0.525 (Fisher's exact test), Q value = 0.88

Table S449.  Gene #46: '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 = 1

Table S450.  Gene #46: '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
'SEH1L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.59

Table S451.  Gene #47: 'SEH1L MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
SEH1L MUTATED 0 3 1 0
SEH1L WILD-TYPE 147 127 184 42
'SEH1L MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0645 (Fisher's exact test), Q value = 0.33

Table S452.  Gene #47: 'SEH1L 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
SEH1L MUTATED 1 3 0 0 0 0 0
SEH1L WILD-TYPE 83 72 94 88 76 74 19
'SEH1L MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S453.  Gene #47: 'SEH1L MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
SEH1L MUTATED 1 3 0
SEH1L WILD-TYPE 138 202 158
'SEH1L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0451 (Fisher's exact test), Q value = 0.26

Table S454.  Gene #47: 'SEH1L MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
SEH1L MUTATED 1 3 0 0
SEH1L WILD-TYPE 175 96 165 62

Figure S95.  Get High-res Image Gene #47: 'SEH1L MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SEH1L MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.81

Table S455.  Gene #47: 'SEH1L MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
SEH1L MUTATED 3 1 0
SEH1L WILD-TYPE 206 150 145
'SEH1L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.098 (Fisher's exact test), Q value = 0.4

Table S456.  Gene #47: 'SEH1L MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
SEH1L MUTATED 1 3 0
SEH1L WILD-TYPE 187 134 180
'SEH1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.49

Table S457.  Gene #47: 'SEH1L 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
SEH1L MUTATED 0 1 3 0 0
SEH1L WILD-TYPE 68 138 90 114 46
'SEH1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S458.  Gene #47: 'SEH1L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
SEH1L MUTATED 1 2 1
SEH1L WILD-TYPE 137 236 83
'CUL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0203 (Fisher's exact test), Q value = 0.17

Table S459.  Gene #48: '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 S96.  Get High-res Image Gene #48: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00375 (Fisher's exact test), Q value = 0.051

Table S460.  Gene #48: '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 S97.  Get High-res Image Gene #48: 'CUL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CUL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.79

Table S461.  Gene #48: 'CUL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
CUL3 MUTATED 2 4 0 2
CUL3 WILD-TYPE 53 48 35 66
'CUL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 0.96

Table S462.  Gene #48: '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 = 0.332 (Fisher's exact test), Q value = 0.75

Table S463.  Gene #48: '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 = 0.0277 (Fisher's exact test), Q value = 0.21

Table S464.  Gene #48: '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 S98.  Get High-res Image Gene #48: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.59

Table S465.  Gene #48: '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 = 1

Table S466.  Gene #48: '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 = 0.00145 (Fisher's exact test), Q value = 0.024

Table S467.  Gene #48: '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 S99.  Get High-res Image Gene #48: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 0.79

Table S468.  Gene #48: '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
'NOTCH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.85

Table S469.  Gene #49: '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 = 0.4 (Fisher's exact test), Q value = 0.81

Table S470.  Gene #49: '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 = 0.075 (Fisher's exact test), Q value = 0.34

Table S471.  Gene #49: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
NOTCH2 MUTATED 4 1 4 1
NOTCH2 WILD-TYPE 51 51 31 67
'NOTCH2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 0.77

Table S472.  Gene #49: '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 = 0.594 (Fisher's exact test), Q value = 0.89

Table S473.  Gene #49: '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 = 0.72

Table S474.  Gene #49: '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 = 0.502 (Fisher's exact test), Q value = 0.86

Table S475.  Gene #49: '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 = 0.486 (Fisher's exact test), Q value = 0.86

Table S476.  Gene #49: '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 = 0.901 (Fisher's exact test), Q value = 1

Table S477.  Gene #49: '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 = 0.599 (Fisher's exact test), Q value = 0.89

Table S478.  Gene #49: '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
'YTHDF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.89

Table S479.  Gene #50: 'YTHDF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
YTHDF1 MUTATED 1 1 3 1
YTHDF1 WILD-TYPE 146 129 182 41
'YTHDF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S480.  Gene #50: 'YTHDF1 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
YTHDF1 MUTATED 0 1 1 1 1 2 0
YTHDF1 WILD-TYPE 84 74 93 87 75 72 19
'YTHDF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S481.  Gene #50: 'YTHDF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
YTHDF1 MUTATED 2 2 2
YTHDF1 WILD-TYPE 137 203 156
'YTHDF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S482.  Gene #50: 'YTHDF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
YTHDF1 MUTATED 2 2 2 0
YTHDF1 WILD-TYPE 174 97 163 62
'YTHDF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 0.89

Table S483.  Gene #50: 'YTHDF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
YTHDF1 MUTATED 4 1 1
YTHDF1 WILD-TYPE 205 150 144
'YTHDF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.88

Table S484.  Gene #50: 'YTHDF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
YTHDF1 MUTATED 2 3 1
YTHDF1 WILD-TYPE 186 134 179
'YTHDF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 0.88

Table S485.  Gene #50: 'YTHDF1 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
YTHDF1 MUTATED 1 2 2 0 0
YTHDF1 WILD-TYPE 67 137 91 114 46
'YTHDF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S486.  Gene #50: 'YTHDF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
YTHDF1 MUTATED 1 3 1
YTHDF1 WILD-TYPE 137 235 83
'FOSL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S487.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
FOSL2 MUTATED 2 2 4 1
FOSL2 WILD-TYPE 145 128 181 41
'FOSL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.415 (Fisher's exact test), Q value = 0.81

Table S488.  Gene #51: 'FOSL2 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
FOSL2 MUTATED 1 0 4 1 1 3 0
FOSL2 WILD-TYPE 83 75 90 87 75 71 19
'FOSL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.72

Table S489.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
FOSL2 MUTATED 1 0 1 4
FOSL2 WILD-TYPE 54 52 34 64
'FOSL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.511 (Fisher's exact test), Q value = 0.87

Table S490.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
FOSL2 MUTATED 1 4 1
FOSL2 WILD-TYPE 77 81 46
'FOSL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.49

Table S491.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
FOSL2 MUTATED 2 2 6
FOSL2 WILD-TYPE 137 203 152
'FOSL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.79

Table S492.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
FOSL2 MUTATED 3 1 6 0
FOSL2 WILD-TYPE 173 98 159 62
'FOSL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 0.99

Table S493.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
FOSL2 MUTATED 4 4 2
FOSL2 WILD-TYPE 205 147 143
'FOSL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.78 (Fisher's exact test), Q value = 0.98

Table S494.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
FOSL2 MUTATED 5 2 3
FOSL2 WILD-TYPE 183 135 177
'FOSL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.42

Table S495.  Gene #51: 'FOSL2 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
FOSL2 MUTATED 1 1 1 6 0
FOSL2 WILD-TYPE 67 138 92 108 46
'FOSL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.44

Table S496.  Gene #51: 'FOSL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
FOSL2 MUTATED 5 2 2
FOSL2 WILD-TYPE 133 236 82
'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.016 (Fisher's exact test), Q value = 0.16

Table S497.  Gene #52: '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 S100.  Get High-res Image Gene #52: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.62

Table S498.  Gene #52: '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 = 0.544 (Fisher's exact test), Q value = 0.89

Table S499.  Gene #52: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
MYH9 MUTATED 3 3 1 1
MYH9 WILD-TYPE 52 49 34 67
'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.47 (Fisher's exact test), Q value = 0.86

Table S500.  Gene #52: '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 = 0.557 (Fisher's exact test), Q value = 0.89

Table S501.  Gene #52: '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 = 0.717 (Fisher's exact test), Q value = 0.96

Table S502.  Gene #52: '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 = 0.704 (Fisher's exact test), Q value = 0.95

Table S503.  Gene #52: '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 = 0.454 (Fisher's exact test), Q value = 0.85

Table S504.  Gene #52: '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 = 0.846 (Fisher's exact test), Q value = 1

Table S505.  Gene #52: '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 = 0.455 (Fisher's exact test), Q value = 0.85

Table S506.  Gene #52: '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
'TP63 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.57

Table S507.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
TP63 MUTATED 2 3 4 3
TP63 WILD-TYPE 145 127 181 39
'TP63 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S508.  Gene #53: 'TP63 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
TP63 MUTATED 2 1 2 2 2 2 1
TP63 WILD-TYPE 82 74 92 86 74 72 18
'TP63 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S509.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
TP63 MUTATED 1 2 1 1
TP63 WILD-TYPE 54 50 34 67
'TP63 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S510.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
TP63 MUTATED 2 2 1
TP63 WILD-TYPE 76 83 46
'TP63 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.86

Table S511.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
TP63 MUTATED 4 3 5
TP63 WILD-TYPE 135 202 153
'TP63 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 0.96

Table S512.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
TP63 MUTATED 6 1 4 1
TP63 WILD-TYPE 170 98 161 61
'TP63 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0414 (Fisher's exact test), Q value = 0.25

Table S513.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
TP63 MUTATED 1 6 5
TP63 WILD-TYPE 208 145 140

Figure S101.  Get High-res Image Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP63 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.427 (Fisher's exact test), Q value = 0.83

Table S514.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
TP63 MUTATED 7 2 3
TP63 WILD-TYPE 181 135 177
'TP63 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 0.98

Table S515.  Gene #53: 'TP63 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
TP63 MUTATED 2 5 2 2 0
TP63 WILD-TYPE 66 134 91 112 46
'TP63 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.549 (Fisher's exact test), Q value = 0.89

Table S516.  Gene #53: 'TP63 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
TP63 MUTATED 5 5 1
TP63 WILD-TYPE 133 233 83
'DYSF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S517.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
DYSF MUTATED 6 7 7 1
DYSF WILD-TYPE 141 123 178 41
'DYSF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0186 (Fisher's exact test), Q value = 0.16

Table S518.  Gene #54: 'DYSF 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
DYSF MUTATED 1 9 1 4 2 4 0
DYSF WILD-TYPE 83 66 93 84 74 70 19

Figure S102.  Get High-res Image Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DYSF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.45

Table S519.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
DYSF MUTATED 1 5 1 1
DYSF WILD-TYPE 54 47 34 67
'DYSF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 0.96

Table S520.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
DYSF MUTATED 2 4 2
DYSF WILD-TYPE 76 81 45
'DYSF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0921 (Fisher's exact test), Q value = 0.39

Table S521.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
DYSF MUTATED 4 13 3
DYSF WILD-TYPE 135 192 155
'DYSF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0166 (Fisher's exact test), Q value = 0.16

Table S522.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
DYSF MUTATED 4 10 5 1
DYSF WILD-TYPE 172 89 160 61

Figure S103.  Get High-res Image Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DYSF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.244 (Fisher's exact test), Q value = 0.63

Table S523.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
DYSF MUTATED 9 9 3
DYSF WILD-TYPE 200 142 142
'DYSF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 0.6

Table S524.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
DYSF MUTATED 5 9 7
DYSF WILD-TYPE 183 128 173
'DYSF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0389 (Fisher's exact test), Q value = 0.24

Table S525.  Gene #54: 'DYSF 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
DYSF MUTATED 2 5 10 2 1
DYSF WILD-TYPE 66 134 83 112 45

Figure S104.  Get High-res Image Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'DYSF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0764 (Fisher's exact test), Q value = 0.34

Table S526.  Gene #54: 'DYSF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
DYSF MUTATED 2 15 3
DYSF WILD-TYPE 136 223 81
'TMEM2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.7

Table S527.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
TMEM2 MUTATED 6 7 4 0
TMEM2 WILD-TYPE 141 123 181 42
'TMEM2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0751 (Fisher's exact test), Q value = 0.34

Table S528.  Gene #55: 'TMEM2 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
TMEM2 MUTATED 1 7 2 4 1 1 1
TMEM2 WILD-TYPE 83 68 92 84 75 73 18
'TMEM2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S529.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
TMEM2 MUTATED 4 2 1 4
TMEM2 WILD-TYPE 51 50 34 64
'TMEM2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.49

Table S530.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
TMEM2 MUTATED 5 6 0
TMEM2 WILD-TYPE 73 79 47
'TMEM2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.73

Table S531.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
TMEM2 MUTATED 4 10 3
TMEM2 WILD-TYPE 135 195 155
'TMEM2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 0.86

Table S532.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
TMEM2 MUTATED 5 6 4 2
TMEM2 WILD-TYPE 171 93 161 60
'TMEM2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 0.95

Table S533.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
TMEM2 MUTATED 9 4 4
TMEM2 WILD-TYPE 200 147 141
'TMEM2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.88

Table S534.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
TMEM2 MUTATED 7 6 4
TMEM2 WILD-TYPE 181 131 176
'TMEM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 0.96

Table S535.  Gene #55: 'TMEM2 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
TMEM2 MUTATED 2 2 4 4 1
TMEM2 WILD-TYPE 66 137 89 110 45
'TMEM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 0.89

Table S536.  Gene #55: 'TMEM2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
TMEM2 MUTATED 3 9 1
TMEM2 WILD-TYPE 135 229 83
'PTPN14 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.16

Table S537.  Gene #56: '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 S105.  Get High-res Image Gene #56: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTPN14 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.43

Table S538.  Gene #56: '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 = 0.848 (Fisher's exact test), Q value = 1

Table S539.  Gene #56: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
PTPN14 MUTATED 2 2 1 1
PTPN14 WILD-TYPE 53 50 34 67
'PTPN14 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 0.89

Table S540.  Gene #56: '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 = 0.226 (Fisher's exact test), Q value = 0.61

Table S541.  Gene #56: '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 = 0.721 (Fisher's exact test), Q value = 0.96

Table S542.  Gene #56: '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 = 0.0451 (Fisher's exact test), Q value = 0.26

Table S543.  Gene #56: '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 S106.  Get High-res Image Gene #56: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PTPN14 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 0.91

Table S544.  Gene #56: '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 = 0.263 (Fisher's exact test), Q value = 0.66

Table S545.  Gene #56: '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 = 0.451 (Fisher's exact test), Q value = 0.85

Table S546.  Gene #56: '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
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 0.85

Table S547.  Gene #57: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
RBM10 MUTATED 0 1 3 0
RBM10 WILD-TYPE 147 129 182 42
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.88

Table S548.  Gene #57: 'RBM10 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
RBM10 MUTATED 2 0 0 1 0 1 0
RBM10 WILD-TYPE 82 75 94 87 76 73 19
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.692 (Fisher's exact test), Q value = 0.95

Table S549.  Gene #57: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
RBM10 MUTATED 2 1 1
RBM10 WILD-TYPE 137 204 157
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 0.93

Table S550.  Gene #57: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
RBM10 MUTATED 2 0 1 1
RBM10 WILD-TYPE 174 99 164 61
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 0.95

Table S551.  Gene #57: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
RBM10 MUTATED 1 1 2
RBM10 WILD-TYPE 208 150 143
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 0.89

Table S552.  Gene #57: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
RBM10 MUTATED 2 0 2
RBM10 WILD-TYPE 186 137 178
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.806 (Fisher's exact test), Q value = 1

Table S553.  Gene #57: 'RBM10 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
RBM10 MUTATED 0 1 1 1 1
RBM10 WILD-TYPE 68 138 92 113 45
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 0.92

Table S554.  Gene #57: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
RBM10 MUTATED 2 2 0
RBM10 WILD-TYPE 136 236 84
'IRF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.066 (Fisher's exact test), Q value = 0.33

Table S555.  Gene #58: 'IRF2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
IRF2 MUTATED 1 0 4 2
IRF2 WILD-TYPE 146 130 181 40
'IRF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.44

Table S556.  Gene #58: 'IRF2 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
IRF2 MUTATED 0 0 1 1 2 4 0
IRF2 WILD-TYPE 84 75 93 87 74 70 19
'IRF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.21

Table S557.  Gene #58: 'IRF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
IRF2 MUTATED 0 2 6
IRF2 WILD-TYPE 139 203 152

Figure S107.  Get High-res Image Gene #58: 'IRF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'IRF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0799 (Fisher's exact test), Q value = 0.35

Table S558.  Gene #58: 'IRF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
IRF2 MUTATED 1 0 6 1
IRF2 WILD-TYPE 175 99 159 61
'IRF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S559.  Gene #58: 'IRF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
IRF2 MUTATED 4 2 1
IRF2 WILD-TYPE 205 149 144
'IRF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.349 (Fisher's exact test), Q value = 0.77

Table S560.  Gene #58: 'IRF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
IRF2 MUTATED 1 2 4
IRF2 WILD-TYPE 187 135 176
'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.84

Table S561.  Gene #58: 'IRF2 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
IRF2 MUTATED 1 4 0 1 1
IRF2 WILD-TYPE 67 135 93 113 45
'IRF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 0.95

Table S562.  Gene #58: 'IRF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
IRF2 MUTATED 1 5 1
IRF2 WILD-TYPE 137 233 83
'AMPD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.43

Table S563.  Gene #59: 'AMPD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
AMPD1 MUTATED 3 2 0 1
AMPD1 WILD-TYPE 144 128 185 41
'AMPD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 0.91

Table S564.  Gene #59: 'AMPD1 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
AMPD1 MUTATED 0 2 1 2 0 1 0
AMPD1 WILD-TYPE 84 73 93 86 76 73 19
'AMPD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.75

Table S565.  Gene #59: 'AMPD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
AMPD1 MUTATED 0 3 3
AMPD1 WILD-TYPE 139 202 155
'AMPD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.51

Table S566.  Gene #59: 'AMPD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
AMPD1 MUTATED 0 2 3 1
AMPD1 WILD-TYPE 176 97 162 61
'AMPD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.7

Table S567.  Gene #59: 'AMPD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
AMPD1 MUTATED 3 3 0
AMPD1 WILD-TYPE 206 148 145
'AMPD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0309 (Fisher's exact test), Q value = 0.22

Table S568.  Gene #59: 'AMPD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
AMPD1 MUTATED 0 4 2
AMPD1 WILD-TYPE 188 133 178

Figure S108.  Get High-res Image Gene #59: 'AMPD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'AMPD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.837 (Fisher's exact test), Q value = 1

Table S569.  Gene #59: 'AMPD1 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
AMPD1 MUTATED 0 3 1 1 0
AMPD1 WILD-TYPE 68 136 92 113 46
'AMPD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.43

Table S570.  Gene #59: 'AMPD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
AMPD1 MUTATED 0 5 0
AMPD1 WILD-TYPE 138 233 84
'ZMYM1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S571.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
ZMYM1 MUTATED 3 3 3 0
ZMYM1 WILD-TYPE 144 127 182 42
'ZMYM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.44

Table S572.  Gene #60: 'ZMYM1 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
ZMYM1 MUTATED 0 0 2 5 1 1 0
ZMYM1 WILD-TYPE 84 75 92 83 75 73 19
'ZMYM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.87

Table S573.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
ZMYM1 MUTATED 0 2 1 1
ZMYM1 WILD-TYPE 55 50 34 67
'ZMYM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.545 (Fisher's exact test), Q value = 0.89

Table S574.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ZMYM1 MUTATED 1 3 0
ZMYM1 WILD-TYPE 77 82 47
'ZMYM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.534 (Fisher's exact test), Q value = 0.88

Table S575.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
ZMYM1 MUTATED 1 4 4
ZMYM1 WILD-TYPE 138 201 154
'ZMYM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.721 (Fisher's exact test), Q value = 0.96

Table S576.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
ZMYM1 MUTATED 3 2 2 2
ZMYM1 WILD-TYPE 173 97 163 60
'ZMYM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 0.97

Table S577.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
ZMYM1 MUTATED 5 2 2
ZMYM1 WILD-TYPE 204 149 143
'ZMYM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S578.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
ZMYM1 MUTATED 3 2 4
ZMYM1 WILD-TYPE 185 135 176
'ZMYM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 0.96

Table S579.  Gene #60: 'ZMYM1 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
ZMYM1 MUTATED 0 3 1 3 1
ZMYM1 WILD-TYPE 68 136 92 111 45
'ZMYM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 0.91

Table S580.  Gene #60: 'ZMYM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
ZMYM1 MUTATED 1 5 2
ZMYM1 WILD-TYPE 137 233 82
'LCP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0738 (Fisher's exact test), Q value = 0.34

Table S581.  Gene #61: '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 = 0.0899 (Fisher's exact test), Q value = 0.38

Table S582.  Gene #61: '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 = 0.754 (Fisher's exact test), Q value = 0.97

Table S583.  Gene #61: 'LCP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
LCP1 MUTATED 2 1 2 4
LCP1 WILD-TYPE 53 51 33 64
'LCP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 1

Table S584.  Gene #61: '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 = 0.755 (Fisher's exact test), Q value = 0.97

Table S585.  Gene #61: '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 = 0.0721 (Fisher's exact test), Q value = 0.34

Table S586.  Gene #61: '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 = 0.946 (Fisher's exact test), Q value = 1

Table S587.  Gene #61: '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 = 0.896 (Fisher's exact test), Q value = 1

Table S588.  Gene #61: '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 = 0.736 (Fisher's exact test), Q value = 0.96

Table S589.  Gene #61: '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 = 0.255 (Fisher's exact test), Q value = 0.64

Table S590.  Gene #61: '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
'SLC9A6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00883 (Fisher's exact test), Q value = 0.1

Table S591.  Gene #62: '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 S109.  Get High-res Image Gene #62: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SLC9A6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0937 (Fisher's exact test), Q value = 0.39

Table S592.  Gene #62: '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 = 0.873 (Fisher's exact test), Q value = 1

Table S593.  Gene #62: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 55 52 35 68
SLC9A6 MUTATED 1 0 1 1
SLC9A6 WILD-TYPE 54 52 34 67
'SLC9A6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.43

Table S594.  Gene #62: '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 = 0.113 (Fisher's exact test), Q value = 0.42

Table S595.  Gene #62: '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 = 0.37 (Fisher's exact test), Q value = 0.79

Table S596.  Gene #62: '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 = 0.0501 (Fisher's exact test), Q value = 0.28

Table S597.  Gene #62: '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 = 0.23 (Fisher's exact test), Q value = 0.61

Table S598.  Gene #62: '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 = 0.569 (Fisher's exact test), Q value = 0.89

Table S599.  Gene #62: '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 = 0.0281 (Fisher's exact test), Q value = 0.21

Table S600.  Gene #62: '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 S110.  Get High-res Image Gene #62: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CCNG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.24

Table S601.  Gene #63: 'CCNG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
CCNG2 MUTATED 0 2 0 1
CCNG2 WILD-TYPE 147 128 185 41

Figure S111.  Get High-res Image Gene #63: 'CCNG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CCNG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 0.89

Table S602.  Gene #63: 'CCNG2 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
CCNG2 MUTATED 1 1 0 0 1 0 0
CCNG2 WILD-TYPE 83 74 94 88 75 74 19
'CCNG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S603.  Gene #63: 'CCNG2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
CCNG2 MUTATED 1 1 1
CCNG2 WILD-TYPE 138 204 157
'CCNG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 0.96

Table S604.  Gene #63: 'CCNG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
CCNG2 MUTATED 1 0 2 0
CCNG2 WILD-TYPE 175 99 163 62
'CCNG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.86

Table S605.  Gene #63: 'CCNG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
CCNG2 MUTATED 1 2 0
CCNG2 WILD-TYPE 208 149 145
'CCNG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S606.  Gene #63: 'CCNG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
CCNG2 MUTATED 1 1 1
CCNG2 WILD-TYPE 187 136 179
'TACR2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S607.  Gene #64: 'TACR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 147 130 185 42
TACR2 MUTATED 1 1 2 0
TACR2 WILD-TYPE 146 129 183 42
'TACR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S608.  Gene #64: 'TACR2 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
TACR2 MUTATED 1 1 1 0 0 1 0
TACR2 WILD-TYPE 83 74 93 88 76 73 19
'TACR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S609.  Gene #64: 'TACR2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 139 205 158
TACR2 MUTATED 1 2 1
TACR2 WILD-TYPE 138 203 157
'TACR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S610.  Gene #64: 'TACR2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 99 165 62
TACR2 MUTATED 1 1 2 0
TACR2 WILD-TYPE 175 98 163 62
'TACR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S611.  Gene #64: 'TACR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 209 151 145
TACR2 MUTATED 2 1 1
TACR2 WILD-TYPE 207 150 144
'TACR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 0.95

Table S612.  Gene #64: 'TACR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 188 137 180
TACR2 MUTATED 1 2 1
TACR2 WILD-TYPE 187 135 179
'TACR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S613.  Gene #64: 'TACR2 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
TACR2 MUTATED 1 1 1 1 0
TACR2 WILD-TYPE 67 138 92 113 46
'TACR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S614.  Gene #64: 'TACR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 138 238 84
TACR2 MUTATED 1 2 1
TACR2 WILD-TYPE 137 236 83
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/15648707/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/15111022/HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 510

  • Number of significantly mutated genes = 64

  • 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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