Correlation between gene mutation status and molecular subtypes
Head and Neck Squamous Cell Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1NK3DFR
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1NK3DFR
Overview
Introduction

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

Summary

Testing the association between mutation status of 62 genes and 10 molecular subtypes across 511 patients, 110 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_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • MLL2 mutation correlated to 'METHLYATION_CNMF'.

  • TGFBR2 mutation correlated to 'CN_CNMF' and 'METHLYATION_CNMF'.

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

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

  • FAT1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • JUB mutation correlated to 'MIRSEQ_CNMF'.

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

  • NFE2L2 mutation correlated to 'METHLYATION_CNMF'.

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

  • EPHA2 mutation correlated to 'METHLYATION_CNMF'.

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

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

  • EP300 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • OR6C65 mutation correlated to 'MIRSEQ_CNMF'.

  • PIK3CA mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • MAPK1 mutation correlated to 'CN_CNMF'.

  • KDM6A mutation correlated to 'RPPA_CNMF'.

  • RB1 mutation correlated to 'MRNASEQ_CNMF'.

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

  • PTPN14 mutation correlated to 'METHLYATION_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • KRTAP5-5 mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CNMF'.

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

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

  • VEZF1 mutation correlated to 'MIRSEQ_CNMF'.

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

  • IRS4 mutation correlated to 'CN_CNMF' and 'MIRSEQ_MATURE_CNMF'.

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

  • THSD7A mutation correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • KIAA1267 mutation correlated to 'CN_CNMF'.

  • ASXL1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • GAGE2A mutation correlated to 'CN_CNMF'.

  • KRTAP5-7 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • SLC9A6 mutation correlated to 'MRNASEQ_CNMF'.

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

  • HNRNPL mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • NOTCH2 mutation correlated to 'RPPA_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 62 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, 110 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 62 (12%) 449 0.00722
(0.0915) 		1e-05
(0.00031) 		0.00729
(0.0915) 		0.0143
(0.135) 		1e-05
(0.00031) 		1e-05
(0.00031) 		0.00251
(0.038) 		0.00013
(0.00322) 		0.219
(0.597) 		0.00012
(0.0031)
TP53 364 (71%) 147 1e-05
(0.00031) 		1e-05
(0.00031) 		0.142
(0.456) 		0.748
(0.941) 		1e-05
(0.00031) 		1e-05
(0.00031) 		1e-05
(0.00031) 		1e-05
(0.00031) 		0.00161
(0.0256) 		1e-05
(0.00031)
CDKN2A 112 (22%) 399 4e-05
(0.00108) 		1e-05
(0.00031) 		0.0105
(0.109) 		0.814
(0.976) 		0.0863
(0.332) 		1e-05
(0.00031) 		0.0452
(0.252) 		0.0421
(0.24) 		0.908
(1.00) 		0.0153
(0.14)
CASP8 54 (11%) 457 1e-05
(0.00031) 		1e-05
(0.00031) 		0.0877
(0.336) 		0.35
(0.699) 		1e-05
(0.00031) 		1e-05
(0.00031) 		1e-05
(0.00031) 		0.571
(0.857) 		0.112
(0.396) 		0.0108
(0.109)
NOTCH1 90 (18%) 421 0.0343
(0.22) 		2e-05
(0.000564) 		0.308
(0.671) 		0.0592
(0.296) 		0.00028
(0.00599) 		0.00319
(0.046) 		0.00017
(0.00405) 		0.0789
(0.328) 		0.0686
(0.308) 		0.0118
(0.115)
HLA-A 22 (4%) 489 0.00068
(0.0128) 		0.0182
(0.154) 		0.964
(1.00) 		0.64
(0.905) 		0.0392
(0.232) 		0.00066
(0.0128) 		0.307
(0.671) 		0.0311
(0.203) 		0.317
(0.683) 		0.0216
(0.169)
FAT1 112 (22%) 399 0.0301
(0.199) 		1e-05
(0.00031) 		0.925
(1.00) 		0.488
(0.803) 		0.0186
(0.154) 		0.00072
(0.0131) 		0.0264
(0.182) 		0.592
(0.87) 		0.251
(0.627) 		0.269
(0.654)
HRAS 31 (6%) 480 1e-05
(0.00031) 		1e-05
(0.00031) 		0.577
(0.858) 		0.651
(0.905) 		0.00051
(0.0102) 		0.0254
(0.181) 		0.00043
(0.00889) 		0.109
(0.391) 		0.57
(0.857) 		0.491
(0.803)
HLA-B 24 (5%) 487 0.00273
(0.0403) 		0.00844
(0.0987) 		0.852
(0.986) 		0.224
(0.597) 		0.0263
(0.182) 		0.0702
(0.311) 		0.0696
(0.311) 		0.194
(0.553) 		0.00684
(0.0902) 		0.0464
(0.255)
ZNF750 21 (4%) 490 0.19
(0.553) 		0.0162
(0.144) 		0.623
(0.897) 		0.285
(0.666) 		0.0379
(0.228) 		0.00832
(0.0987) 		0.00026
(0.00576) 		0.215
(0.595) 		1
(1.00) 		0.199
(0.557)
RAC1 15 (3%) 496 0.0039
(0.0537) 		0.0364
(0.226) 		0.705
(0.925) 		0.834
(0.976) 		0.00389
(0.0537) 		0.0784
(0.328) 		1
(1.00) 		0.344
(0.695) 		0.462
(0.781) 		0.585
(0.864)
EP300 38 (7%) 473 0.037
(0.227) 		0.0165
(0.144) 		0.395
(0.73) 		0.0851
(0.332) 		0.0557
(0.29) 		0.0599
(0.297) 		0.313
(0.678) 		0.0421
(0.24) 		0.429
(0.758) 		0.235
(0.61)
PTPN14 16 (3%) 495 0.451
(0.771) 		0.0277
(0.189) 		0.198
(0.557) 		0.579
(0.859) 		0.36
(0.711) 		0.669
(0.906) 		0.0347
(0.22) 		0.502
(0.813) 		0.0378
(0.228) 		0.294
(0.666)
CUL3 16 (3%) 495 0.0348
(0.22) 		0.0101
(0.108) 		0.508
(0.815) 		0.733
(0.934) 		0.275
(0.659) 		0.0193
(0.158) 		0.0463
(0.255) 		0.902
(0.999) 		0.464
(0.781) 		0.447
(0.769)
MLL4 19 (4%) 492 0.00097
(0.0167) 		0.00174
(0.027) 		0.832
(0.976) 		0.382
(0.727) 		0.125
(0.42) 		0.169
(0.525) 		0.0206
(0.164) 		0.915
(1.00) 		0.123
(0.413) 		0.626
(0.897)
THSD7A 32 (6%) 479 0.686
(0.912) 		0.12
(0.409) 		0.471
(0.788) 		0.249
(0.627) 		0.00497
(0.067) 		0.0657
(0.303) 		0.27
(0.654) 		0.0385
(0.229) 		0.0807
(0.329) 		0.0232
(0.169)
TGFBR2 24 (5%) 487 0.00161
(0.0256) 		0.029
(0.195) 		0.564
(0.856) 		0.901
(0.999) 		0.437
(0.763) 		0.953
(1.00) 		0.307
(0.671) 		0.781
(0.963) 		0.436
(0.763) 		0.417
(0.75)
KEAP1 22 (4%) 489 0.419
(0.75) 		0.132
(0.434) 		0.766
(0.952) 		0.827
(0.976) 		0.332
(0.69) 		0.00106
(0.0178) 		0.787
(0.968) 		0.0411
(0.24) 		0.37
(0.719) 		0.318
(0.683)
KRTAP5-5 4 (1%) 507 0.642
(0.905) 		0.918
(1.00) 		1
(1.00) 		0.795
(0.969) 		0.0145
(0.135) 		0.547
(0.841) 		0.0106
(0.109) 		0.26
(0.638) 		1
(1.00) 		0.354
(0.705)
CREBBP 34 (7%) 477 0.116
(0.405) 		0.451
(0.771) 		0.305
(0.671) 		0.932
(1.00) 		0.0852
(0.332) 		0.0739
(0.321) 		0.712
(0.928) 		0.0232
(0.169) 		0.121
(0.409) 		0.0115
(0.113)
IRS4 17 (3%) 494 0.0198
(0.159) 		0.552
(0.847) 		0.195
(0.553) 		0.791
(0.969) 		0.409
(0.742) 		0.0659
(0.303) 		0.546
(0.841) 		0.05
(0.267) 		0.0352
(0.221) 		0.132
(0.434)
HUWE1 46 (9%) 465 0.00898
(0.101) 		0.00082
(0.0145) 		0.728
(0.934) 		0.637
(0.904) 		0.234
(0.61) 		0.0805
(0.329) 		0.743
(0.94) 		0.462
(0.781) 		0.71
(0.928) 		0.617
(0.894)
DYSF 20 (4%) 491 0.647
(0.905) 		0.0097
(0.106) 		0.56
(0.855) 		0.732
(0.934) 		0.194
(0.553) 		0.0091
(0.101) 		0.606
(0.885) 		0.219
(0.597) 		0.293
(0.666) 		0.161
(0.504)
CTCF 15 (3%) 496 0.0122
(0.116) 		0.00769
(0.0935) 		0.902
(0.999) 		0.526
(0.83) 		0.607
(0.885) 		0.412
(0.744) 		0.697
(0.919) 		0.717
(0.93) 		1
(1.00) 		0.716
(0.93)
MLL2 81 (16%) 430 0.18
(0.547) 		0.0224
(0.169) 		0.653
(0.905) 		0.52
(0.826) 		0.214
(0.595) 		0.29
(0.666) 		0.246
(0.623) 		0.0526
(0.276) 		0.543
(0.841) 		0.113
(0.398)
JUB 34 (7%) 477 0.894
(0.995) 		0.4
(0.735) 		0.0853
(0.332) 		0.637
(0.904) 		0.119
(0.409) 		0.772
(0.954) 		0.0298
(0.199) 		0.355
(0.705) 		0.321
(0.684) 		0.393
(0.73)
NFE2L2 27 (5%) 484 0.541
(0.841) 		2e-05
(0.000564) 		0.0831
(0.332) 		0.874
(0.986) 		0.912
(1.00) 		0.284
(0.666) 		0.0964
(0.358) 		0.343
(0.694) 		0.817
(0.976) 		0.633
(0.902)
EPHA2 24 (5%) 487 0.324
(0.687) 		0.00026
(0.00576) 		0.972
(1.00) 		0.93
(1.00) 		0.374
(0.722) 		0.317
(0.683) 		0.661
(0.906) 		0.189
(0.553) 		0.438
(0.763) 		0.321
(0.684)
OR6C65 16 (3%) 495 0.963
(1.00) 		0.273
(0.657) 		0.645
(0.905) 		0.432
(0.759) 		0.678
(0.91) 		0.748
(0.941) 		0.0415
(0.24) 		0.695
(0.919) 		0.0774
(0.327) 		0.915
(1.00)
PIK3CA 94 (18%) 417 0.0588
(0.296) 		0.159
(0.504) 		0.983
(1.00) 		0.0628
(0.299) 		0.0921
(0.348) 		0.329
(0.69) 		0.0901
(0.343) 		0.0229
(0.169) 		0.0932
(0.35) 		0.194
(0.553)
MAPK1 9 (2%) 502 0.0115
(0.113) 		0.623
(0.897) 		0.602
(0.882) 		0.833
(0.976) 		0.706
(0.925) 		0.919
(1.00) 		0.192
(0.553) 		0.836
(0.976) 		0.84
(0.976) 		0.169
(0.525)
KDM6A 17 (3%) 494 0.19
(0.553) 		0.376
(0.722) 		0.0443
(0.25) 		1
(1.00) 		0.929
(1.00) 		0.363
(0.711) 		0.651
(0.905) 		0.907
(1.00) 		0.407
(0.739) 		0.331
(0.69)
RB1 17 (3%) 494 0.337
(0.693) 		0.197
(0.557) 		0.238
(0.616) 		0.273
(0.657) 		0.0185
(0.154) 		0.253
(0.627) 		0.101
(0.37) 		0.264
(0.645) 		0.132
(0.434) 		0.304
(0.671)
VEZF1 8 (2%) 503 0.444
(0.768) 		0.0506
(0.268) 		0.964
(1.00) 		0.0588
(0.296) 		0.863
(0.986) 		0.494
(0.803) 		0.0227
(0.169) 		0.26
(0.638) 		0.279
(0.664) 		0.631
(0.902)
KIAA1267 11 (2%) 500 0.00738
(0.0915) 		0.668
(0.906) 		0.0856
(0.332) 		0.0621
(0.299) 		0.975
(1.00) 		1
(1.00) 		0.391
(0.73) 		0.927
(1.00) 		0.471
(0.788) 		0.677
(0.91)
ASXL1 16 (3%) 495 0.623
(0.897) 		0.985
(1.00) 		0.216
(0.595) 		0.873
(0.986) 		0.0764
(0.327) 		0.0177
(0.152) 		0.0665
(0.303) 		0.0656
(0.303) 		0.562
(0.855) 		0.0776
(0.327)
GAGE2A 4 (1%) 507 0.00862
(0.099) 		0.0948
(0.354) 		0.47
(0.788) 		0.794
(0.969) 		0.84
(0.976) 		0.484
(0.801) 		0.174
(0.533) 		0.685
(0.912) 		1
(1.00) 		1
(1.00)
KRTAP5-7 5 (1%) 506 0.835
(0.976) 		0.937
(1.00) 		0.688
(0.913) 		0.242
(0.617) 		0.664
(0.906) 		0.023
(0.169) 		0.695
(0.919) 		0.547
(0.841)
SLC9A6 5 (1%) 506 0.135
(0.44) 		0.0818
(0.332) 		1
(1.00) 		0.115
(0.401) 		0.0264
(0.182) 		0.365
(0.712) 		0.422
(0.75) 		0.229
(0.608) 		0.523
(0.827) 		0.0757
(0.326)
HNRNPL 11 (2%) 500 0.458
(0.778) 		0.28
(0.664) 		0.375
(0.722) 		0.456
(0.777) 		0.662
(0.906) 		0.334
(0.692) 		0.151
(0.48) 		0.0156
(0.14) 		0.292
(0.666) 		0.655
(0.905)
NOTCH2 21 (4%) 490 0.924
(1.00) 		0.983
(1.00) 		0.024
(0.173) 		0.488
(0.803) 		0.243
(0.618) 		0.447
(0.769) 		0.574
(0.858) 		0.668
(0.906) 		0.757
(0.944) 		0.39
(0.73)
FBXW7 33 (6%) 478 0.0612
(0.299) 		0.0583
(0.296) 		0.182
(0.55) 		0.232
(0.608) 		0.0979
(0.361) 		0.443
(0.768) 		0.476
(0.789) 		0.523
(0.827) 		0.104
(0.381) 		0.422
(0.75)
PTEN 14 (3%) 497 0.789
(0.969) 		0.131
(0.434) 		0.404
(0.739) 		0.834
(0.976) 		0.662
(0.906) 		0.232
(0.608) 		0.591
(0.87) 		0.224
(0.597) 		0.744
(0.94) 		0.0794
(0.328)
RASA1 18 (4%) 493 0.375
(0.722) 		0.189
(0.553) 		0.185
(0.55) 		0.713
(0.928) 		0.217
(0.595) 		0.205
(0.573) 		0.872
(0.986) 		0.627
(0.897) 		0.475
(0.789) 		0.679
(0.91)
NUDT11 9 (2%) 502 0.89
(0.992) 		0.611
(0.889) 		0.364
(0.711) 		0.733
(0.934) 		0.91
(1.00) 		0.679
(0.91) 		0.809
(0.976) 		0.401
(0.735) 		0.889
(0.992) 		0.792
(0.969)
KRT17 6 (1%) 505 0.932
(1.00) 		0.294
(0.666) 		0.303
(0.671) 		0.655
(0.905) 		0.772
(0.954) 		0.294
(0.666) 		0.974
(1.00) 		0.881
(0.99) 		0.0612
(0.299) 		1
(1.00)
RHOA 10 (2%) 501 0.301
(0.671) 		0.648
(0.905) 		0.395
(0.73) 		0.242
(0.617) 		1
(1.00) 		1
(1.00) 		0.868
(0.986) 		0.565
(0.856) 		0.733
(0.934) 		0.658
(0.906)
ZNF623 12 (2%) 499 0.72
(0.931) 		0.665
(0.906) 		0.24
(0.617) 		0.34
(0.694) 		0.83
(0.976) 		0.108
(0.391) 		0.822
(0.976) 		0.0578
(0.296) 		0.883
(0.99) 		0.0731
(0.319)
TIGD4 7 (1%) 504 0.655
(0.905) 		0.938
(1.00) 		0.816
(0.976) 		0.835
(0.976) 		0.504
(0.813) 		0.391
(0.73) 		0.856
(0.986) 		0.395
(0.73) 		0.576
(0.858) 		0.539
(0.841)
NAP1L2 7 (1%) 504 0.944
(1.00) 		0.0627
(0.299) 		0.514
(0.82) 		1
(1.00) 		0.395
(0.73) 		0.448
(0.769) 		0.977
(1.00) 		0.568
(0.857) 		0.308
(0.671) 		0.889
(0.992)
C3ORF59 10 (2%) 501 0.514
(0.82) 		0.345
(0.695) 		0.834
(0.976) 		0.558
(0.854) 		0.989
(1.00) 		0.724
(0.934) 		1
(1.00) 		0.378
(0.724)
ZNF233 9 (2%) 502 0.734
(0.934) 		0.381
(0.727) 		0.297
(0.668) 		0.287
(0.666) 		0.339
(0.694) 		1
(1.00) 		0.183
(0.55) 		0.641
(0.905) 		0.175
(0.535) 		0.285
(0.666)
SMAD4 13 (3%) 498 0.25
(0.627) 		0.346
(0.695) 		0.12
(0.409) 		0.874
(0.986) 		0.34
(0.694) 		0.568
(0.857) 		0.185
(0.55) 		0.494
(0.803) 		0.509
(0.815) 		0.232
(0.608)
EMG1 3 (1%) 508 0.841
(0.976) 		0.869
(0.986) 		0.224
(0.597) 		0.741
(0.94) 		0.529
(0.832) 		1
(1.00)
PIK3R1 8 (2%) 503 0.87
(0.986) 		0.332
(0.69) 		0.0709
(0.312) 		0.111
(0.396) 		0.395
(0.73) 		0.294
(0.666) 		1
(1.00) 		0.342
(0.694)
ELF4 7 (1%) 504 0.77
(0.954) 		0.797
(0.969) 		0.297
(0.668) 		0.336
(0.693) 		0.876
(0.986) 		0.86
(0.986) 		0.145
(0.464) 		0.802
(0.973) 		0.391
(0.73) 		0.616
(0.894)
ZFP36L2 8 (2%) 503 0.223
(0.597) 		0.0481
(0.262) 		0.706
(0.925) 		0.356
(0.706) 		0.864
(0.986) 		0.494
(0.803) 		0.416
(0.749) 		0.678
(0.91) 		1
(1.00) 		0.758
(0.944)
MYH9 21 (4%) 490 0.252
(0.627) 		0.363
(0.711) 		0.0665
(0.303) 		0.753
(0.943) 		0.931
(1.00) 		0.742
(0.94) 		0.822
(0.976) 		0.405
(0.739) 		0.581
(0.86) 		0.754
(0.943)
NCOR1 17 (3%) 494 0.868
(0.986) 		0.421
(0.75) 		0.476
(0.789) 		0.494
(0.803) 		0.818
(0.976) 		0.254
(0.628) 		0.825
(0.976) 		0.222
(0.597) 		0.868
(0.986) 		0.813
(0.976)
AK5 13 (3%) 498 0.754
(0.943) 		0.28
(0.664) 		0.426
(0.755) 		0.545
(0.841) 		0.847
(0.982) 		0.575
(0.858) 		0.0498
(0.267) 		0.0851
(0.332) 		0.171
(0.526) 		0.0824
(0.332)
SPTY2D1 10 (2%) 501 0.109
(0.391) 		0.136
(0.442) 		0.065
(0.303) 		0.286
(0.666) 		0.326
(0.689) 		0.858
(0.986) 		0.327
(0.689) 		0.31
(0.674) 		0.505
(0.814) 		0.543
(0.841)
PIWIL2 8 (2%) 503 0.731
(0.934) 		0.119
(0.409) 		0.82
(0.976) 		0.682
(0.912) 		0.185
(0.55) 		0.532
(0.836) 		0.14
(0.452) 		0.0685
(0.308) 		0.43
(0.758) 		0.16
(0.504)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
TP53 MUTATED 181 94 50 35
TP53 WILD-TYPE 18 27 89 11

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 = 0.00031

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 86 82 102 88 73 75 5
TP53 MUTATED 62 72 69 80 8 70 3
TP53 WILD-TYPE 24 10 33 8 65 5 2

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 = 0.142 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
TP53 MUTATED 39 19 25 23 59
TP53 WILD-TYPE 12 11 8 4 10
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.748 (Fisher's exact test), Q value = 0.94

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 35
TP53 WILD-TYPE 16 17 12
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
TP53 MUTATED 110 73 93 83
TP53 WILD-TYPE 23 37 70 14

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 = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
TP53 MUTATED 145 82 122 10
TP53 WILD-TYPE 31 15 46 52

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 = 1e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
TP53 MUTATED 69 99 58 75 60
TP53 WILD-TYPE 8 36 70 14 17

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 = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
TP53 MUTATED 158 117 86
TP53 WILD-TYPE 32 23 90

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 = 0.00161 (Fisher's exact test), Q value = 0.026

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
TP53 MUTATED 116 123 92
TP53 WILD-TYPE 24 62 45

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 = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
TP53 MUTATED 141 75 115
TP53 WILD-TYPE 30 24 77

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 = 4e-05 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
CDKN2A MUTATED 53 20 18 20
CDKN2A WILD-TYPE 146 101 121 26

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 = 0.00031

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 86 82 102 88 73 75 5
CDKN2A MUTATED 19 14 33 22 1 23 0
CDKN2A WILD-TYPE 67 68 69 66 72 52 5

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 = 0.0105 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
CDKN2A MUTATED 11 5 5 14 22
CDKN2A WILD-TYPE 40 25 28 13 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 = 0.814 (Fisher's exact test), Q value = 0.98

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 21 13
CDKN2A WILD-TYPE 55 64 34
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0863 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
CDKN2A MUTATED 28 32 27 24
CDKN2A WILD-TYPE 105 78 136 73
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
CDKN2A MUTATED 47 22 41 1
CDKN2A WILD-TYPE 129 75 127 61

Figure S12.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0452 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
CDKN2A MUTATED 14 39 18 21 19
CDKN2A WILD-TYPE 63 96 110 68 58

Figure S13.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.24

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
CDKN2A MUTATED 53 27 31
CDKN2A WILD-TYPE 137 113 145

Figure S14.  Get High-res Image Gene #2: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
CDKN2A MUTATED 31 43 29
CDKN2A WILD-TYPE 109 142 108
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0153 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
CDKN2A MUTATED 49 23 31
CDKN2A WILD-TYPE 122 76 161

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

'NSD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00722 (Fisher's exact test), Q value = 0.092

Table S21.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
NSD1 MUTATED 25 24 9 3
NSD1 WILD-TYPE 174 97 130 43

Figure S16.  Get High-res Image Gene #3: '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 = 0.00031

Table S22.  Gene #3: '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 86 82 102 88 73 75 5
NSD1 MUTATED 4 48 3 1 5 1 0
NSD1 WILD-TYPE 82 34 99 87 68 74 5

Figure S17.  Get High-res Image Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NSD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00729 (Fisher's exact test), Q value = 0.092

Table S23.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
NSD1 MUTATED 7 1 8 3 2
NSD1 WILD-TYPE 44 29 25 24 67

Figure S18.  Get High-res Image Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NSD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.13

Table S24.  Gene #3: '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 S19.  Get High-res Image Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S25.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
NSD1 MUTATED 11 6 39 5
NSD1 WILD-TYPE 122 104 124 92

Figure S20.  Get High-res Image Gene #3: '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 = 0.00031

Table S26.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
NSD1 MUTATED 10 39 5 7
NSD1 WILD-TYPE 166 58 163 55

Figure S21.  Get High-res Image Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00251 (Fisher's exact test), Q value = 0.038

Table S27.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
NSD1 MUTATED 18 15 18 3 8
NSD1 WILD-TYPE 59 120 110 86 69

Figure S22.  Get High-res Image Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00013 (Fisher's exact test), Q value = 0.0032

Table S28.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
NSD1 MUTATED 13 31 18
NSD1 WILD-TYPE 177 109 158

Figure S23.  Get High-res Image Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.6

Table S29.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
NSD1 MUTATED 12 27 19
NSD1 WILD-TYPE 128 158 118
'NSD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0031

Table S30.  Gene #3: 'NSD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
NSD1 MUTATED 14 5 39
NSD1 WILD-TYPE 157 94 153

Figure S24.  Get High-res Image Gene #3: '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 = 0.00031

Table S31.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
CASP8 MUTATED 6 2 36 9
CASP8 WILD-TYPE 193 119 103 37

Figure S25.  Get High-res Image Gene #4: '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 = 0.00031

Table S32.  Gene #4: '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 86 82 102 88 73 75 5
CASP8 MUTATED 8 3 39 0 0 4 0
CASP8 WILD-TYPE 78 79 63 88 73 71 5

Figure S26.  Get High-res Image Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CASP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0877 (Fisher's exact test), Q value = 0.34

Table S33.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
CASP8 MUTATED 5 2 1 7 7
CASP8 WILD-TYPE 46 28 32 20 62
'CASP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.7

Table S34.  Gene #4: '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 = 0.00031

Table S35.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
CASP8 MUTATED 19 26 4 5
CASP8 WILD-TYPE 114 84 159 92

Figure S27.  Get High-res Image Gene #4: '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 = 0.00031

Table S36.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
CASP8 MUTATED 16 4 34 0
CASP8 WILD-TYPE 160 93 134 62

Figure S28.  Get High-res Image Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S37.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
CASP8 MUTATED 5 28 3 14 3
CASP8 WILD-TYPE 72 107 125 75 74

Figure S29.  Get High-res Image Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CASP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 0.86

Table S38.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
CASP8 MUTATED 18 18 17
CASP8 WILD-TYPE 172 122 159
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.4

Table S39.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
CASP8 MUTATED 12 27 11
CASP8 WILD-TYPE 128 158 126
'CASP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0108 (Fisher's exact test), Q value = 0.11

Table S40.  Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
CASP8 MUTATED 17 19 14
CASP8 WILD-TYPE 154 80 178

Figure S30.  Get High-res Image Gene #4: 'CASP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 0.55

Table S41.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
MLL2 MUTATED 28 27 18 7
MLL2 WILD-TYPE 171 94 121 39
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0224 (Fisher's exact test), Q value = 0.17

Table S42.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
MLL2 MUTATED 7 19 14 20 11 8 2
MLL2 WILD-TYPE 79 63 88 68 62 67 3

Figure S31.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S43.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
MLL2 MUTATED 8 6 9 4 11
MLL2 WILD-TYPE 43 24 24 23 58
'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 0.83

Table S44.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
MLL2 MUTATED 14 18 6
MLL2 WILD-TYPE 64 67 41
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S45.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
MLL2 MUTATED 21 14 33 11
MLL2 WILD-TYPE 112 96 130 86
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.67

Table S46.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
MLL2 MUTATED 21 19 30 9
MLL2 WILD-TYPE 155 78 138 53
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.62

Table S47.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
MLL2 MUTATED 17 18 24 13 8
MLL2 WILD-TYPE 60 117 104 76 69
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0526 (Fisher's exact test), Q value = 0.28

Table S48.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
MLL2 MUTATED 22 30 28
MLL2 WILD-TYPE 168 110 148
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 0.84

Table S49.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
MLL2 MUTATED 20 26 25
MLL2 WILD-TYPE 120 159 112
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.4

Table S50.  Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
MLL2 MUTATED 20 21 30
MLL2 WILD-TYPE 151 78 162
'TGFBR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00161 (Fisher's exact test), Q value = 0.026

Table S51.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
TGFBR2 MUTATED 6 1 14 3
TGFBR2 WILD-TYPE 193 120 125 43

Figure S32.  Get High-res Image Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.029 (Fisher's exact test), Q value = 0.2

Table S52.  Gene #6: '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 86 82 102 88 73 75 5
TGFBR2 MUTATED 4 5 10 1 1 2 1
TGFBR2 WILD-TYPE 82 77 92 87 72 73 4

Figure S33.  Get High-res Image Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TGFBR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 0.86

Table S53.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
TGFBR2 MUTATED 3 1 0 0 4
TGFBR2 WILD-TYPE 48 29 33 27 65
'TGFBR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S54.  Gene #6: '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 = 0.437 (Fisher's exact test), Q value = 0.76

Table S55.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
TGFBR2 MUTATED 7 8 5 4
TGFBR2 WILD-TYPE 126 102 158 93
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.953 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
TGFBR2 MUTATED 9 4 9 2
TGFBR2 WILD-TYPE 167 93 159 60
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.67

Table S57.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
TGFBR2 MUTATED 2 8 3 7 4
TGFBR2 WILD-TYPE 75 127 125 82 73
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S58.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
TGFBR2 MUTATED 9 8 7
TGFBR2 WILD-TYPE 181 132 169
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.76

Table S59.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
TGFBR2 MUTATED 10 8 5
TGFBR2 WILD-TYPE 130 177 132
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.417 (Fisher's exact test), Q value = 0.75

Table S60.  Gene #6: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
TGFBR2 MUTATED 9 7 7
TGFBR2 WILD-TYPE 162 92 185
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00273 (Fisher's exact test), Q value = 0.04

Table S61.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
HLA-B MUTATED 3 4 13 4
HLA-B WILD-TYPE 196 117 126 42

Figure S34.  Get High-res Image Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00844 (Fisher's exact test), Q value = 0.099

Table S62.  Gene #7: '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 86 82 102 88 73 75 5
HLA-B MUTATED 1 1 13 4 3 2 0
HLA-B WILD-TYPE 85 81 89 84 70 73 5

Figure S35.  Get High-res Image Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 0.99

Table S63.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
HLA-B MUTATED 1 2 1 1 2
HLA-B WILD-TYPE 50 28 32 26 67
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.6

Table S64.  Gene #7: '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 = 0.0263 (Fisher's exact test), Q value = 0.18

Table S65.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
HLA-B MUTATED 6 11 4 2
HLA-B WILD-TYPE 127 99 159 95

Figure S36.  Get High-res Image Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0702 (Fisher's exact test), Q value = 0.31

Table S66.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
HLA-B MUTATED 4 5 13 1
HLA-B WILD-TYPE 172 92 155 61
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0696 (Fisher's exact test), Q value = 0.31

Table S67.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
HLA-B MUTATED 7 8 5 4 0
HLA-B WILD-TYPE 70 127 123 85 77
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.55

Table S68.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
HLA-B MUTATED 5 8 11
HLA-B WILD-TYPE 185 132 165
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00684 (Fisher's exact test), Q value = 0.09

Table S69.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
HLA-B MUTATED 1 14 8
HLA-B WILD-TYPE 139 171 129

Figure S37.  Get High-res Image Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0464 (Fisher's exact test), Q value = 0.25

Table S70.  Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
HLA-B MUTATED 4 9 10
HLA-B WILD-TYPE 167 90 182

Figure S38.  Get High-res Image Gene #7: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0612 (Fisher's exact test), Q value = 0.3

Table S71.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
FBXW7 MUTATED 7 13 11 2
FBXW7 WILD-TYPE 192 108 128 44
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0583 (Fisher's exact test), Q value = 0.3

Table S72.  Gene #8: '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 86 82 102 88 73 75 5
FBXW7 MUTATED 1 7 10 8 3 3 1
FBXW7 WILD-TYPE 85 75 92 80 70 72 4
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.55

Table S73.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
FBXW7 MUTATED 1 0 4 1 4
FBXW7 WILD-TYPE 50 30 29 26 65
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S74.  Gene #8: '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 = 0.0979 (Fisher's exact test), Q value = 0.36

Table S75.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
FBXW7 MUTATED 5 11 13 3
FBXW7 WILD-TYPE 128 99 150 94
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.443 (Fisher's exact test), Q value = 0.77

Table S76.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
FBXW7 MUTATED 8 9 12 3
FBXW7 WILD-TYPE 168 88 156 59
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.79

Table S77.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
FBXW7 MUTATED 3 13 8 6 3
FBXW7 WILD-TYPE 74 122 120 83 74
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.523 (Fisher's exact test), Q value = 0.83

Table S78.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
FBXW7 MUTATED 11 12 10
FBXW7 WILD-TYPE 179 128 166
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.38

Table S79.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
FBXW7 MUTATED 5 17 7
FBXW7 WILD-TYPE 135 168 130
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.422 (Fisher's exact test), Q value = 0.75

Table S80.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
FBXW7 MUTATED 9 9 11
FBXW7 WILD-TYPE 162 90 181
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
NOTCH1 MUTATED 32 13 33 10
NOTCH1 WILD-TYPE 167 108 106 36

Figure S39.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00056

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 86 82 102 88 73 75 5
NOTCH1 MUTATED 20 9 33 14 3 9 2
NOTCH1 WILD-TYPE 66 73 69 74 70 66 3

Figure S40.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
NOTCH1 MUTATED 11 7 2 5 14
NOTCH1 WILD-TYPE 40 23 31 22 55
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0592 (Fisher's exact test), Q value = 0.3

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 = 0.00028 (Fisher's exact test), Q value = 0.006

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
NOTCH1 MUTATED 23 29 14 23
NOTCH1 WILD-TYPE 110 81 149 74

Figure S41.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00319 (Fisher's exact test), Q value = 0.046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
NOTCH1 MUTATED 38 12 36 3
NOTCH1 WILD-TYPE 138 85 132 59

Figure S42.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0041

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
NOTCH1 MUTATED 10 33 8 19 19
NOTCH1 WILD-TYPE 67 102 120 70 58

Figure S43.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0789 (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 190 140 176
NOTCH1 MUTATED 42 24 23
NOTCH1 WILD-TYPE 148 116 153
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0686 (Fisher's exact test), Q value = 0.31

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
NOTCH1 MUTATED 31 32 16
NOTCH1 WILD-TYPE 109 153 121
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0118 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
NOTCH1 MUTATED 41 14 24
NOTCH1 WILD-TYPE 130 85 168

Figure S44.  Get High-res Image Gene #9: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0301 (Fisher's exact test), Q value = 0.2

Table S91.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
FAT1 MUTATED 33 25 38 15
FAT1 WILD-TYPE 166 96 101 31

Figure S45.  Get High-res Image Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

Table S92.  Gene #10: '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 86 82 102 88 73 75 5
FAT1 MUTATED 16 17 42 22 2 12 1
FAT1 WILD-TYPE 70 65 60 66 71 63 4

Figure S46.  Get High-res Image Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.925 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
FAT1 MUTATED 12 7 7 4 16
FAT1 WILD-TYPE 39 23 26 23 53
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 0.8

Table S94.  Gene #10: '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 = 0.0186 (Fisher's exact test), Q value = 0.15

Table S95.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
FAT1 MUTATED 32 34 25 19
FAT1 WILD-TYPE 101 76 138 78

Figure S47.  Get High-res Image Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00072 (Fisher's exact test), Q value = 0.013

Table S96.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
FAT1 MUTATED 41 19 47 3
FAT1 WILD-TYPE 135 78 121 59

Figure S48.  Get High-res Image Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.18

Table S97.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
FAT1 MUTATED 18 34 16 26 16
FAT1 WILD-TYPE 59 101 112 63 61

Figure S49.  Get High-res Image Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 0.87

Table S98.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
FAT1 MUTATED 46 29 35
FAT1 WILD-TYPE 144 111 141
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.63

Table S99.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
FAT1 MUTATED 30 48 25
FAT1 WILD-TYPE 110 137 112
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.269 (Fisher's exact test), Q value = 0.65

Table S100.  Gene #10: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
FAT1 MUTATED 44 23 36
FAT1 WILD-TYPE 127 76 156
'JUB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
JUB MUTATED 14 8 8 4
JUB WILD-TYPE 185 113 131 42
'JUB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
JUB MUTATED 3 5 10 8 2 6 0
JUB WILD-TYPE 83 77 92 80 71 69 5
'JUB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0853 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
JUB MUTATED 6 1 3 3 1
JUB WILD-TYPE 45 29 30 24 68
'JUB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
JUB MUTATED 7 5 2
JUB WILD-TYPE 71 80 45
'JUB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
JUB MUTATED 13 8 11 2
JUB WILD-TYPE 120 102 152 95
'JUB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.772 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
JUB MUTATED 10 8 13 3
JUB WILD-TYPE 166 89 155 59
'JUB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0298 (Fisher's exact test), Q value = 0.2

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
JUB MUTATED 8 12 8 6 0
JUB WILD-TYPE 69 123 120 83 77

Figure S50.  Get High-res Image Gene #11: 'JUB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'JUB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.355 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
JUB MUTATED 9 12 13
JUB WILD-TYPE 181 128 163
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
JUB MUTATED 8 12 14
JUB WILD-TYPE 132 173 123
'JUB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 0.73

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
JUB MUTATED 9 9 16
JUB WILD-TYPE 162 90 176
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.55

Table S111.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
ZNF750 MUTATED 5 9 6 1
ZNF750 WILD-TYPE 194 112 133 45
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.14

Table S112.  Gene #12: '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 86 82 102 88 73 75 5
ZNF750 MUTATED 1 3 3 6 8 0 0
ZNF750 WILD-TYPE 85 79 99 82 65 75 5

Figure S51.  Get High-res Image Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 0.9

Table S113.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
ZNF750 MUTATED 1 0 2 0 2
ZNF750 WILD-TYPE 50 30 31 27 67
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 0.67

Table S114.  Gene #12: '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 = 0.0379 (Fisher's exact test), Q value = 0.23

Table S115.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
ZNF750 MUTATED 4 1 12 2
ZNF750 WILD-TYPE 129 109 151 95

Figure S52.  Get High-res Image Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00832 (Fisher's exact test), Q value = 0.099

Table S116.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
ZNF750 MUTATED 3 5 4 7
ZNF750 WILD-TYPE 173 92 164 55

Figure S53.  Get High-res Image Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0058

Table S117.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
ZNF750 MUTATED 6 1 12 0 2
ZNF750 WILD-TYPE 71 134 116 89 75

Figure S54.  Get High-res Image Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
ZNF750 MUTATED 5 5 11
ZNF750 WILD-TYPE 185 135 165
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S119.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
ZNF750 MUTATED 6 9 6
ZNF750 WILD-TYPE 134 176 131
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 0.56

Table S120.  Gene #12: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
ZNF750 MUTATED 5 3 13
ZNF750 WILD-TYPE 166 96 179
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.84

Table S121.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
NFE2L2 MUTATED 8 7 8 4
NFE2L2 WILD-TYPE 191 114 131 42
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00056

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 86 82 102 88 73 75 5
NFE2L2 MUTATED 1 3 7 15 1 0 0
NFE2L2 WILD-TYPE 85 79 95 73 72 75 5

Figure S55.  Get High-res Image Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0831 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
NFE2L2 MUTATED 3 2 5 2 1
NFE2L2 WILD-TYPE 48 28 28 25 68
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.874 (Fisher's exact test), Q value = 0.99

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 = 0.912 (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 CLUS_4
ALL 133 110 163 97
NFE2L2 MUTATED 7 7 9 4
NFE2L2 WILD-TYPE 126 103 154 93
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.67

Table S126.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
NFE2L2 MUTATED 7 9 9 2
NFE2L2 WILD-TYPE 169 88 159 60
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0964 (Fisher's exact test), Q value = 0.36

Table S127.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
NFE2L2 MUTATED 5 2 8 8 4
NFE2L2 WILD-TYPE 72 133 120 81 73
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.69

Table S128.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
NFE2L2 MUTATED 9 5 13
NFE2L2 WILD-TYPE 181 135 163
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 0.98

Table S129.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
NFE2L2 MUTATED 9 9 8
NFE2L2 WILD-TYPE 131 176 129
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 0.9

Table S130.  Gene #13: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
NFE2L2 MUTATED 9 4 13
NFE2L2 WILD-TYPE 162 95 179
'HLA-A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00068 (Fisher's exact test), Q value = 0.013

Table S131.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
HLA-A MUTATED 4 1 13 4
HLA-A WILD-TYPE 195 120 126 42

Figure S56.  Get High-res Image Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HLA-A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0182 (Fisher's exact test), Q value = 0.15

Table S132.  Gene #14: '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 86 82 102 88 73 75 5
HLA-A MUTATED 2 1 12 3 3 1 0
HLA-A WILD-TYPE 84 81 90 85 70 74 5

Figure S57.  Get High-res Image Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HLA-A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.964 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
HLA-A MUTATED 1 0 1 1 2
HLA-A WILD-TYPE 50 30 32 26 67
'HLA-A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.64 (Fisher's exact test), Q value = 0.9

Table S134.  Gene #14: '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 = 0.0392 (Fisher's exact test), Q value = 0.23

Table S135.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
HLA-A MUTATED 9 8 4 1
HLA-A WILD-TYPE 124 102 159 96

Figure S58.  Get High-res Image Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HLA-A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00066 (Fisher's exact test), Q value = 0.013

Table S136.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
HLA-A MUTATED 2 1 16 3
HLA-A WILD-TYPE 174 96 152 59

Figure S59.  Get High-res Image Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.67

Table S137.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
HLA-A MUTATED 3 10 4 4 1
HLA-A WILD-TYPE 74 125 124 85 76
'HLA-A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.2

Table S138.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
HLA-A MUTATED 3 10 9
HLA-A WILD-TYPE 187 130 167

Figure S60.  Get High-res Image Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.68

Table S139.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
HLA-A MUTATED 4 12 6
HLA-A WILD-TYPE 136 173 131
'HLA-A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.17

Table S140.  Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
HLA-A MUTATED 4 10 8
HLA-A WILD-TYPE 167 89 184

Figure S61.  Get High-res Image Gene #14: 'HLA-A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPHA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.69

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
EPHA2 MUTATED 8 3 10 2
EPHA2 WILD-TYPE 191 118 129 44
'EPHA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00026 (Fisher's exact test), Q value = 0.0058

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
EPHA2 MUTATED 0 5 13 0 2 4 0
EPHA2 WILD-TYPE 86 77 89 88 71 71 5

Figure S62.  Get High-res Image Gene #15: 'EPHA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPHA2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.972 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
EPHA2 MUTATED 4 1 2 1 4
EPHA2 WILD-TYPE 47 29 31 26 65
'EPHA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

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

P value = 0.374 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
EPHA2 MUTATED 10 5 5 4
EPHA2 WILD-TYPE 123 105 158 93
'EPHA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
EPHA2 MUTATED 8 3 12 1
EPHA2 WILD-TYPE 168 94 156 61
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
EPHA2 MUTATED 5 8 4 4 2
EPHA2 WILD-TYPE 72 127 124 85 75
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
EPHA2 MUTATED 8 10 5
EPHA2 WILD-TYPE 182 130 171
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.76

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
EPHA2 MUTATED 5 11 4
EPHA2 WILD-TYPE 135 174 133
'EPHA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
EPHA2 MUTATED 7 7 6
EPHA2 WILD-TYPE 164 92 186
'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.054

Table S151.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
RAC1 MUTATED 2 1 10 2
RAC1 WILD-TYPE 197 120 129 44

Figure S63.  Get High-res Image Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.23

Table S152.  Gene #16: '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 86 82 102 88 73 75 5
RAC1 MUTATED 4 0 8 1 1 1 0
RAC1 WILD-TYPE 82 82 94 87 72 74 5

Figure S64.  Get High-res Image Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S153.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
RAC1 MUTATED 1 1 0 1 1
RAC1 WILD-TYPE 50 29 33 26 68
'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 0.98

Table S154.  Gene #16: '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 = 0.00389 (Fisher's exact test), Q value = 0.054

Table S155.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
RAC1 MUTATED 1 9 3 1
RAC1 WILD-TYPE 132 101 160 96

Figure S65.  Get High-res Image Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0784 (Fisher's exact test), Q value = 0.33

Table S156.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
RAC1 MUTATED 2 1 9 2
RAC1 WILD-TYPE 174 96 159 60
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S157.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
RAC1 MUTATED 2 4 4 3 2
RAC1 WILD-TYPE 75 131 124 86 75
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.69

Table S158.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
RAC1 MUTATED 4 3 8
RAC1 WILD-TYPE 186 137 168
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.78

Table S159.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
RAC1 MUTATED 2 7 4
RAC1 WILD-TYPE 138 178 133
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 0.86

Table S160.  Gene #16: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
RAC1 MUTATED 3 3 7
RAC1 WILD-TYPE 168 96 185
'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
HRAS MUTATED 1 0 25 4
HRAS WILD-TYPE 198 121 114 42

Figure S66.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00031

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
HRAS MUTATED 5 2 20 1 1 2 0
HRAS WILD-TYPE 81 80 82 87 72 73 5

Figure S67.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.577 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
HRAS MUTATED 2 0 2 2 2
HRAS WILD-TYPE 49 30 31 25 67
'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 0.9

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

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

P value = 0.00051 (Fisher's exact test), Q value = 0.01

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
HRAS MUTATED 11 14 2 4
HRAS WILD-TYPE 122 96 161 93

Figure S68.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0254 (Fisher's exact test), Q value = 0.18

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
HRAS MUTATED 9 3 18 1
HRAS WILD-TYPE 167 94 150 61

Figure S69.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
HRAS MUTATED 3 19 2 5 2
HRAS WILD-TYPE 74 116 126 84 75

Figure S70.  Get High-res Image Gene #17: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.39

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
HRAS MUTATED 10 5 16
HRAS WILD-TYPE 180 135 160
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
HRAS MUTATED 8 15 7
HRAS WILD-TYPE 132 170 130
'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 0.8

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
HRAS MUTATED 10 9 11
HRAS WILD-TYPE 161 90 181
'EP300 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.037 (Fisher's exact test), Q value = 0.23

Table S171.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
EP300 MUTATED 10 6 18 4
EP300 WILD-TYPE 189 115 121 42

Figure S71.  Get High-res Image Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EP300 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0165 (Fisher's exact test), Q value = 0.14

Table S172.  Gene #18: '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 86 82 102 88 73 75 5
EP300 MUTATED 5 2 13 8 9 1 0
EP300 WILD-TYPE 81 80 89 80 64 74 5

Figure S72.  Get High-res Image Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EP300 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.73

Table S173.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
EP300 MUTATED 3 2 1 4 3
EP300 WILD-TYPE 48 28 32 23 66
'EP300 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.33

Table S174.  Gene #18: '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 = 0.0557 (Fisher's exact test), Q value = 0.29

Table S175.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
EP300 MUTATED 10 15 8 5
EP300 WILD-TYPE 123 95 155 92
'EP300 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0599 (Fisher's exact test), Q value = 0.3

Table S176.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
EP300 MUTATED 13 2 18 5
EP300 WILD-TYPE 163 95 150 57
'EP300 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.68

Table S177.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
EP300 MUTATED 4 12 9 9 2
EP300 WILD-TYPE 73 123 119 80 75
'EP300 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0421 (Fisher's exact test), Q value = 0.24

Table S178.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
EP300 MUTATED 12 5 19
EP300 WILD-TYPE 178 135 157

Figure S73.  Get High-res Image Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.76

Table S179.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
EP300 MUTATED 7 15 12
EP300 WILD-TYPE 133 170 125
'EP300 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.61

Table S180.  Gene #18: 'EP300 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
EP300 MUTATED 10 5 19
EP300 WILD-TYPE 161 94 173
'OR6C65 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.963 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
OR6C65 MUTATED 7 3 5 1
OR6C65 WILD-TYPE 192 118 134 45
'OR6C65 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.66

Table S182.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
OR6C65 MUTATED 2 2 4 1 6 1 0
OR6C65 WILD-TYPE 84 80 98 87 67 74 5
'OR6C65 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 0.9

Table S183.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
OR6C65 MUTATED 2 2 0 1 2
OR6C65 WILD-TYPE 49 28 33 26 67
'OR6C65 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 0.76

Table S184.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
OR6C65 MUTATED 3 4 0
OR6C65 WILD-TYPE 75 81 47
'OR6C65 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 0.91

Table S185.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
OR6C65 MUTATED 3 3 5 5
OR6C65 WILD-TYPE 130 107 158 92
'OR6C65 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.748 (Fisher's exact test), Q value = 0.94

Table S186.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
OR6C65 MUTATED 6 3 4 3
OR6C65 WILD-TYPE 170 94 164 59
'OR6C65 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0415 (Fisher's exact test), Q value = 0.24

Table S187.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
OR6C65 MUTATED 0 6 7 0 3
OR6C65 WILD-TYPE 77 129 121 89 74

Figure S74.  Get High-res Image Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'OR6C65 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 0.92

Table S188.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
OR6C65 MUTATED 6 3 7
OR6C65 WILD-TYPE 184 137 169
'OR6C65 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0774 (Fisher's exact test), Q value = 0.33

Table S189.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
OR6C65 MUTATED 0 6 4
OR6C65 WILD-TYPE 140 179 133
'OR6C65 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S190.  Gene #19: 'OR6C65 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
OR6C65 MUTATED 3 2 5
OR6C65 WILD-TYPE 168 97 187
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0588 (Fisher's exact test), Q value = 0.3

Table S191.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
PIK3CA MUTATED 25 24 32 10
PIK3CA WILD-TYPE 174 97 107 36
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.5

Table S192.  Gene #20: '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 86 82 102 88 73 75 5
PIK3CA MUTATED 16 13 17 18 21 8 1
PIK3CA WILD-TYPE 70 69 85 70 52 67 4
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.983 (Fisher's exact test), Q value = 1

Table S193.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
PIK3CA MUTATED 10 6 7 4 13
PIK3CA WILD-TYPE 41 24 26 23 56
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0628 (Fisher's exact test), Q value = 0.3

Table S194.  Gene #20: '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 = 0.0921 (Fisher's exact test), Q value = 0.35

Table S195.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
PIK3CA MUTATED 19 22 39 13
PIK3CA WILD-TYPE 114 88 124 84
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 0.69

Table S196.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
PIK3CA MUTATED 27 18 32 16
PIK3CA WILD-TYPE 149 79 136 46
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0901 (Fisher's exact test), Q value = 0.34

Table S197.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
PIK3CA MUTATED 13 24 34 14 9
PIK3CA WILD-TYPE 64 111 94 75 68
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.17

Table S198.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
PIK3CA MUTATED 31 19 44
PIK3CA WILD-TYPE 159 121 132

Figure S75.  Get High-res Image Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0932 (Fisher's exact test), Q value = 0.35

Table S199.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
PIK3CA MUTATED 22 30 34
PIK3CA WILD-TYPE 118 155 103
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.55

Table S200.  Gene #20: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
PIK3CA MUTATED 31 13 42
PIK3CA WILD-TYPE 140 86 150
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
PTEN MUTATED 5 4 3 2
PTEN WILD-TYPE 194 117 136 44
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.43

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
PTEN MUTATED 1 3 1 3 4 1 1
PTEN WILD-TYPE 85 79 101 85 69 74 4
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.404 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
PTEN MUTATED 1 2 0 0 1
PTEN WILD-TYPE 50 28 33 27 68
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 0.98

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

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

P value = 0.662 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
PTEN MUTATED 3 2 7 2
PTEN WILD-TYPE 130 108 156 95
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
PTEN MUTATED 2 4 5 3
PTEN WILD-TYPE 174 93 163 59
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 0.87

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
PTEN MUTATED 2 3 6 1 1
PTEN WILD-TYPE 75 132 122 88 76
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
PTEN MUTATED 2 5 6
PTEN WILD-TYPE 188 135 170
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 0.94

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
PTEN MUTATED 2 5 4
PTEN WILD-TYPE 138 180 133
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0794 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
PTEN MUTATED 1 2 8
PTEN WILD-TYPE 170 97 184
'RASA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.72

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
RASA1 MUTATED 8 6 2 1
RASA1 WILD-TYPE 191 115 137 45
'RASA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
RASA1 MUTATED 4 1 3 6 0 4 0
RASA1 WILD-TYPE 82 81 99 82 73 71 5
'RASA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
RASA1 MUTATED 2 4 0 1 3
RASA1 WILD-TYPE 49 26 33 26 66
'RASA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 0.93

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

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

P value = 0.217 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
RASA1 MUTATED 5 1 6 6
RASA1 WILD-TYPE 128 109 157 91
'RASA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.205 (Fisher's exact test), Q value = 0.57

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
RASA1 MUTATED 7 6 5 0
RASA1 WILD-TYPE 169 91 163 62
'RASA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.872 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
RASA1 MUTATED 4 4 4 4 2
RASA1 WILD-TYPE 73 131 124 85 75
'RASA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
RASA1 MUTATED 9 4 5
RASA1 WILD-TYPE 181 136 171
'RASA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
RASA1 MUTATED 7 6 3
RASA1 WILD-TYPE 133 179 134
'RASA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.91

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
RASA1 MUTATED 7 4 5
RASA1 WILD-TYPE 164 95 187
'MAPK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0115 (Fisher's exact test), Q value = 0.11

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
MAPK1 MUTATED 0 2 6 1
MAPK1 WILD-TYPE 199 119 133 45

Figure S76.  Get High-res Image Gene #23: 'MAPK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MAPK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
MAPK1 MUTATED 2 1 2 1 3 0 0
MAPK1 WILD-TYPE 84 81 100 87 70 75 5
'MAPK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
MAPK1 MUTATED 2 0 0 1 1
MAPK1 WILD-TYPE 49 30 33 26 68
'MAPK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.833 (Fisher's exact test), Q value = 0.98

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

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

P value = 0.706 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
MAPK1 MUTATED 1 3 3 1
MAPK1 WILD-TYPE 132 107 160 96
'MAPK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.919 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
MAPK1 MUTATED 2 2 3 1
MAPK1 WILD-TYPE 174 95 165 61
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.55

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
MAPK1 MUTATED 0 3 5 0 1
MAPK1 WILD-TYPE 77 132 123 89 76
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
MAPK1 MUTATED 3 2 4
MAPK1 WILD-TYPE 187 138 172
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
MAPK1 MUTATED 2 4 3
MAPK1 WILD-TYPE 138 181 134
'MAPK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.53

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
MAPK1 MUTATED 3 0 6
MAPK1 WILD-TYPE 168 99 186
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 0.99

Table S231.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
NUDT11 MUTATED 4 3 2 0
NUDT11 WILD-TYPE 195 118 137 46
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 0.89

Table S232.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
NUDT11 MUTATED 0 3 2 1 1 2 0
NUDT11 WILD-TYPE 86 79 100 87 72 73 5
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 0.71

Table S233.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
NUDT11 MUTATED 3 0 0 1 1
NUDT11 WILD-TYPE 48 30 33 26 68
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 0.93

Table S234.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NUDT11 MUTATED 3 1 1
NUDT11 WILD-TYPE 75 84 46
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S235.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
NUDT11 MUTATED 3 2 2 2
NUDT11 WILD-TYPE 130 108 161 95
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.91

Table S236.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
NUDT11 MUTATED 2 3 3 1
NUDT11 WILD-TYPE 174 94 165 61
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.809 (Fisher's exact test), Q value = 0.98

Table S237.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
NUDT11 MUTATED 1 4 1 2 1
NUDT11 WILD-TYPE 76 131 127 87 76
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.74

Table S238.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
NUDT11 MUTATED 2 2 5
NUDT11 WILD-TYPE 188 138 171
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 0.99

Table S239.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
NUDT11 MUTATED 3 2 2
NUDT11 WILD-TYPE 137 183 135
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 0.97

Table S240.  Gene #24: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
NUDT11 MUTATED 2 1 4
NUDT11 WILD-TYPE 169 98 188
'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.55

Table S241.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
KDM6A MUTATED 10 5 2 0
KDM6A WILD-TYPE 189 116 137 46
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.72

Table S242.  Gene #25: '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 86 82 102 88 73 75 5
KDM6A MUTATED 0 5 4 3 2 3 0
KDM6A WILD-TYPE 86 77 98 85 71 72 5
'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0443 (Fisher's exact test), Q value = 0.25

Table S243.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
KDM6A MUTATED 1 0 3 1 0
KDM6A WILD-TYPE 50 30 30 26 69

Figure S77.  Get High-res Image Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S244.  Gene #25: '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 = 0.929 (Fisher's exact test), Q value = 1

Table S245.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
KDM6A MUTATED 5 4 5 2
KDM6A WILD-TYPE 128 106 158 95
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.71

Table S246.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
KDM6A MUTATED 5 6 4 1
KDM6A WILD-TYPE 171 91 164 61
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.651 (Fisher's exact test), Q value = 0.9

Table S247.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
KDM6A MUTATED 2 7 5 2 1
KDM6A WILD-TYPE 75 128 123 87 76
'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S248.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
KDM6A MUTATED 7 5 5
KDM6A WILD-TYPE 183 135 171
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.74

Table S249.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
KDM6A MUTATED 3 9 4
KDM6A WILD-TYPE 137 176 133
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 0.69

Table S250.  Gene #25: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
KDM6A MUTATED 5 6 5
KDM6A WILD-TYPE 166 93 187
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.69

Table S251.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
RB1 MUTATED 4 5 5 3
RB1 WILD-TYPE 195 116 134 43
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.56

Table S252.  Gene #26: '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 86 82 102 88 73 75 5
RB1 MUTATED 1 3 2 3 5 2 1
RB1 WILD-TYPE 85 79 100 85 68 73 4
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.62

Table S253.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
RB1 MUTATED 0 2 0 0 2
RB1 WILD-TYPE 51 28 33 27 67
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.66

Table S254.  Gene #26: '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 = 0.0185 (Fisher's exact test), Q value = 0.15

Table S255.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
RB1 MUTATED 1 4 11 1
RB1 WILD-TYPE 132 106 152 96

Figure S78.  Get High-res Image Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.63

Table S256.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
RB1 MUTATED 4 6 4 3
RB1 WILD-TYPE 172 91 164 59
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.37

Table S257.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
RB1 MUTATED 4 4 7 0 1
RB1 WILD-TYPE 73 131 121 89 76
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 0.64

Table S258.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
RB1 MUTATED 3 6 7
RB1 WILD-TYPE 187 134 169
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.43

Table S259.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
RB1 MUTATED 2 5 8
RB1 WILD-TYPE 138 180 129
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.67

Table S260.  Gene #26: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
RB1 MUTATED 3 3 9
RB1 WILD-TYPE 168 96 183
'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 0.75

Table S261.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
KEAP1 MUTATED 6 8 7 1
KEAP1 WILD-TYPE 193 113 132 45
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.43

Table S262.  Gene #27: '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 86 82 102 88 73 75 5
KEAP1 MUTATED 3 5 4 8 0 2 0
KEAP1 WILD-TYPE 83 77 98 80 73 73 5
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S263.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
KEAP1 MUTATED 2 2 2 0 3
KEAP1 WILD-TYPE 49 28 31 27 66
'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 0.98

Table S264.  Gene #27: '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 = 0.332 (Fisher's exact test), Q value = 0.69

Table S265.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
KEAP1 MUTATED 8 2 9 3
KEAP1 WILD-TYPE 125 108 154 94
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00106 (Fisher's exact test), Q value = 0.018

Table S266.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
KEAP1 MUTATED 3 11 8 0
KEAP1 WILD-TYPE 173 86 160 62

Figure S79.  Get High-res Image Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.787 (Fisher's exact test), Q value = 0.97

Table S267.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
KEAP1 MUTATED 3 4 8 4 3
KEAP1 WILD-TYPE 74 131 120 85 74
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.24

Table S268.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
KEAP1 MUTATED 4 11 7
KEAP1 WILD-TYPE 186 129 169

Figure S80.  Get High-res Image Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 0.72

Table S269.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
KEAP1 MUTATED 6 10 3
KEAP1 WILD-TYPE 134 175 134
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.68

Table S270.  Gene #27: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
KEAP1 MUTATED 4 5 10
KEAP1 WILD-TYPE 167 94 182
'KRT17 MUTATION STATUS' versus 'CN_CNMF'

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

Table S271.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
KRT17 MUTATED 2 2 2 0
KRT17 WILD-TYPE 197 119 137 46
'KRT17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 0.67

Table S272.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
KRT17 MUTATED 0 0 3 2 1 0 0
KRT17 WILD-TYPE 86 82 99 86 72 75 5
'KRT17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.67

Table S273.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
KRT17 MUTATED 0 2 1 0 3
KRT17 WILD-TYPE 51 28 32 27 66
'KRT17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 0.9

Table S274.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
KRT17 MUTATED 1 3 2
KRT17 WILD-TYPE 77 82 45
'KRT17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 0.95

Table S275.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
KRT17 MUTATED 2 1 1 2
KRT17 WILD-TYPE 131 109 162 95
'KRT17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 0.67

Table S276.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
KRT17 MUTATED 2 3 1 0
KRT17 WILD-TYPE 174 94 167 62
'KRT17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S277.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
KRT17 MUTATED 1 1 2 1 1
KRT17 WILD-TYPE 76 134 126 88 76
'KRT17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.881 (Fisher's exact test), Q value = 0.99

Table S278.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
KRT17 MUTATED 3 1 2
KRT17 WILD-TYPE 187 139 174
'KRT17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0612 (Fisher's exact test), Q value = 0.3

Table S279.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
KRT17 MUTATED 3 0 3
KRT17 WILD-TYPE 137 185 134
'KRT17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S280.  Gene #28: 'KRT17 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
KRT17 MUTATED 2 1 3
KRT17 WILD-TYPE 169 98 189
'RHOA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 0.67

Table S281.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
RHOA MUTATED 3 1 4 2
RHOA WILD-TYPE 196 120 135 44
'RHOA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.648 (Fisher's exact test), Q value = 0.9

Table S282.  Gene #29: '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 86 82 102 88 73 75 5
RHOA MUTATED 2 3 2 0 1 2 0
RHOA WILD-TYPE 84 79 100 88 72 73 5
'RHOA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.73

Table S283.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
RHOA MUTATED 0 0 0 0 3
RHOA WILD-TYPE 51 30 33 27 66
'RHOA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.62

Table S284.  Gene #29: '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 S285.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
RHOA MUTATED 3 2 3 2
RHOA WILD-TYPE 130 108 160 95
'RHOA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S286.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
RHOA MUTATED 4 2 3 1
RHOA WILD-TYPE 172 95 165 61
'RHOA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 0.99

Table S287.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
RHOA MUTATED 1 3 2 3 1
RHOA WILD-TYPE 76 132 126 86 76
'RHOA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.565 (Fisher's exact test), Q value = 0.86

Table S288.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
RHOA MUTATED 4 4 2
RHOA WILD-TYPE 186 136 174
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 0.93

Table S289.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
RHOA MUTATED 4 3 3
RHOA WILD-TYPE 136 182 134
'RHOA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 0.91

Table S290.  Gene #29: 'RHOA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
RHOA MUTATED 4 3 3
RHOA WILD-TYPE 167 96 189
'PTPN14 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 0.77

Table S291.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
PTPN14 MUTATED 7 3 3 3
PTPN14 WILD-TYPE 192 118 136 43
'PTPN14 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.19

Table S292.  Gene #30: '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 86 82 102 88 73 75 5
PTPN14 MUTATED 0 4 8 2 0 2 0
PTPN14 WILD-TYPE 86 78 94 86 73 73 5

Figure S81.  Get High-res Image Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PTPN14 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.56

Table S293.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
PTPN14 MUTATED 2 2 1 1 0
PTPN14 WILD-TYPE 49 28 32 26 69
'PTPN14 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.579 (Fisher's exact test), Q value = 0.86

Table S294.  Gene #30: '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 = 0.36 (Fisher's exact test), Q value = 0.71

Table S295.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
PTPN14 MUTATED 5 6 3 2
PTPN14 WILD-TYPE 128 104 160 95
'PTPN14 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.669 (Fisher's exact test), Q value = 0.91

Table S296.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
PTPN14 MUTATED 4 4 7 1
PTPN14 WILD-TYPE 172 93 161 61
'PTPN14 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.22

Table S297.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
PTPN14 MUTATED 2 10 1 2 1
PTPN14 WILD-TYPE 75 125 127 87 76

Figure S82.  Get High-res Image Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PTPN14 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.502 (Fisher's exact test), Q value = 0.81

Table S298.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
PTPN14 MUTATED 4 6 6
PTPN14 WILD-TYPE 186 134 170
'PTPN14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0378 (Fisher's exact test), Q value = 0.23

Table S299.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
PTPN14 MUTATED 1 10 3
PTPN14 WILD-TYPE 139 175 134

Figure S83.  Get High-res Image Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PTPN14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 0.67

Table S300.  Gene #30: 'PTPN14 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
PTPN14 MUTATED 3 5 6
PTPN14 WILD-TYPE 168 94 186
'KRTAP5-5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.9

Table S301.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
KRTAP5-5 MUTATED 3 0 1 0
KRTAP5-5 WILD-TYPE 196 121 138 46
'KRTAP5-5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S302.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
KRTAP5-5 MUTATED 1 1 1 0 0 1 0
KRTAP5-5 WILD-TYPE 85 81 101 88 73 74 5
'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S303.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
KRTAP5-5 MUTATED 1 0 0 0 2
KRTAP5-5 WILD-TYPE 50 30 33 27 67
'KRTAP5-5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 0.97

Table S304.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
KRTAP5-5 MUTATED 1 2 0
KRTAP5-5 WILD-TYPE 77 83 47
'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.13

Table S305.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
KRTAP5-5 MUTATED 0 1 0 3
KRTAP5-5 WILD-TYPE 133 109 163 94

Figure S84.  Get High-res Image Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRTAP5-5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.547 (Fisher's exact test), Q value = 0.84

Table S306.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
KRTAP5-5 MUTATED 3 0 1 0
KRTAP5-5 WILD-TYPE 173 97 167 62
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.11

Table S307.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
KRTAP5-5 MUTATED 0 0 0 1 3
KRTAP5-5 WILD-TYPE 77 135 128 88 74

Figure S85.  Get High-res Image Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.64

Table S308.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
KRTAP5-5 MUTATED 3 1 0
KRTAP5-5 WILD-TYPE 187 139 176
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S309.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
KRTAP5-5 MUTATED 1 2 1
KRTAP5-5 WILD-TYPE 139 183 136
'KRTAP5-5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.71

Table S310.  Gene #31: 'KRTAP5-5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
KRTAP5-5 MUTATED 3 0 1
KRTAP5-5 WILD-TYPE 168 99 191
'ZNF623 MUTATION STATUS' versus 'CN_CNMF'

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

Table S311.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
ZNF623 MUTATED 3 4 3 1
ZNF623 WILD-TYPE 196 117 136 45
'ZNF623 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 0.91

Table S312.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
ZNF623 MUTATED 1 2 5 1 2 1 0
ZNF623 WILD-TYPE 85 80 97 87 71 74 5
'ZNF623 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.62

Table S313.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
ZNF623 MUTATED 2 0 3 1 1
ZNF623 WILD-TYPE 49 30 30 26 68
'ZNF623 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.34 (Fisher's exact test), Q value = 0.69

Table S314.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ZNF623 MUTATED 4 1 2
ZNF623 WILD-TYPE 74 84 45
'ZNF623 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 0.98

Table S315.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
ZNF623 MUTATED 4 3 4 1
ZNF623 WILD-TYPE 129 107 159 96
'ZNF623 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.39

Table S316.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
ZNF623 MUTATED 1 2 7 2
ZNF623 WILD-TYPE 175 95 161 60
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 0.98

Table S317.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
ZNF623 MUTATED 2 5 2 2 1
ZNF623 WILD-TYPE 75 130 126 87 76
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0578 (Fisher's exact test), Q value = 0.3

Table S318.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
ZNF623 MUTATED 1 6 5
ZNF623 WILD-TYPE 189 134 171
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 0.99

Table S319.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
ZNF623 MUTATED 2 3 1
ZNF623 WILD-TYPE 138 182 136
'ZNF623 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0731 (Fisher's exact test), Q value = 0.32

Table S320.  Gene #32: 'ZNF623 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
ZNF623 MUTATED 0 3 3
ZNF623 WILD-TYPE 171 96 189
'TIGD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 0.9

Table S321.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
TIGD4 MUTATED 2 3 2 0
TIGD4 WILD-TYPE 197 118 137 46
'TIGD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S322.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
TIGD4 MUTATED 1 1 2 2 1 0 0
TIGD4 WILD-TYPE 85 81 100 86 72 75 5
'TIGD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 0.98

Table S323.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
TIGD4 MUTATED 1 0 1 1 1
TIGD4 WILD-TYPE 50 30 32 26 68
'TIGD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 0.98

Table S324.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
TIGD4 MUTATED 2 1 1
TIGD4 WILD-TYPE 76 84 46
'TIGD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 0.81

Table S325.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
TIGD4 MUTATED 2 1 4 0
TIGD4 WILD-TYPE 131 109 159 97
'TIGD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.73

Table S326.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
TIGD4 MUTATED 1 2 4 0
TIGD4 WILD-TYPE 175 95 164 62
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 0.99

Table S327.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
TIGD4 MUTATED 0 2 2 2 1
TIGD4 WILD-TYPE 77 133 126 87 76
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.73

Table S328.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
TIGD4 MUTATED 1 3 3
TIGD4 WILD-TYPE 189 137 173
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 0.86

Table S329.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
TIGD4 MUTATED 1 4 2
TIGD4 WILD-TYPE 139 181 135
'TIGD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.539 (Fisher's exact test), Q value = 0.84

Table S330.  Gene #33: 'TIGD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
TIGD4 MUTATED 1 2 4
TIGD4 WILD-TYPE 170 97 188
'NAP1L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S331.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
NAP1L2 MUTATED 4 1 2 0
NAP1L2 WILD-TYPE 195 120 137 46
'NAP1L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0627 (Fisher's exact test), Q value = 0.3

Table S332.  Gene #34: '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 86 82 102 88 73 75 5
NAP1L2 MUTATED 1 0 1 2 0 2 1
NAP1L2 WILD-TYPE 85 82 101 86 73 73 4
'NAP1L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 0.82

Table S333.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
NAP1L2 MUTATED 0 0 0 1 2
NAP1L2 WILD-TYPE 51 30 33 26 67
'NAP1L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S334.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NAP1L2 MUTATED 1 1 1
NAP1L2 WILD-TYPE 77 84 46
'NAP1L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.73

Table S335.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
NAP1L2 MUTATED 3 2 1 0
NAP1L2 WILD-TYPE 130 108 162 97
'NAP1L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 0.77

Table S336.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
NAP1L2 MUTATED 1 1 4 0
NAP1L2 WILD-TYPE 175 96 164 62
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.977 (Fisher's exact test), Q value = 1

Table S337.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
NAP1L2 MUTATED 1 3 1 1 1
NAP1L2 WILD-TYPE 76 132 127 88 76
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.86

Table S338.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
NAP1L2 MUTATED 2 1 4
NAP1L2 WILD-TYPE 188 139 172
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 0.67

Table S339.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
NAP1L2 MUTATED 1 5 1
NAP1L2 WILD-TYPE 139 180 136
'NAP1L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.889 (Fisher's exact test), Q value = 0.99

Table S340.  Gene #34: 'NAP1L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
NAP1L2 MUTATED 2 2 3
NAP1L2 WILD-TYPE 169 97 189
'CUL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0348 (Fisher's exact test), Q value = 0.22

Table S341.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
CUL3 MUTATED 7 8 1 0
CUL3 WILD-TYPE 192 113 138 46

Figure S86.  Get High-res Image Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0101 (Fisher's exact test), Q value = 0.11

Table S342.  Gene #35: '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 86 82 102 88 73 75 5
CUL3 MUTATED 1 6 1 7 0 1 0
CUL3 WILD-TYPE 85 76 101 81 73 74 5

Figure S87.  Get High-res Image Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CUL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 0.81

Table S343.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
CUL3 MUTATED 2 1 3 0 2
CUL3 WILD-TYPE 49 29 30 27 67
'CUL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 0.93

Table S344.  Gene #35: '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 = 0.275 (Fisher's exact test), Q value = 0.66

Table S345.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
CUL3 MUTATED 5 1 8 2
CUL3 WILD-TYPE 128 109 155 95
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0193 (Fisher's exact test), Q value = 0.16

Table S346.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
CUL3 MUTATED 5 8 3 0
CUL3 WILD-TYPE 171 89 165 62

Figure S88.  Get High-res Image Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.25

Table S347.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
CUL3 MUTATED 5 3 7 0 1
CUL3 WILD-TYPE 72 132 121 89 76

Figure S89.  Get High-res Image Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CUL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S348.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
CUL3 MUTATED 7 4 5
CUL3 WILD-TYPE 183 136 171
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 0.78

Table S349.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
CUL3 MUTATED 2 7 4
CUL3 WILD-TYPE 138 178 133
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 0.77

Table S350.  Gene #35: 'CUL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
CUL3 MUTATED 5 1 7
CUL3 WILD-TYPE 166 98 185
'CREBBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.4

Table S351.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
CREBBP MUTATED 7 11 12 3
CREBBP WILD-TYPE 192 110 127 43
'CREBBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 0.77

Table S352.  Gene #36: '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 86 82 102 88 73 75 5
CREBBP MUTATED 5 9 8 7 2 3 0
CREBBP WILD-TYPE 81 73 94 81 71 72 5
'CREBBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.67

Table S353.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
CREBBP MUTATED 4 1 4 0 3
CREBBP WILD-TYPE 47 29 29 27 66
'CREBBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S354.  Gene #36: '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 = 0.0852 (Fisher's exact test), Q value = 0.33

Table S355.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
CREBBP MUTATED 15 4 11 4
CREBBP WILD-TYPE 118 106 152 93
'CREBBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0739 (Fisher's exact test), Q value = 0.32

Table S356.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
CREBBP MUTATED 6 10 15 3
CREBBP WILD-TYPE 170 87 153 59
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 0.93

Table S357.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
CREBBP MUTATED 7 11 7 4 5
CREBBP WILD-TYPE 70 124 121 85 72
'CREBBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.17

Table S358.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
CREBBP MUTATED 7 16 11
CREBBP WILD-TYPE 183 124 165

Figure S90.  Get High-res Image Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.41

Table S359.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
CREBBP MUTATED 6 18 7
CREBBP WILD-TYPE 134 167 130
'CREBBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0115 (Fisher's exact test), Q value = 0.11

Table S360.  Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
CREBBP MUTATED 5 12 14
CREBBP WILD-TYPE 166 87 178

Figure S91.  Get High-res Image Gene #36: 'CREBBP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'VEZF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.77

Table S361.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
VEZF1 MUTATED 2 4 2 0
VEZF1 WILD-TYPE 197 117 137 46
'VEZF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0506 (Fisher's exact test), Q value = 0.27

Table S362.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
VEZF1 MUTATED 0 3 2 1 0 1 1
VEZF1 WILD-TYPE 86 79 100 87 73 74 4
'VEZF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.964 (Fisher's exact test), Q value = 1

Table S363.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
VEZF1 MUTATED 1 0 1 1 2
VEZF1 WILD-TYPE 50 30 32 26 67
'VEZF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0588 (Fisher's exact test), Q value = 0.3

Table S364.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
VEZF1 MUTATED 0 2 3
VEZF1 WILD-TYPE 78 83 44
'VEZF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 0.99

Table S365.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
VEZF1 MUTATED 3 1 3 1
VEZF1 WILD-TYPE 130 109 160 96
'VEZF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.8

Table S366.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
VEZF1 MUTATED 2 3 3 0
VEZF1 WILD-TYPE 174 94 165 62
'VEZF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.17

Table S367.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
VEZF1 MUTATED 4 3 0 0 1
VEZF1 WILD-TYPE 73 132 128 89 76

Figure S92.  Get High-res Image Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'VEZF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.64

Table S368.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
VEZF1 MUTATED 3 4 1
VEZF1 WILD-TYPE 187 136 175
'VEZF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.66

Table S369.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
VEZF1 MUTATED 3 2 0
VEZF1 WILD-TYPE 137 183 137
'VEZF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.631 (Fisher's exact test), Q value = 0.9

Table S370.  Gene #37: 'VEZF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
VEZF1 MUTATED 3 1 1
VEZF1 WILD-TYPE 168 98 191
'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00097 (Fisher's exact test), Q value = 0.017

Table S371.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
MLL4 MUTATED 1 4 10 4
MLL4 WILD-TYPE 198 117 129 42

Figure S93.  Get High-res Image Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'MLL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00174 (Fisher's exact test), Q value = 0.027

Table S372.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
MLL4 MUTATED 2 2 11 2 1 0 1
MLL4 WILD-TYPE 84 80 91 86 72 75 4

Figure S94.  Get High-res Image Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'MLL4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 0.98

Table S373.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
MLL4 MUTATED 2 0 1 0 3
MLL4 WILD-TYPE 49 30 32 27 66
'MLL4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.73

Table S374.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
MLL4 MUTATED 2 4 0
MLL4 WILD-TYPE 76 81 47
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.42

Table S375.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
MLL4 MUTATED 4 8 5 1
MLL4 WILD-TYPE 129 102 158 96
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.53

Table S376.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
MLL4 MUTATED 5 3 10 0
MLL4 WILD-TYPE 171 94 158 62
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.16

Table S377.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
MLL4 MUTATED 2 12 2 2 1
MLL4 WILD-TYPE 75 123 126 87 76

Figure S95.  Get High-res Image Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MLL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S378.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
MLL4 MUTATED 7 6 6
MLL4 WILD-TYPE 183 134 170
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.41

Table S379.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
MLL4 MUTATED 2 10 3
MLL4 WILD-TYPE 138 175 134
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.9

Table S380.  Gene #38: 'MLL4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
MLL4 MUTATED 5 2 8
MLL4 WILD-TYPE 166 97 184
'IRS4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0198 (Fisher's exact test), Q value = 0.16

Table S381.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
IRS4 MUTATED 5 1 10 0
IRS4 WILD-TYPE 194 120 129 46

Figure S96.  Get High-res Image Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IRS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.552 (Fisher's exact test), Q value = 0.85

Table S382.  Gene #39: '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 86 82 102 88 73 75 5
IRS4 MUTATED 4 2 2 3 5 1 0
IRS4 WILD-TYPE 82 80 100 85 68 74 5
'IRS4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.55

Table S383.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
IRS4 MUTATED 1 1 1 3 1
IRS4 WILD-TYPE 50 29 32 24 68
'IRS4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 0.97

Table S384.  Gene #39: '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 = 0.409 (Fisher's exact test), Q value = 0.74

Table S385.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
IRS4 MUTATED 3 3 9 2
IRS4 WILD-TYPE 130 107 154 95
'IRS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0659 (Fisher's exact test), Q value = 0.3

Table S386.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
IRS4 MUTATED 3 5 4 5
IRS4 WILD-TYPE 173 92 164 57
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.546 (Fisher's exact test), Q value = 0.84

Table S387.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
IRS4 MUTATED 4 4 6 1 2
IRS4 WILD-TYPE 73 131 122 88 75
'IRS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.05 (Fisher's exact test), Q value = 0.27

Table S388.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
IRS4 MUTATED 2 6 9
IRS4 WILD-TYPE 188 134 167
'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0352 (Fisher's exact test), Q value = 0.22

Table S389.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
IRS4 MUTATED 2 4 9
IRS4 WILD-TYPE 138 181 128

Figure S97.  Get High-res Image Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'IRS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.43

Table S390.  Gene #39: 'IRS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
IRS4 MUTATED 4 1 10
IRS4 WILD-TYPE 167 98 182
'HUWE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00898 (Fisher's exact test), Q value = 0.1

Table S391.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
HUWE1 MUTATED 17 4 21 3
HUWE1 WILD-TYPE 182 117 118 43

Figure S98.  Get High-res Image Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HUWE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00082 (Fisher's exact test), Q value = 0.015

Table S392.  Gene #40: '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 86 82 102 88 73 75 5
HUWE1 MUTATED 8 1 20 4 8 5 0
HUWE1 WILD-TYPE 78 81 82 84 65 70 5

Figure S99.  Get High-res Image Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HUWE1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 0.93

Table S393.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
HUWE1 MUTATED 4 1 1 3 5
HUWE1 WILD-TYPE 47 29 32 24 64
'HUWE1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 0.9

Table S394.  Gene #40: '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 = 0.234 (Fisher's exact test), Q value = 0.61

Table S395.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
HUWE1 MUTATED 14 14 10 7
HUWE1 WILD-TYPE 119 96 153 90
'HUWE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0805 (Fisher's exact test), Q value = 0.33

Table S396.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
HUWE1 MUTATED 13 5 23 4
HUWE1 WILD-TYPE 163 92 145 58
'HUWE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S397.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
HUWE1 MUTATED 5 13 10 11 7
HUWE1 WILD-TYPE 72 122 118 78 70
'HUWE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.462 (Fisher's exact test), Q value = 0.78

Table S398.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
HUWE1 MUTATED 15 11 20
HUWE1 WILD-TYPE 175 129 156
'HUWE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 0.93

Table S399.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
HUWE1 MUTATED 12 21 13
HUWE1 WILD-TYPE 128 164 124
'HUWE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.617 (Fisher's exact test), Q value = 0.89

Table S400.  Gene #40: 'HUWE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
HUWE1 MUTATED 14 11 21
HUWE1 WILD-TYPE 157 88 171
'THSD7A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.91

Table S401.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
THSD7A MUTATED 15 8 6 3
THSD7A WILD-TYPE 184 113 133 43
'THSD7A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.41

Table S402.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
THSD7A MUTATED 2 10 8 4 6 2 0
THSD7A WILD-TYPE 84 72 94 84 67 73 5
'THSD7A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.79

Table S403.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
THSD7A MUTATED 4 3 3 4 3
THSD7A WILD-TYPE 47 27 30 23 66
'THSD7A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.63

Table S404.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
THSD7A MUTATED 7 4 6
THSD7A WILD-TYPE 71 81 41
'THSD7A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00497 (Fisher's exact test), Q value = 0.067

Table S405.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
THSD7A MUTATED 9 7 16 0
THSD7A WILD-TYPE 124 103 147 97

Figure S100.  Get High-res Image Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'THSD7A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0657 (Fisher's exact test), Q value = 0.3

Table S406.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
THSD7A MUTATED 7 12 9 4
THSD7A WILD-TYPE 169 85 159 58
'THSD7A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.65

Table S407.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
THSD7A MUTATED 7 9 7 6 1
THSD7A WILD-TYPE 70 126 121 83 76
'THSD7A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.23

Table S408.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
THSD7A MUTATED 5 11 14
THSD7A WILD-TYPE 185 129 162

Figure S101.  Get High-res Image Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'THSD7A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0807 (Fisher's exact test), Q value = 0.33

Table S409.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
THSD7A MUTATED 3 13 10
THSD7A WILD-TYPE 137 172 127
'THSD7A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0232 (Fisher's exact test), Q value = 0.17

Table S410.  Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
THSD7A MUTATED 4 5 17
THSD7A WILD-TYPE 167 94 175

Figure S102.  Get High-res Image Gene #41: 'THSD7A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'C3ORF59 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.514 (Fisher's exact test), Q value = 0.82

Table S411.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
C3ORF59 MUTATED 2 3 4 1
C3ORF59 WILD-TYPE 197 118 135 45
'C3ORF59 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.69

Table S412.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
C3ORF59 MUTATED 0 2 5 1 1 1 0
C3ORF59 WILD-TYPE 86 80 97 87 72 74 5
'C3ORF59 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 0.98

Table S413.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
C3ORF59 MUTATED 2 3 4 1
C3ORF59 WILD-TYPE 131 107 159 96
'C3ORF59 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 0.85

Table S414.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
C3ORF59 MUTATED 4 1 5 0
C3ORF59 WILD-TYPE 172 96 163 62
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.989 (Fisher's exact test), Q value = 1

Table S415.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
C3ORF59 MUTATED 1 3 2 2 2
C3ORF59 WILD-TYPE 76 132 126 87 75
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 0.93

Table S416.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
C3ORF59 MUTATED 3 4 3
C3ORF59 WILD-TYPE 187 136 173
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S417.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
C3ORF59 MUTATED 3 4 3
C3ORF59 WILD-TYPE 137 181 134
'C3ORF59 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 0.72

Table S418.  Gene #42: 'C3ORF59 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
C3ORF59 MUTATED 3 4 3
C3ORF59 WILD-TYPE 168 95 189
'DYSF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 0.9

Table S419.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
DYSF MUTATED 6 7 5 2
DYSF WILD-TYPE 193 114 134 44
'DYSF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0097 (Fisher's exact test), Q value = 0.11

Table S420.  Gene #43: '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 86 82 102 88 73 75 5
DYSF MUTATED 1 9 6 3 1 0 0
DYSF WILD-TYPE 85 73 96 85 72 75 5

Figure S103.  Get High-res Image Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DYSF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 0.86

Table S421.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
DYSF MUTATED 1 1 3 1 2
DYSF WILD-TYPE 50 29 30 26 67
'DYSF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 0.93

Table S422.  Gene #43: '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 = 0.194 (Fisher's exact test), Q value = 0.55

Table S423.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
DYSF MUTATED 2 3 10 4
DYSF WILD-TYPE 131 107 153 93
'DYSF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0091 (Fisher's exact test), Q value = 0.1

Table S424.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
DYSF MUTATED 4 10 4 1
DYSF WILD-TYPE 172 87 164 61

Figure S104.  Get High-res Image Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DYSF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.89

Table S425.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
DYSF MUTATED 4 6 6 1 3
DYSF WILD-TYPE 73 129 122 88 74
'DYSF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.219 (Fisher's exact test), Q value = 0.6

Table S426.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
DYSF MUTATED 5 9 6
DYSF WILD-TYPE 185 131 170
'DYSF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.67

Table S427.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
DYSF MUTATED 3 8 8
DYSF WILD-TYPE 137 177 129
'DYSF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.5

Table S428.  Gene #43: 'DYSF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
DYSF MUTATED 4 3 12
DYSF WILD-TYPE 167 96 180
'ZNF233 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 0.93

Table S429.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
ZNF233 MUTATED 2 2 3 0
ZNF233 WILD-TYPE 197 119 136 46
'ZNF233 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.73

Table S430.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
ZNF233 MUTATED 3 0 2 3 1 0 0
ZNF233 WILD-TYPE 83 82 100 85 72 75 5
'ZNF233 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.67

Table S431.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
ZNF233 MUTATED 0 0 2 1 2
ZNF233 WILD-TYPE 51 30 31 26 67
'ZNF233 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.67

Table S432.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ZNF233 MUTATED 1 4 0
ZNF233 WILD-TYPE 77 81 47
'ZNF233 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.69

Table S433.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
ZNF233 MUTATED 3 0 3 3
ZNF233 WILD-TYPE 130 110 160 94
'ZNF233 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S434.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
ZNF233 MUTATED 3 2 3 1
ZNF233 WILD-TYPE 173 95 165 61
'ZNF233 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.55

Table S435.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
ZNF233 MUTATED 2 1 5 0 1
ZNF233 WILD-TYPE 75 134 123 89 76
'ZNF233 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.9

Table S436.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
ZNF233 MUTATED 5 2 2
ZNF233 WILD-TYPE 185 138 174
'ZNF233 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.54

Table S437.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
ZNF233 MUTATED 4 1 4
ZNF233 WILD-TYPE 136 184 133
'ZNF233 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.285 (Fisher's exact test), Q value = 0.67

Table S438.  Gene #44: 'ZNF233 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
ZNF233 MUTATED 5 0 4
ZNF233 WILD-TYPE 166 99 188
'KIAA1267 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00738 (Fisher's exact test), Q value = 0.092

Table S439.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
KIAA1267 MUTATED 0 3 6 2
KIAA1267 WILD-TYPE 199 118 133 44

Figure S105.  Get High-res Image Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KIAA1267 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 0.91

Table S440.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
KIAA1267 MUTATED 1 1 5 2 1 1 0
KIAA1267 WILD-TYPE 85 81 97 86 72 74 5
'KIAA1267 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0856 (Fisher's exact test), Q value = 0.33

Table S441.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
KIAA1267 MUTATED 3 0 0 0 0
KIAA1267 WILD-TYPE 48 30 33 27 69
'KIAA1267 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0621 (Fisher's exact test), Q value = 0.3

Table S442.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
KIAA1267 MUTATED 3 0 0
KIAA1267 WILD-TYPE 75 85 47
'KIAA1267 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.975 (Fisher's exact test), Q value = 1

Table S443.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
KIAA1267 MUTATED 3 3 3 2
KIAA1267 WILD-TYPE 130 107 160 95
'KIAA1267 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S444.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
KIAA1267 MUTATED 4 2 4 1
KIAA1267 WILD-TYPE 172 95 164 61
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.73

Table S445.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
KIAA1267 MUTATED 0 5 2 3 1
KIAA1267 WILD-TYPE 77 130 126 86 76
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S446.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
KIAA1267 MUTATED 5 3 3
KIAA1267 WILD-TYPE 185 137 173
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.79

Table S447.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
KIAA1267 MUTATED 3 3 5
KIAA1267 WILD-TYPE 137 182 132
'KIAA1267 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.677 (Fisher's exact test), Q value = 0.91

Table S448.  Gene #45: 'KIAA1267 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
KIAA1267 MUTATED 5 1 5
KIAA1267 WILD-TYPE 166 98 187
'ASXL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.623 (Fisher's exact test), Q value = 0.9

Table S449.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
ASXL1 MUTATED 6 4 6 0
ASXL1 WILD-TYPE 193 117 133 46
'ASXL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.985 (Fisher's exact test), Q value = 1

Table S450.  Gene #46: '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 86 82 102 88 73 75 5
ASXL1 MUTATED 3 2 3 4 2 2 0
ASXL1 WILD-TYPE 83 80 99 84 71 73 5
'ASXL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.59

Table S451.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
ASXL1 MUTATED 1 2 0 2 1
ASXL1 WILD-TYPE 50 28 33 25 68
'ASXL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.873 (Fisher's exact test), Q value = 0.99

Table S452.  Gene #46: '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 = 0.0764 (Fisher's exact test), Q value = 0.33

Table S453.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
ASXL1 MUTATED 7 5 4 0
ASXL1 WILD-TYPE 126 105 159 97
'ASXL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0177 (Fisher's exact test), Q value = 0.15

Table S454.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
ASXL1 MUTATED 1 4 10 1
ASXL1 WILD-TYPE 175 93 158 61

Figure S106.  Get High-res Image Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0665 (Fisher's exact test), Q value = 0.3

Table S455.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
ASXL1 MUTATED 4 4 2 6 0
ASXL1 WILD-TYPE 73 131 126 83 77
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0656 (Fisher's exact test), Q value = 0.3

Table S456.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
ASXL1 MUTATED 2 7 7
ASXL1 WILD-TYPE 188 133 169
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 0.86

Table S457.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
ASXL1 MUTATED 3 7 6
ASXL1 WILD-TYPE 137 178 131
'ASXL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0776 (Fisher's exact test), Q value = 0.33

Table S458.  Gene #46: 'ASXL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
ASXL1 MUTATED 2 4 10
ASXL1 WILD-TYPE 169 95 182
'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 0.63

Table S459.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
SMAD4 MUTATED 7 4 1 0
SMAD4 WILD-TYPE 192 117 138 46
'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.69

Table S460.  Gene #47: '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 86 82 102 88 73 75 5
SMAD4 MUTATED 1 1 4 2 2 2 1
SMAD4 WILD-TYPE 85 81 98 86 71 73 4
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.41

Table S461.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
SMAD4 MUTATED 3 1 2 0 0
SMAD4 WILD-TYPE 48 29 31 27 69
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.874 (Fisher's exact test), Q value = 0.99

Table S462.  Gene #47: '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 = 0.34 (Fisher's exact test), Q value = 0.69

Table S463.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
SMAD4 MUTATED 2 3 3 5
SMAD4 WILD-TYPE 131 107 160 92
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.568 (Fisher's exact test), Q value = 0.86

Table S464.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
SMAD4 MUTATED 7 1 4 1
SMAD4 WILD-TYPE 169 96 164 61
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.55

Table S465.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
SMAD4 MUTATED 1 1 3 4 4
SMAD4 WILD-TYPE 76 134 125 85 73
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.8

Table S466.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
SMAD4 MUTATED 7 3 3
SMAD4 WILD-TYPE 183 137 173
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.81

Table S467.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
SMAD4 MUTATED 5 3 3
SMAD4 WILD-TYPE 135 182 134
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S468.  Gene #47: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
SMAD4 MUTATED 5 4 2
SMAD4 WILD-TYPE 166 95 190
'GAGE2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00862 (Fisher's exact test), Q value = 0.099

Table S469.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
GAGE2A MUTATED 0 4 0 0
GAGE2A WILD-TYPE 199 117 139 46

Figure S107.  Get High-res Image Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'GAGE2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0948 (Fisher's exact test), Q value = 0.35

Table S470.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
GAGE2A MUTATED 0 1 0 3 0 0 0
GAGE2A WILD-TYPE 86 81 102 85 73 75 5
'GAGE2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.79

Table S471.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
GAGE2A MUTATED 0 0 1 1 1
GAGE2A WILD-TYPE 51 30 32 26 68
'GAGE2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.794 (Fisher's exact test), Q value = 0.97

Table S472.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
GAGE2A MUTATED 1 2 0
GAGE2A WILD-TYPE 77 83 47
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 0.98

Table S473.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
GAGE2A MUTATED 1 0 2 1
GAGE2A WILD-TYPE 132 110 161 96
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.8

Table S474.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
GAGE2A MUTATED 1 2 1 0
GAGE2A WILD-TYPE 175 95 167 62
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.53

Table S475.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
GAGE2A MUTATED 0 0 3 1 0
GAGE2A WILD-TYPE 77 135 125 88 77
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.685 (Fisher's exact test), Q value = 0.91

Table S476.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
GAGE2A MUTATED 1 2 1
GAGE2A WILD-TYPE 189 138 175
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S477.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
GAGE2A MUTATED 1 2 1
GAGE2A WILD-TYPE 139 183 136
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S478.  Gene #48: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
GAGE2A MUTATED 1 1 2
GAGE2A WILD-TYPE 170 98 190
'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 0.98

Table S479.  Gene #49: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
EMG1 MUTATED 2 0 1 0
EMG1 WILD-TYPE 197 121 138 46
'EMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 0.99

Table S480.  Gene #49: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
EMG1 MUTATED 1 0 1 0 0 1 0
EMG1 WILD-TYPE 85 82 101 88 73 74 5
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.6

Table S481.  Gene #49: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
EMG1 MUTATED 1 2 0 0
EMG1 WILD-TYPE 132 108 163 97
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 0.94

Table S482.  Gene #49: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
EMG1 MUTATED 1 0 2 0
EMG1 WILD-TYPE 175 97 166 62
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.529 (Fisher's exact test), Q value = 0.83

Table S483.  Gene #49: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
EMG1 MUTATED 0 2 0 1 0
EMG1 WILD-TYPE 77 133 128 88 77
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S484.  Gene #49: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
EMG1 MUTATED 1 1 1
EMG1 WILD-TYPE 189 139 175
'PIK3R1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.87 (Fisher's exact test), Q value = 0.99

Table S485.  Gene #50: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
PIK3R1 MUTATED 3 3 2 0
PIK3R1 WILD-TYPE 196 118 137 46
'PIK3R1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.69

Table S486.  Gene #50: '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 86 82 102 88 73 75 5
PIK3R1 MUTATED 1 2 2 0 3 0 0
PIK3R1 WILD-TYPE 85 80 100 88 70 75 5
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0709 (Fisher's exact test), Q value = 0.31

Table S487.  Gene #50: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
PIK3R1 MUTATED 0 1 6 1
PIK3R1 WILD-TYPE 133 109 157 96
'PIK3R1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.4

Table S488.  Gene #50: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
PIK3R1 MUTATED 1 2 2 3
PIK3R1 WILD-TYPE 175 95 166 59
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.73

Table S489.  Gene #50: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
PIK3R1 MUTATED 0 2 4 2 0
PIK3R1 WILD-TYPE 77 133 124 87 77
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 0.67

Table S490.  Gene #50: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
PIK3R1 MUTATED 1 3 4
PIK3R1 WILD-TYPE 189 137 172
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S491.  Gene #50: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
PIK3R1 MUTATED 2 3 2
PIK3R1 WILD-TYPE 138 182 135
'PIK3R1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 0.69

Table S492.  Gene #50: 'PIK3R1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
PIK3R1 MUTATED 1 1 5
PIK3R1 WILD-TYPE 170 98 187
'KRTAP5-7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.835 (Fisher's exact test), Q value = 0.98

Table S493.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
KRTAP5-7 MUTATED 2 2 1 0
KRTAP5-7 WILD-TYPE 197 119 138 46
'KRTAP5-7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S494.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
KRTAP5-7 MUTATED 1 1 1 0 1 1 0
KRTAP5-7 WILD-TYPE 85 81 101 88 72 74 5
'KRTAP5-7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.91

Table S495.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
KRTAP5-7 MUTATED 1 2 2 0
KRTAP5-7 WILD-TYPE 132 108 161 97
'KRTAP5-7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.62

Table S496.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
KRTAP5-7 MUTATED 0 1 3 1
KRTAP5-7 WILD-TYPE 176 96 165 61
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 0.91

Table S497.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
KRTAP5-7 MUTATED 0 2 1 2 0
KRTAP5-7 WILD-TYPE 77 133 127 87 77
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.023 (Fisher's exact test), Q value = 0.17

Table S498.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
KRTAP5-7 MUTATED 0 4 1
KRTAP5-7 WILD-TYPE 190 136 175

Figure S108.  Get High-res Image Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 0.92

Table S499.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
KRTAP5-7 MUTATED 1 1 2
KRTAP5-7 WILD-TYPE 139 184 135
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.547 (Fisher's exact test), Q value = 0.84

Table S500.  Gene #51: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
KRTAP5-7 MUTATED 1 0 3
KRTAP5-7 WILD-TYPE 170 99 189
'SLC9A6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.44

Table S501.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
SLC9A6 MUTATED 4 0 0 1
SLC9A6 WILD-TYPE 195 121 139 45
'SLC9A6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0818 (Fisher's exact test), Q value = 0.33

Table S502.  Gene #52: '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 86 82 102 88 73 75 5
SLC9A6 MUTATED 0 0 2 0 0 3 0
SLC9A6 WILD-TYPE 86 82 100 88 73 72 5
'SLC9A6 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S503.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
SLC9A6 MUTATED 1 0 0 0 2
SLC9A6 WILD-TYPE 50 30 33 27 67
'SLC9A6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.4

Table S504.  Gene #52: '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 = 0.0264 (Fisher's exact test), Q value = 0.18

Table S505.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
SLC9A6 MUTATED 0 3 0 2
SLC9A6 WILD-TYPE 133 107 163 95

Figure S109.  Get High-res Image Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SLC9A6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.365 (Fisher's exact test), Q value = 0.71

Table S506.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
SLC9A6 MUTATED 4 0 1 0
SLC9A6 WILD-TYPE 172 97 167 62
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.75

Table S507.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
SLC9A6 MUTATED 1 1 0 2 1
SLC9A6 WILD-TYPE 76 134 128 87 76
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.61

Table S508.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
SLC9A6 MUTATED 4 0 1
SLC9A6 WILD-TYPE 186 140 175
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.83

Table S509.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
SLC9A6 MUTATED 3 1 1
SLC9A6 WILD-TYPE 137 184 136
'SLC9A6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0757 (Fisher's exact test), Q value = 0.33

Table S510.  Gene #52: 'SLC9A6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
SLC9A6 MUTATED 4 1 0
SLC9A6 WILD-TYPE 167 98 192
'ELF4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 0.95

Table S511.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
ELF4 MUTATED 2 2 2 1
ELF4 WILD-TYPE 197 119 137 45
'ELF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 0.97

Table S512.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
ELF4 MUTATED 1 1 2 0 2 1 0
ELF4 WILD-TYPE 85 81 100 88 71 74 5
'ELF4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.67

Table S513.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
ELF4 MUTATED 2 0 1 0 0
ELF4 WILD-TYPE 49 30 32 27 69
'ELF4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.336 (Fisher's exact test), Q value = 0.69

Table S514.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ELF4 MUTATED 2 0 1
ELF4 WILD-TYPE 76 85 46
'ELF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 0.99

Table S515.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
ELF4 MUTATED 1 2 3 1
ELF4 WILD-TYPE 132 108 160 96
'ELF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.86 (Fisher's exact test), Q value = 0.99

Table S516.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
ELF4 MUTATED 2 2 2 1
ELF4 WILD-TYPE 174 95 166 61
'ELF4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.46

Table S517.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
ELF4 MUTATED 1 0 1 3 2
ELF4 WILD-TYPE 76 135 127 86 75
'ELF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.802 (Fisher's exact test), Q value = 0.97

Table S518.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
ELF4 MUTATED 3 1 3
ELF4 WILD-TYPE 187 139 173
'ELF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.73

Table S519.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
ELF4 MUTATED 3 1 3
ELF4 WILD-TYPE 137 184 134
'ELF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S520.  Gene #53: 'ELF4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
ELF4 MUTATED 4 1 2
ELF4 WILD-TYPE 167 98 190
'CTCF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0122 (Fisher's exact test), Q value = 0.12

Table S521.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
CTCF MUTATED 4 1 10 0
CTCF WILD-TYPE 195 120 129 46

Figure S110.  Get High-res Image Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTCF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00769 (Fisher's exact test), Q value = 0.093

Table S522.  Gene #54: '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 86 82 102 88 73 75 5
CTCF MUTATED 1 3 9 0 0 2 0
CTCF WILD-TYPE 85 79 93 88 73 73 5

Figure S111.  Get High-res Image Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTCF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S523.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
CTCF MUTATED 2 1 1 0 4
CTCF WILD-TYPE 49 29 32 27 65
'CTCF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.526 (Fisher's exact test), Q value = 0.83

Table S524.  Gene #54: '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 = 0.607 (Fisher's exact test), Q value = 0.89

Table S525.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
CTCF MUTATED 4 5 3 2
CTCF WILD-TYPE 129 105 160 95
'CTCF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 0.74

Table S526.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
CTCF MUTATED 4 3 7 0
CTCF WILD-TYPE 172 94 161 62
'CTCF MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.92

Table S527.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
CTCF MUTATED 1 6 4 3 1
CTCF WILD-TYPE 76 129 124 86 76
'CTCF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.717 (Fisher's exact test), Q value = 0.93

Table S528.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
CTCF MUTATED 7 4 4
CTCF WILD-TYPE 183 136 172
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S529.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
CTCF MUTATED 4 5 4
CTCF WILD-TYPE 136 180 133
'CTCF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 0.93

Table S530.  Gene #54: 'CTCF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
CTCF MUTATED 6 3 4
CTCF WILD-TYPE 165 96 188
'HNRNPL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.78

Table S531.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
HNRNPL MUTATED 5 1 3 2
HNRNPL WILD-TYPE 194 120 136 44
'HNRNPL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.66

Table S532.  Gene #55: '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 86 82 102 88 73 75 5
HNRNPL MUTATED 3 3 4 1 0 0 0
HNRNPL WILD-TYPE 83 79 98 87 73 75 5
'HNRNPL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.72

Table S533.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
HNRNPL MUTATED 1 0 1 2 1
HNRNPL WILD-TYPE 50 30 32 25 68
'HNRNPL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.78

Table S534.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
HNRNPL MUTATED 2 1 2
HNRNPL WILD-TYPE 76 84 45
'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 0.91

Table S535.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
HNRNPL MUTATED 3 4 3 1
HNRNPL WILD-TYPE 130 106 160 96
'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.69

Table S536.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
HNRNPL MUTATED 6 3 2 0
HNRNPL WILD-TYPE 170 94 166 62
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.48

Table S537.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
HNRNPL MUTATED 3 4 0 3 1
HNRNPL WILD-TYPE 74 131 128 86 76
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.14

Table S538.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
HNRNPL MUTATED 5 6 0
HNRNPL WILD-TYPE 185 134 176

Figure S112.  Get High-res Image Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.67

Table S539.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
HNRNPL MUTATED 5 2 3
HNRNPL WILD-TYPE 135 183 134
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.655 (Fisher's exact test), Q value = 0.9

Table S540.  Gene #55: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
HNRNPL MUTATED 4 3 3
HNRNPL WILD-TYPE 167 96 189
'ZFP36L2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S541.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
ZFP36L2 MUTATED 5 2 0 1
ZFP36L2 WILD-TYPE 194 119 139 45
'ZFP36L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.26

Table S542.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
ZFP36L2 MUTATED 0 2 1 3 0 1 1
ZFP36L2 WILD-TYPE 86 80 101 85 73 74 4

Figure S113.  Get High-res Image Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ZFP36L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 0.93

Table S543.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
ZFP36L2 MUTATED 1 1 0 1 1
ZFP36L2 WILD-TYPE 50 29 33 26 68
'ZFP36L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.71

Table S544.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
ZFP36L2 MUTATED 3 1 0
ZFP36L2 WILD-TYPE 75 84 47
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 0.99

Table S545.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
ZFP36L2 MUTATED 3 1 3 1
ZFP36L2 WILD-TYPE 130 109 160 96
'ZFP36L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.8

Table S546.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
ZFP36L2 MUTATED 2 3 3 0
ZFP36L2 WILD-TYPE 174 94 165 62
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.416 (Fisher's exact test), Q value = 0.75

Table S547.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
ZFP36L2 MUTATED 2 2 1 3 0
ZFP36L2 WILD-TYPE 75 133 127 86 77
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.678 (Fisher's exact test), Q value = 0.91

Table S548.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
ZFP36L2 MUTATED 2 2 4
ZFP36L2 WILD-TYPE 188 138 172
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S549.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
ZFP36L2 MUTATED 2 2 2
ZFP36L2 WILD-TYPE 138 183 135
'ZFP36L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.758 (Fisher's exact test), Q value = 0.94

Table S550.  Gene #56: 'ZFP36L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
ZFP36L2 MUTATED 2 2 2
ZFP36L2 WILD-TYPE 169 97 190
'MYH9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.63

Table S551.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
MYH9 MUTATED 8 2 9 2
MYH9 WILD-TYPE 191 119 130 44
'MYH9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.71

Table S552.  Gene #57: '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 86 82 102 88 73 75 5
MYH9 MUTATED 4 2 8 2 4 1 0
MYH9 WILD-TYPE 82 80 94 86 69 74 5
'MYH9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0665 (Fisher's exact test), Q value = 0.3

Table S553.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
MYH9 MUTATED 3 3 2 1 0
MYH9 WILD-TYPE 48 27 31 26 69
'MYH9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 0.94

Table S554.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
MYH9 MUTATED 3 3 3
MYH9 WILD-TYPE 75 82 44
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S555.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
MYH9 MUTATED 6 4 6 5
MYH9 WILD-TYPE 127 106 157 92
'MYH9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.742 (Fisher's exact test), Q value = 0.94

Table S556.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
MYH9 MUTATED 10 3 6 2
MYH9 WILD-TYPE 166 94 162 60
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 0.98

Table S557.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
MYH9 MUTATED 2 7 4 5 3
MYH9 WILD-TYPE 75 128 124 84 74
'MYH9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.74

Table S558.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
MYH9 MUTATED 11 4 6
MYH9 WILD-TYPE 179 136 170
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 0.86

Table S559.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
MYH9 MUTATED 5 10 4
MYH9 WILD-TYPE 135 175 133
'MYH9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 0.94

Table S560.  Gene #57: 'MYH9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
MYH9 MUTATED 6 5 8
MYH9 WILD-TYPE 165 94 184
'NOTCH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.924 (Fisher's exact test), Q value = 1

Table S561.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
NOTCH2 MUTATED 9 4 6 1
NOTCH2 WILD-TYPE 190 117 133 45
'NOTCH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.983 (Fisher's exact test), Q value = 1

Table S562.  Gene #58: '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 86 82 102 88 73 75 5
NOTCH2 MUTATED 4 3 4 4 2 4 0
NOTCH2 WILD-TYPE 82 79 98 84 71 71 5
'NOTCH2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.024 (Fisher's exact test), Q value = 0.17

Table S563.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
NOTCH2 MUTATED 3 3 0 4 1
NOTCH2 WILD-TYPE 48 27 33 23 68

Figure S114.  Get High-res Image Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NOTCH2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 0.8

Table S564.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
NOTCH2 MUTATED 6 3 2
NOTCH2 WILD-TYPE 72 82 45
'NOTCH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.243 (Fisher's exact test), Q value = 0.62

Table S565.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
NOTCH2 MUTATED 8 6 3 4
NOTCH2 WILD-TYPE 125 104 160 93
'NOTCH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 0.77

Table S566.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
NOTCH2 MUTATED 11 3 6 1
NOTCH2 WILD-TYPE 165 94 162 61
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.86

Table S567.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
NOTCH2 MUTATED 2 9 4 4 2
NOTCH2 WILD-TYPE 75 126 124 85 75
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.91

Table S568.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
NOTCH2 MUTATED 10 5 6
NOTCH2 WILD-TYPE 180 135 170
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 0.94

Table S569.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
NOTCH2 MUTATED 7 6 5
NOTCH2 WILD-TYPE 133 179 132
'NOTCH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.73

Table S570.  Gene #58: 'NOTCH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
NOTCH2 MUTATED 9 4 5
NOTCH2 WILD-TYPE 162 95 187
'NCOR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 0.99

Table S571.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
NCOR1 MUTATED 6 3 6 1
NCOR1 WILD-TYPE 193 118 133 45
'NCOR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.75

Table S572.  Gene #59: '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 86 82 102 88 73 75 5
NCOR1 MUTATED 2 3 6 4 2 0 0
NCOR1 WILD-TYPE 84 79 96 84 71 75 5
'NCOR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.476 (Fisher's exact test), Q value = 0.79

Table S573.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
NCOR1 MUTATED 1 1 1 3 4
NCOR1 WILD-TYPE 50 29 32 24 65
'NCOR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.8

Table S574.  Gene #59: '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 = 0.818 (Fisher's exact test), Q value = 0.98

Table S575.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
NCOR1 MUTATED 6 4 5 2
NCOR1 WILD-TYPE 127 106 158 95
'NCOR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 0.63

Table S576.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
NCOR1 MUTATED 3 5 8 1
NCOR1 WILD-TYPE 173 92 160 61
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 0.98

Table S577.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
NCOR1 MUTATED 4 4 3 3 3
NCOR1 WILD-TYPE 73 131 125 86 74
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.6

Table S578.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
NCOR1 MUTATED 5 8 4
NCOR1 WILD-TYPE 185 132 172
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 0.99

Table S579.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
NCOR1 MUTATED 6 7 4
NCOR1 WILD-TYPE 134 178 133
'NCOR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.813 (Fisher's exact test), Q value = 0.98

Table S580.  Gene #59: 'NCOR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
NCOR1 MUTATED 5 4 8
NCOR1 WILD-TYPE 166 95 184
'AK5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.754 (Fisher's exact test), Q value = 0.94

Table S581.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
AK5 MUTATED 5 3 5 0
AK5 WILD-TYPE 194 118 134 46
'AK5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.66

Table S582.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
AK5 MUTATED 1 3 5 0 1 3 0
AK5 WILD-TYPE 85 79 97 88 72 72 5
'AK5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 0.75

Table S583.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
AK5 MUTATED 0 1 0 0 3
AK5 WILD-TYPE 51 29 33 27 66
'AK5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.545 (Fisher's exact test), Q value = 0.84

Table S584.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
AK5 MUTATED 1 3 0
AK5 WILD-TYPE 77 82 47
'AK5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.847 (Fisher's exact test), Q value = 0.98

Table S585.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
AK5 MUTATED 4 2 3 3
AK5 WILD-TYPE 129 108 160 94
'AK5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.575 (Fisher's exact test), Q value = 0.86

Table S586.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
AK5 MUTATED 4 2 6 0
AK5 WILD-TYPE 172 95 162 62
'AK5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.27

Table S587.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
AK5 MUTATED 3 5 0 1 4
AK5 WILD-TYPE 74 130 128 88 73

Figure S115.  Get High-res Image Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AK5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.33

Table S588.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
AK5 MUTATED 7 5 1
AK5 WILD-TYPE 183 135 175
'AK5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 0.53

Table S589.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
AK5 MUTATED 6 6 1
AK5 WILD-TYPE 134 179 136
'AK5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0824 (Fisher's exact test), Q value = 0.33

Table S590.  Gene #60: 'AK5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
AK5 MUTATED 6 5 2
AK5 WILD-TYPE 165 94 190
'SPTY2D1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.39

Table S591.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
SPTY2D1 MUTATED 3 3 1 3
SPTY2D1 WILD-TYPE 196 118 138 43
'SPTY2D1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.44

Table S592.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
SPTY2D1 MUTATED 0 1 2 3 2 1 1
SPTY2D1 WILD-TYPE 86 81 100 85 71 74 4
'SPTY2D1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.065 (Fisher's exact test), Q value = 0.3

Table S593.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
SPTY2D1 MUTATED 0 3 0 0 2
SPTY2D1 WILD-TYPE 51 27 33 27 67
'SPTY2D1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.67

Table S594.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
SPTY2D1 MUTATED 1 4 0
SPTY2D1 WILD-TYPE 77 81 47
'SPTY2D1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.69

Table S595.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
SPTY2D1 MUTATED 4 0 4 2
SPTY2D1 WILD-TYPE 129 110 159 95
'SPTY2D1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 0.99

Table S596.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
SPTY2D1 MUTATED 3 2 3 2
SPTY2D1 WILD-TYPE 173 95 165 60
'SPTY2D1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.69

Table S597.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
SPTY2D1 MUTATED 1 2 5 0 2
SPTY2D1 WILD-TYPE 76 133 123 89 75
'SPTY2D1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.31 (Fisher's exact test), Q value = 0.67

Table S598.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
SPTY2D1 MUTATED 3 5 2
SPTY2D1 WILD-TYPE 187 135 174
'SPTY2D1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.81

Table S599.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
SPTY2D1 MUTATED 1 3 3
SPTY2D1 WILD-TYPE 139 182 134
'SPTY2D1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.84

Table S600.  Gene #61: 'SPTY2D1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
SPTY2D1 MUTATED 1 2 4
SPTY2D1 WILD-TYPE 170 97 188
'PIWIL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.731 (Fisher's exact test), Q value = 0.93

Table S601.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 199 121 139 46
PIWIL2 MUTATED 2 2 3 0
PIWIL2 WILD-TYPE 197 119 136 46
'PIWIL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.41

Table S602.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 86 82 102 88 73 75 5
PIWIL2 MUTATED 4 0 3 1 0 0 0
PIWIL2 WILD-TYPE 82 82 99 87 73 75 5
'PIWIL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 0.98

Table S603.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 51 30 33 27 69
PIWIL2 MUTATED 1 0 1 1 1
PIWIL2 WILD-TYPE 50 30 32 26 68
'PIWIL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 0.91

Table S604.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 78 85 47
PIWIL2 MUTATED 2 2 0
PIWIL2 WILD-TYPE 76 83 47
'PIWIL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.55

Table S605.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 133 110 163 97
PIWIL2 MUTATED 2 1 1 4
PIWIL2 WILD-TYPE 131 109 162 93
'PIWIL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 0.84

Table S606.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 176 97 168 62
PIWIL2 MUTATED 5 1 2 0
PIWIL2 WILD-TYPE 171 96 166 62
'PIWIL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.45

Table S607.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 77 135 128 89 77
PIWIL2 MUTATED 0 2 1 1 4
PIWIL2 WILD-TYPE 77 133 127 88 73
'PIWIL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0685 (Fisher's exact test), Q value = 0.31

Table S608.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 190 140 176
PIWIL2 MUTATED 5 3 0
PIWIL2 WILD-TYPE 185 137 176
'PIWIL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.76

Table S609.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 140 185 137
PIWIL2 MUTATED 4 2 1
PIWIL2 WILD-TYPE 136 183 136
'PIWIL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.5

Table S610.  Gene #62: 'PIWIL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 171 99 192
PIWIL2 MUTATED 5 1 1
PIWIL2 WILD-TYPE 166 98 191
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/22815321/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/22541004/HNSC-TP.transferedmergedcluster.txt

  • Number of patients = 511

  • Number of significantly mutated genes = 62

  • 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.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

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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