Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 60 genes and 10 molecular subtypes across 185 patients, 38 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • CDKN2A mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • NFE2L2 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ZNF750 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • ARID1A mutation correlated to 'RPPA_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ERBB2 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ASTE1 mutation correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ANAPC1 mutation correlated to 'CN_CNMF'.

  • IVL mutation correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RB1 mutation correlated to 'CN_CNMF'.

  • NOTCH1 mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • RAD17 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • TCHH mutation correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 60 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, 38 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
NFE2L2 16 (9%) 169 2e-05
(0.0024) 		1e-05
(0.002) 		0.0944
(0.587) 		0.341
(0.819) 		1e-05
(0.002) 		0.0019
(0.06) 		0.00305
(0.0832) 		0.001
(0.0408) 		2e-05
(0.0024) 		0.00184
(0.06)
IVL 15 (8%) 170 0.00579
(0.124) 		0.0245
(0.319) 		0.157
(0.661) 		0.00388
(0.0956) 		0.00351
(0.0916) 		0.00019
(0.0127) 		0.0395
(0.388) 		0.00076
(0.0351) 		0.00819
(0.149) 		0.00035
(0.0191)
ERBB2 11 (6%) 174 0.0427
(0.388) 		0.0105
(0.18) 		0.0232
(0.316) 		0.00032
(0.0191) 		0.0282
(0.348) 		0.00142
(0.0532) 		0.00403
(0.0956) 		0.00048
(0.024)
TP53 153 (83%) 32 1e-05
(0.002) 		5e-05
(0.00429) 		0.141
(0.661) 		0.134
(0.651) 		0.0303
(0.357) 		0.00761
(0.145) 		0.4
(0.838) 		0.0266
(0.34) 		0.00287
(0.082) 		0.0324
(0.367)
ARID1A 15 (8%) 170 0.0374
(0.387) 		0.218
(0.736) 		0.0043
(0.0956) 		0.0355
(0.378) 		0.0781
(0.551) 		0.00772
(0.145) 		0.119
(0.625) 		0.0359
(0.378) 		0.146
(0.661) 		0.0117
(0.195)
ASTE1 5 (3%) 180 0.0828
(0.569) 		0.0605
(0.469) 		0.753
(0.99) 		0.36
(0.834) 		0.436
(0.857) 		0.0148
(0.233) 		0.609
(0.963) 		0.00161
(0.0568) 		0.0828
(0.569) 		0.00102
(0.0408)
NOTCH1 18 (10%) 167 0.0576
(0.462) 		0.00426
(0.0956) 		0.157
(0.661) 		0.092
(0.583) 		0.059
(0.466) 		0.0889
(0.573) 		0.0179
(0.276) 		0.00931
(0.164) 		0.0549
(0.457) 		0.062
(0.471)
CDKN2A 19 (10%) 166 0.224
(0.744) 		0.626
(0.963) 		0.921
(1.00) 		0.621
(0.963) 		0.14
(0.661) 		0.00616
(0.124) 		0.362
(0.834) 		0.105
(0.618) 		0.672
(0.964) 		0.0411
(0.388)
ZNF750 10 (5%) 175 0.0834
(0.569) 		0.204
(0.713) 		0.331
(0.816) 		0.459
(0.872) 		0.176
(0.69) 		0.0199
(0.284) 		0.0188
(0.283) 		4e-05
(0.004) 		0.0655
(0.489) 		0.0292
(0.35)
ANAPC1 5 (3%) 180 0.00016
(0.012) 		0.311
(0.808) 		0.676
(0.964) 		0.456
(0.872) 		0.763
(0.99) 		0.804
(0.994) 		0.892
(1.00) 		0.176
(0.69) 		0.879
(1.00) 		0.647
(0.963)
RB1 7 (4%) 178 0.00242
(0.0726) 		0.974
(1.00) 		0.39
(0.838) 		0.408
(0.838) 		0.788
(0.994) 		0.867
(1.00) 		0.673
(0.964) 		0.9
(1.00) 		0.453
(0.872) 		1
(1.00)
RAD17 4 (2%) 181 1
(1.00) 		0.231
(0.746) 		0.382
(0.838) 		0.634
(0.963) 		0.633
(0.963) 		0.774
(0.993) 		0.259
(0.781) 		0.00618
(0.124) 		0.178
(0.69) 		0.383
(0.838)
TCHH 14 (8%) 171 0.441
(0.864) 		0.0146
(0.233) 		0.532
(0.927) 		0.773
(0.993) 		0.309
(0.808) 		0.554
(0.936) 		0.619
(0.963) 		0.318
(0.812) 		0.895
(1.00) 		0.626
(0.963)
SMAD4 13 (7%) 172 0.0284
(0.348) 		0.35
(0.824) 		0.273
(0.787) 		0.115
(0.625) 		0.533
(0.927) 		0.0659
(0.489) 		0.555
(0.936) 		0.16
(0.662) 		0.572
(0.949) 		0.114
(0.625)
MLL2 32 (17%) 153 0.666
(0.964) 		0.289
(0.808) 		0.0409
(0.388) 		0.397
(0.838) 		0.495
(0.898) 		0.158
(0.661) 		0.101
(0.615) 		0.13
(0.651) 		0.061
(0.469) 		0.26
(0.781)
TGFBR2 15 (8%) 170 0.0231
(0.316) 		0.258
(0.781) 		0.743
(0.99) 		0.263
(0.786) 		0.784
(0.994) 		0.533
(0.927) 		0.797
(0.994) 		0.926
(1.00) 		1
(1.00) 		1
(1.00)
FBXW7 13 (7%) 172 0.187
(0.705) 		0.434
(0.856) 		0.655
(0.963) 		0.596
(0.963) 		0.119
(0.625) 		0.119
(0.625) 		0.315
(0.81) 		0.276
(0.787) 		0.325
(0.812) 		0.224
(0.744)
PKD2 7 (4%) 178 0.396
(0.838) 		0.136
(0.651) 		0.781
(0.994) 		0.0404
(0.388) 		0.332
(0.817) 		0.634
(0.963) 		0.233
(0.747) 		0.131
(0.651) 		0.12
(0.625) 		0.168
(0.684)
PTCH1 12 (6%) 173 0.0413
(0.388) 		0.252
(0.777) 		0.404
(0.838) 		0.958
(1.00) 		0.0875
(0.571) 		0.341
(0.819) 		0.378
(0.838) 		0.322
(0.812) 		0.204
(0.713) 		0.392
(0.838)
KIAA2018 13 (7%) 172 0.236
(0.749) 		0.598
(0.963) 		0.226
(0.744) 		0.198
(0.713) 		0.554
(0.936) 		0.227
(0.744) 		0.388
(0.838) 		0.221
(0.74) 		0.639
(0.963) 		0.128
(0.646)
FAM108A1 4 (2%) 181 0.829
(0.995) 		0.59
(0.957) 		0.203
(0.713) 		0.541
(0.934) 		0.634
(0.963) 		0.566
(0.946) 		0.268
(0.787) 		0.748
(0.99) 		0.758
(0.99) 		0.818
(0.994)
PAXIP1 10 (5%) 175 0.688
(0.967) 		0.942
(1.00) 		0.55
(0.936) 		0.865
(1.00) 		0.288
(0.808) 		0.895
(1.00) 		0.147
(0.661) 		0.0578
(0.462) 		0.297
(0.808) 		1
(1.00)
MGC29506 4 (2%) 181 0.301
(0.808) 		1
(1.00) 		0.323
(0.812) 		1
(1.00) 		0.411
(0.839) 		0.216
(0.731) 		0.762
(0.99) 		0.647
(0.963)
C10ORF76 6 (3%) 179 0.0324
(0.367) 		0.777
(0.994) 		0.555
(0.936) 		0.469
(0.882) 		0.483
(0.889) 		1
(1.00) 		0.811
(0.994) 		0.344
(0.822) 		0.256
(0.781) 		0.572
(0.949)
IPP 6 (3%) 179 0.869
(1.00) 		0.814
(0.994) 		0.423
(0.851) 		0.494
(0.898) 		0.357
(0.83) 		0.85
(1.00) 		0.116
(0.625) 		0.364
(0.834) 		0.348
(0.824) 		0.243
(0.763)
DNAH10 19 (10%) 166 0.856
(1.00) 		0.425
(0.851) 		0.413
(0.839) 		0.298
(0.808) 		0.376
(0.838) 		0.151
(0.661) 		0.31
(0.808) 		0.599
(0.963) 		0.606
(0.963) 		0.415
(0.839)
RIC3 4 (2%) 181 0.303
(0.808) 		0.326
(0.812) 		1
(1.00) 		0.823
(0.995) 		0.929
(1.00) 		0.434
(0.856) 		1
(1.00) 		0.674
(0.964) 		0.876
(1.00) 		0.485
(0.889)
HMMR 4 (2%) 181 0.105
(0.618) 		0.307
(0.808) 		0.642
(0.963) 		0.519
(0.919) 		0.871
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.878
(1.00) 		0.817
(0.994)
PIAS1 5 (3%) 180 0.336
(0.819) 		0.786
(0.994) 		0.558
(0.937) 		0.138
(0.656) 		0.206
(0.713) 		0.803
(0.994) 		0.509
(0.912) 		0.648
(0.963) 		0.813
(0.994) 		0.704
(0.974)
ITGA6 7 (4%) 178 0.878
(1.00) 		0.371
(0.838) 		0.356
(0.83) 		0.847
(1.00) 		0.527
(0.927) 		1
(1.00) 		0.914
(1.00) 		0.949
(1.00) 		0.929
(1.00) 		1
(1.00)
KPNA1 6 (3%) 179 0.491
(0.898) 		0.727
(0.98) 		0.457
(0.872) 		0.0695
(0.509) 		0.197
(0.713) 		0.847
(1.00) 		0.229
(0.746) 		0.754
(0.99) 		1
(1.00) 		0.306
(0.808)
LIMA1 8 (4%) 177 0.639
(0.963) 		0.676
(0.964) 		0.35
(0.824) 		0.135
(0.651) 		0.425
(0.851) 		0.101
(0.615) 		0.298
(0.808) 		0.127
(0.646) 		0.155
(0.661) 		0.134
(0.651)
FAM65B 8 (4%) 177 1
(1.00) 		0.665
(0.964) 		0.389
(0.838) 		0.286
(0.807) 		0.927
(1.00) 		0.88
(1.00) 		0.176
(0.69) 		0.0425
(0.388) 		0.686
(0.967) 		0.38
(0.838)
CORO7 7 (4%) 178 0.235
(0.749) 		0.377
(0.838) 		0.614
(0.963) 		0.156
(0.661) 		0.497
(0.898) 		0.209
(0.72) 		0.283
(0.8) 		0.0356
(0.378) 		0.0237
(0.316) 		0.159
(0.662)
PIK3CA 19 (10%) 166 0.505
(0.907) 		0.271
(0.787) 		0.252
(0.777) 		0.304
(0.808) 		0.154
(0.661) 		0.481
(0.889) 		0.177
(0.69) 		0.329
(0.816) 		0.105
(0.618) 		0.249
(0.774)
EIF4EBP2 3 (2%) 182 0.044
(0.394) 		0.553
(0.936) 		0.726
(0.98) 		0.0761
(0.544) 		0.69
(0.967) 		0.212
(0.728) 		0.0523
(0.442) 		0.145
(0.661)
SCD 3 (2%) 182 0.582
(0.95) 		0.767
(0.99) 		0.801
(0.994) 		0.696
(0.967) 		0.579
(0.95) 		0.639
(0.963) 		0.686
(0.967) 		0.741
(0.99)
MKL2 6 (3%) 179 0.106
(0.619) 		0.309
(0.808) 		0.499
(0.899) 		0.767
(0.99) 		0.664
(0.964) 		0.154
(0.661) 		0.63
(0.963) 		0.32
(0.812) 		0.404
(0.838) 		0.114
(0.625)
KLF3 3 (2%) 182 0.0423
(0.388) 		0.169
(0.684) 		0.724
(0.98) 		0.124
(0.642) 		0.687
(0.967) 		0.312
(0.808) 		0.454
(0.872) 		0.144
(0.661)
IL10RA 3 (2%) 182 0.789
(0.994) 		1
(1.00) 		0.754
(0.99) 		0.357
(0.83) 		0.511
(0.912) 		0.695
(0.967) 		0.815
(0.994) 		0.875
(1.00) 		0.686
(0.967) 		0.741
(0.99)
KPNB1 6 (3%) 179 0.184
(0.702) 		0.0875
(0.571) 		0.308
(0.808) 		0.657
(0.963) 		0.348
(0.824) 		0.391
(0.838) 		0.181
(0.695) 		0.698
(0.967) 		0.89
(1.00) 		0.574
(0.949)
ZBED4 5 (3%) 180 0.405
(0.838) 		0.64
(0.963) 		0.363
(0.834) 		0.801
(0.994) 		0.0346
(0.378) 		0.668
(0.964) 		0.095
(0.587) 		0.483
(0.889) 		0.888
(1.00) 		0.573
(0.949)
NAA16 6 (3%) 179 0.871
(1.00) 		0.484
(0.889) 		0.643
(0.963) 		0.459
(0.872) 		0.442
(0.865) 		0.231
(0.746) 		0.903
(1.00) 		0.0924
(0.583) 		0.271
(0.787) 		0.382
(0.838)
CNNM2 7 (4%) 178 0.78
(0.994) 		0.812
(0.994) 		0.277
(0.787) 		0.202
(0.713) 		0.885
(1.00) 		0.206
(0.713) 		0.63
(0.963) 		0.582
(0.95) 		0.763
(0.99) 		0.276
(0.787)
HLA-B 7 (4%) 178 0.0196
(0.284) 		0.937
(1.00) 		0.275
(0.787) 		0.322
(0.812) 		0.654
(0.963) 		1
(1.00) 		0.469
(0.882) 		0.244
(0.763) 		0.769
(0.99) 		0.63
(0.963)
PLXNB2 12 (6%) 173 0.531
(0.927) 		0.878
(1.00) 		0.899
(1.00) 		0.656
(0.963) 		0.868
(1.00) 		0.912
(1.00) 		0.879
(1.00) 		0.787
(0.994) 		0.827
(0.995) 		1
(1.00)
PTEN 7 (4%) 178 0.693
(0.967) 		0.602
(0.963) 		0.467
(0.882) 		0.204
(0.713) 		0.75
(0.99) 		0.434
(0.856) 		0.372
(0.838) 		0.725
(0.98) 		0.546
(0.936) 		0.74
(0.99)
CPT1B 5 (3%) 180 0.61
(0.963) 		0.87
(1.00) 		0.399
(0.838) 		0.559
(0.937) 		0.818
(0.994) 		1
(1.00) 		0.923
(1.00) 		1
(1.00) 		0.452
(0.872) 		0.848
(1.00)
CAMTA1 9 (5%) 176 0.54
(0.934) 		0.119
(0.625) 		0.109
(0.619) 		0.0474
(0.414) 		0.857
(1.00) 		0.415
(0.839) 		0.149
(0.661) 		0.762
(0.99) 		0.652
(0.963) 		0.627
(0.963)
OTUD7B 7 (4%) 178 0.108
(0.619) 		0.389
(0.838) 		1
(1.00) 		0.871
(1.00) 		0.336
(0.819) 		0.525
(0.926) 		0.401
(0.838) 		1
(1.00) 		0.477
(0.889) 		0.868
(1.00)
ARRB1 5 (3%) 180 0.723
(0.98) 		0.384
(0.838) 		0.549
(0.936) 		0.191
(0.708) 		0.413
(0.839) 		0.109
(0.619) 		0.662
(0.964) 		0.747
(0.99) 		0.811
(0.994) 		0.453
(0.872)
KIAA1704 3 (2%) 182 0.0844
(0.569) 		0.766
(0.99) 		0.802
(0.994) 		0.697
(0.967) 		1
(1.00) 		0.875
(1.00) 		0.683
(0.967) 		0.578
(0.95)
RNF169 6 (3%) 179 0.492
(0.898) 		0.981
(1.00) 		0.715
(0.978) 		0.406
(0.838) 		0.967
(1.00) 		0.304
(0.808) 		1
(1.00) 		0.516
(0.916) 		0.836
(1.00) 		0.311
(0.808)
RBPJL 6 (3%) 179 0.645
(0.963) 		0.194
(0.713) 		0.178
(0.69) 		0.166
(0.682) 		0.34
(0.819) 		1
(1.00) 		0.796
(0.994) 		0.715
(0.978) 		1
(1.00) 		0.74
(0.99)
MGAT5B 8 (4%) 177 0.707
(0.976) 		0.258
(0.781) 		0.926
(1.00) 		0.631
(0.963) 		0.516
(0.916) 		1
(1.00) 		0.986
(1.00) 		0.652
(0.963) 		0.126
(0.646) 		0.323
(0.812)
LRRC32 9 (5%) 176 0.195
(0.713) 		0.371
(0.838) 		0.578
(0.95) 		0.92
(1.00) 		1
(1.00) 		0.473
(0.883) 		0.724
(0.98) 		0.806
(0.994) 		0.452
(0.872) 		0.812
(0.994)
SLC22A2 4 (2%) 181 0.185
(0.703) 		0.389
(0.838) 		0.296
(0.808) 		0.432
(0.856) 		0.761
(0.99) 		0.542
(0.934) 		0.274
(0.787) 		0.215
(0.731)
PCDH15 21 (11%) 164 0.714
(0.978) 		0.82
(0.994) 		0.642
(0.963) 		0.397
(0.838) 		0.406
(0.838) 		0.142
(0.661) 		0.926
(1.00) 		0.191
(0.708) 		0.606
(0.963) 		0.338
(0.819)
KIAA1549 8 (4%) 177 0.0571
(0.462) 		0.826
(0.995) 		0.238
(0.751) 		0.827
(0.995) 		0.677
(0.964) 		0.671
(0.964) 		0.985
(1.00) 		0.954
(1.00) 		0.716
(0.978) 		0.867
(1.00)
SETBP1 14 (8%) 171 0.584
(0.95) 		0.189
(0.708) 		0.471
(0.882) 		0.0476
(0.414) 		0.0717
(0.518) 		0.0865
(0.571) 		0.277
(0.787) 		0.17
(0.686) 		0.0482
(0.414) 		0.15
(0.661)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.002

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
TP53 MUTATED 60 17 75
TP53 WILD-TYPE 14 16 2

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 = 5e-05 (Fisher's exact test), Q value = 0.0043

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 37 42 2 41 37 17 9
TP53 MUTATED 29 33 0 41 33 10 7
TP53 WILD-TYPE 8 9 2 0 4 7 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 = 0.141 (Fisher's exact test), Q value = 0.66

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 26 28 30 34 8
TP53 MUTATED 21 22 27 33 7
TP53 WILD-TYPE 5 6 3 1 1
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
TP53 MUTATED 19 16 18 25 32
TP53 WILD-TYPE 4 5 4 1 2
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
TP53 MUTATED 57 12 35 29 6 13
TP53 WILD-TYPE 17 2 7 0 3 3

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 = 0.00761 (Fisher's exact test), Q value = 0.14

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
TP53 MUTATED 49 16 87
TP53 WILD-TYPE 19 4 9

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
TP53 MUTATED 53 13 9 15 24 38
TP53 WILD-TYPE 18 2 1 3 4 4
'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0266 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
TP53 MUTATED 47 19 55 31
TP53 WILD-TYPE 16 7 7 2

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00287 (Fisher's exact test), Q value = 0.082

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
TP53 MUTATED 50 64 28 8
TP53 WILD-TYPE 15 3 7 4

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0324 (Fisher's exact test), Q value = 0.37

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
TP53 MUTATED 43 22 85
TP53 WILD-TYPE 13 7 9

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SMAD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0284 (Fisher's exact test), Q value = 0.35

Table S11.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
SMAD4 MUTATED 10 1 2
SMAD4 WILD-TYPE 64 32 75

Figure S8.  Get High-res Image Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SMAD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.82

Table S12.  Gene #2: '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 37 42 2 41 37 17 9
SMAD4 MUTATED 5 4 0 1 1 2 0
SMAD4 WILD-TYPE 32 38 2 40 36 15 9
'SMAD4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.79

Table S13.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
SMAD4 MUTATED 3 2 0 1 0
SMAD4 WILD-TYPE 23 26 30 33 8
'SMAD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.62

Table S14.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
SMAD4 MUTATED 3 2 0 0 1
SMAD4 WILD-TYPE 20 19 22 26 33
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 0.93

Table S15.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
SMAD4 MUTATED 7 1 3 0 1 1
SMAD4 WILD-TYPE 67 13 39 29 8 15
'SMAD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0659 (Fisher's exact test), Q value = 0.49

Table S16.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
SMAD4 MUTATED 8 2 3
SMAD4 WILD-TYPE 60 18 93
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.94

Table S17.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
SMAD4 MUTATED 8 1 1 0 1 2
SMAD4 WILD-TYPE 63 14 9 18 27 40
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.66

Table S18.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
SMAD4 MUTATED 8 2 2 1
SMAD4 WILD-TYPE 55 24 60 32
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.572 (Fisher's exact test), Q value = 0.95

Table S19.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
SMAD4 MUTATED 6 3 3 0
SMAD4 WILD-TYPE 59 64 32 12
'SMAD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.62

Table S20.  Gene #2: 'SMAD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
SMAD4 MUTATED 6 3 3
SMAD4 WILD-TYPE 50 26 91
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.74

Table S21.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
CDKN2A MUTATED 11 3 5
CDKN2A WILD-TYPE 63 30 72
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 0.96

Table S22.  Gene #3: '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 37 42 2 41 37 17 9
CDKN2A MUTATED 6 6 0 3 2 2 0
CDKN2A WILD-TYPE 31 36 2 38 35 15 9
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
CDKN2A MUTATED 3 2 2 3 1
CDKN2A WILD-TYPE 23 26 28 31 7
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test), Q value = 0.96

Table S24.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
CDKN2A MUTATED 3 2 2 3 1
CDKN2A WILD-TYPE 20 19 20 23 33
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.66

Table S25.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
CDKN2A MUTATED 12 1 1 3 1 0
CDKN2A WILD-TYPE 62 13 41 26 8 16
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00616 (Fisher's exact test), Q value = 0.12

Table S26.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
CDKN2A MUTATED 13 1 4
CDKN2A WILD-TYPE 55 19 92

Figure S9.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 0.83

Table S27.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
CDKN2A MUTATED 10 2 2 0 2 3
CDKN2A WILD-TYPE 61 13 8 18 26 39
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.62

Table S28.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
CDKN2A MUTATED 9 5 4 1
CDKN2A WILD-TYPE 54 21 58 32
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 0.96

Table S29.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
CDKN2A MUTATED 8 5 5 1
CDKN2A WILD-TYPE 57 62 30 11
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0411 (Fisher's exact test), Q value = 0.39

Table S30.  Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
CDKN2A MUTATED 9 5 5
CDKN2A WILD-TYPE 47 24 89

Figure S10.  Get High-res Image Gene #3: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0024

Table S31.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
NFE2L2 MUTATED 1 0 15
NFE2L2 WILD-TYPE 73 33 62

Figure S11.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.002

Table S32.  Gene #4: '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 37 42 2 41 37 17 9
NFE2L2 MUTATED 1 0 0 14 1 0 0
NFE2L2 WILD-TYPE 36 42 2 27 36 17 9

Figure S12.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0944 (Fisher's exact test), Q value = 0.59

Table S33.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
NFE2L2 MUTATED 0 2 3 7 1
NFE2L2 WILD-TYPE 26 26 27 27 7
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.82

Table S34.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
NFE2L2 MUTATED 0 2 2 4 5
NFE2L2 WILD-TYPE 23 19 20 22 29
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.002

Table S35.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
NFE2L2 MUTATED 1 0 3 12 0 0
NFE2L2 WILD-TYPE 73 14 39 17 9 16

Figure S13.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0019 (Fisher's exact test), Q value = 0.06

Table S36.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
NFE2L2 MUTATED 1 0 15
NFE2L2 WILD-TYPE 67 20 81

Figure S14.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00305 (Fisher's exact test), Q value = 0.083

Table S37.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
NFE2L2 MUTATED 1 2 1 5 1 6
NFE2L2 WILD-TYPE 70 13 9 13 27 36

Figure S15.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.001 (Fisher's exact test), Q value = 0.041

Table S38.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
NFE2L2 MUTATED 1 0 12 3
NFE2L2 WILD-TYPE 62 26 50 30

Figure S16.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0024

Table S39.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
NFE2L2 MUTATED 0 15 0 1
NFE2L2 WILD-TYPE 65 52 35 11

Figure S17.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.06

Table S40.  Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
NFE2L2 MUTATED 1 0 15
NFE2L2 WILD-TYPE 55 29 79

Figure S18.  Get High-res Image Gene #4: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.666 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
MLL2 MUTATED 11 7 14
MLL2 WILD-TYPE 63 26 63
'MLL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.81

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 37 42 2 41 37 17 9
MLL2 MUTATED 3 7 0 8 10 4 0
MLL2 WILD-TYPE 34 35 2 33 27 13 9
'MLL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0409 (Fisher's exact test), Q value = 0.39

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 26 28 30 34 8
MLL2 MUTATED 2 5 2 10 3
MLL2 WILD-TYPE 24 23 28 24 5

Figure S19.  Get High-res Image Gene #5: 'MLL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'MLL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
MLL2 MUTATED 2 4 2 5 9
MLL2 WILD-TYPE 21 17 20 21 25
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 0.9

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
MLL2 MUTATED 9 1 10 6 2 3
MLL2 WILD-TYPE 65 13 32 23 7 13
'MLL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.66

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
MLL2 MUTATED 7 4 20
MLL2 WILD-TYPE 61 16 76
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
MLL2 MUTATED 10 1 1 3 3 14
MLL2 WILD-TYPE 61 14 9 15 25 28
'MLL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.13 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
MLL2 MUTATED 9 2 11 10
MLL2 WILD-TYPE 54 24 51 23
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.061 (Fisher's exact test), Q value = 0.47

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
MLL2 MUTATED 10 17 3 0
MLL2 WILD-TYPE 55 50 32 12
'MLL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
MLL2 MUTATED 9 2 19
MLL2 WILD-TYPE 47 27 75
'ZNF750 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0834 (Fisher's exact test), Q value = 0.57

Table S51.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ZNF750 MUTATED 1 2 7
ZNF750 WILD-TYPE 73 31 70
'ZNF750 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.71

Table S52.  Gene #6: '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 37 42 2 41 37 17 9
ZNF750 MUTATED 1 0 0 3 4 2 0
ZNF750 WILD-TYPE 36 42 2 38 33 15 9
'ZNF750 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.82

Table S53.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
ZNF750 MUTATED 2 2 2 1 2
ZNF750 WILD-TYPE 24 26 28 33 6
'ZNF750 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.87

Table S54.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
ZNF750 MUTATED 1 1 0 3 4
ZNF750 WILD-TYPE 22 20 22 23 30
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.69

Table S55.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ZNF750 MUTATED 1 1 4 2 1 1
ZNF750 WILD-TYPE 73 13 38 27 8 15
'ZNF750 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.28

Table S56.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ZNF750 MUTATED 0 1 9
ZNF750 WILD-TYPE 68 19 87

Figure S20.  Get High-res Image Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0188 (Fisher's exact test), Q value = 0.28

Table S57.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ZNF750 MUTATED 1 0 3 1 2 3
ZNF750 WILD-TYPE 70 15 7 17 26 39

Figure S21.  Get High-res Image Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 4e-05 (Fisher's exact test), Q value = 0.004

Table S58.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ZNF750 MUTATED 0 1 1 8
ZNF750 WILD-TYPE 63 25 61 25

Figure S22.  Get High-res Image Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0655 (Fisher's exact test), Q value = 0.49

Table S59.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ZNF750 MUTATED 1 6 1 2
ZNF750 WILD-TYPE 64 61 34 10
'ZNF750 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0292 (Fisher's exact test), Q value = 0.35

Table S60.  Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ZNF750 MUTATED 0 1 9
ZNF750 WILD-TYPE 56 28 85

Figure S23.  Get High-res Image Gene #6: 'ZNF750 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TGFBR2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
TGFBR2 MUTATED 2 6 7
TGFBR2 WILD-TYPE 72 27 70

Figure S24.  Get High-res Image Gene #7: 'TGFBR2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TGFBR2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.78

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
TGFBR2 MUTATED 0 5 0 3 5 1 1
TGFBR2 WILD-TYPE 37 37 2 38 32 16 8
'TGFBR2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
TGFBR2 MUTATED 2 3 1 3 1
TGFBR2 WILD-TYPE 24 25 29 31 7
'TGFBR2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
TGFBR2 MUTATED 3 1 0 4 2
TGFBR2 WILD-TYPE 20 20 22 22 32
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
TGFBR2 MUTATED 6 0 4 4 0 1
TGFBR2 WILD-TYPE 68 14 38 25 9 15
'TGFBR2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
TGFBR2 MUTATED 6 0 9
TGFBR2 WILD-TYPE 62 20 87
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 0.99

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
TGFBR2 MUTATED 6 0 0 1 3 5
TGFBR2 WILD-TYPE 65 15 10 17 25 37
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.926 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
TGFBR2 MUTATED 4 2 6 3
TGFBR2 WILD-TYPE 59 24 56 30
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
TGFBR2 MUTATED 5 5 3 1
TGFBR2 WILD-TYPE 60 62 32 11
'TGFBR2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
TGFBR2 MUTATED 4 2 8
TGFBR2 WILD-TYPE 52 27 86
'FBXW7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.187 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
FBXW7 MUTATED 4 5 4
FBXW7 WILD-TYPE 70 28 73
'FBXW7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.86

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 37 42 2 41 37 17 9
FBXW7 MUTATED 4 3 0 2 1 1 2
FBXW7 WILD-TYPE 33 39 2 39 36 16 7
'FBXW7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 0.96

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 26 28 30 34 8
FBXW7 MUTATED 2 1 0 2 0
FBXW7 WILD-TYPE 24 27 30 32 8
'FBXW7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.96

Table S74.  Gene #8: 'FBXW7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
FBXW7 MUTATED 2 0 0 1 2
FBXW7 WILD-TYPE 21 21 22 25 32
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
FBXW7 MUTATED 6 1 0 2 2 1
FBXW7 WILD-TYPE 68 13 42 27 7 15
'FBXW7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
FBXW7 MUTATED 7 2 3
FBXW7 WILD-TYPE 61 18 93
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
FBXW7 MUTATED 6 0 1 3 2 1
FBXW7 WILD-TYPE 65 15 9 15 26 41
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
FBXW7 MUTATED 8 1 3 1
FBXW7 WILD-TYPE 55 25 59 32
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
FBXW7 MUTATED 8 3 2 0
FBXW7 WILD-TYPE 57 64 33 12
'FBXW7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.74

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
FBXW7 MUTATED 7 1 5
FBXW7 WILD-TYPE 49 28 89
'PKD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.84

Table S81.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PKD2 MUTATED 2 0 5
PKD2 WILD-TYPE 72 33 72
'PKD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.65

Table S82.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
PKD2 MUTATED 0 2 0 4 0 0 1
PKD2 WILD-TYPE 37 40 2 37 37 17 8
'PKD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 0.99

Table S83.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PKD2 MUTATED 1 2 3 1 0
PKD2 WILD-TYPE 25 26 27 33 8
'PKD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0404 (Fisher's exact test), Q value = 0.39

Table S84.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PKD2 MUTATED 0 1 2 4 0
PKD2 WILD-TYPE 23 20 20 22 34

Figure S25.  Get High-res Image Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'PKD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.82

Table S85.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PKD2 MUTATED 2 2 1 1 0 1
PKD2 WILD-TYPE 72 12 41 28 9 15
'PKD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 0.96

Table S86.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PKD2 MUTATED 2 0 5
PKD2 WILD-TYPE 66 20 91
'PKD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.75

Table S87.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PKD2 MUTATED 1 0 0 2 2 1
PKD2 WILD-TYPE 70 15 10 16 26 41
'PKD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.65

Table S88.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PKD2 MUTATED 0 2 3 1
PKD2 WILD-TYPE 63 24 59 32
'PKD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.62

Table S89.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PKD2 MUTATED 0 4 1 1
PKD2 WILD-TYPE 65 63 34 11
'PKD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.68

Table S90.  Gene #9: 'PKD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PKD2 MUTATED 0 2 4
PKD2 WILD-TYPE 56 27 90
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.39

Table S91.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ARID1A MUTATED 9 4 2
ARID1A WILD-TYPE 65 29 75

Figure S26.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.74

Table S92.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
ARID1A MUTATED 3 8 0 2 1 1 0
ARID1A WILD-TYPE 34 34 2 39 36 16 9
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0043 (Fisher's exact test), Q value = 0.096

Table S93.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
ARID1A MUTATED 7 3 0 1 0
ARID1A WILD-TYPE 19 25 30 33 8

Figure S27.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0355 (Fisher's exact test), Q value = 0.38

Table S94.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
ARID1A MUTATED 6 2 1 1 1
ARID1A WILD-TYPE 17 19 21 25 33

Figure S28.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0781 (Fisher's exact test), Q value = 0.55

Table S95.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ARID1A MUTATED 12 0 1 2 0 0
ARID1A WILD-TYPE 62 14 41 27 9 16
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00772 (Fisher's exact test), Q value = 0.14

Table S96.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ARID1A MUTATED 11 1 3
ARID1A WILD-TYPE 57 19 93

Figure S29.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.62

Table S97.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ARID1A MUTATED 11 0 1 1 1 1
ARID1A WILD-TYPE 60 15 9 17 27 41
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0359 (Fisher's exact test), Q value = 0.38

Table S98.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ARID1A MUTATED 8 4 1 2
ARID1A WILD-TYPE 55 22 61 31

Figure S30.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.66

Table S99.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ARID1A MUTATED 7 2 2 2
ARID1A WILD-TYPE 58 65 33 10
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0117 (Fisher's exact test), Q value = 0.19

Table S100.  Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ARID1A MUTATED 7 4 2
ARID1A WILD-TYPE 49 25 92

Figure S31.  Get High-res Image Gene #10: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.39

Table S101.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ERBB2 MUTATED 7 3 1
ERBB2 WILD-TYPE 67 30 76

Figure S32.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.18

Table S102.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
ERBB2 MUTATED 4 7 0 0 0 0 0
ERBB2 WILD-TYPE 33 35 2 41 37 17 9

Figure S33.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.32

Table S103.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ERBB2 MUTATED 9 2 0 0 0 0
ERBB2 WILD-TYPE 65 12 42 29 9 16

Figure S34.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00032 (Fisher's exact test), Q value = 0.019

Table S104.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ERBB2 MUTATED 9 2 0
ERBB2 WILD-TYPE 59 18 96

Figure S35.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0282 (Fisher's exact test), Q value = 0.35

Table S105.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ERBB2 MUTATED 9 1 1 0 0 0
ERBB2 WILD-TYPE 62 14 9 18 28 42

Figure S36.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.053

Table S106.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ERBB2 MUTATED 7 4 0 0
ERBB2 WILD-TYPE 56 22 62 33

Figure S37.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00403 (Fisher's exact test), Q value = 0.096

Table S107.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ERBB2 MUTATED 9 0 1 0
ERBB2 WILD-TYPE 56 67 34 12

Figure S38.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00048 (Fisher's exact test), Q value = 0.024

Table S108.  Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ERBB2 MUTATED 6 4 0
ERBB2 WILD-TYPE 50 25 94

Figure S39.  Get High-res Image Gene #11: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0413 (Fisher's exact test), Q value = 0.39

Table S109.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PTCH1 MUTATED 1 3 8
PTCH1 WILD-TYPE 73 30 69

Figure S40.  Get High-res Image Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.78

Table S110.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
PTCH1 MUTATED 0 3 0 6 2 1 0
PTCH1 WILD-TYPE 37 39 2 35 35 16 9
'PTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.404 (Fisher's exact test), Q value = 0.84

Table S111.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PTCH1 MUTATED 0 2 1 4 0
PTCH1 WILD-TYPE 26 26 29 30 8
'PTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.958 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PTCH1 MUTATED 1 1 1 1 3
PTCH1 WILD-TYPE 22 20 21 25 31
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0875 (Fisher's exact test), Q value = 0.57

Table S113.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PTCH1 MUTATED 3 0 2 6 0 1
PTCH1 WILD-TYPE 71 14 40 23 9 15
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.82

Table S114.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PTCH1 MUTATED 3 0 9
PTCH1 WILD-TYPE 65 20 87
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.84

Table S115.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PTCH1 MUTATED 2 1 1 1 2 5
PTCH1 WILD-TYPE 69 14 9 17 26 37
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 0.81

Table S116.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PTCH1 MUTATED 2 1 7 2
PTCH1 WILD-TYPE 61 25 55 31
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.71

Table S117.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PTCH1 MUTATED 2 8 2 0
PTCH1 WILD-TYPE 63 59 33 12
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 0.84

Table S118.  Gene #12: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PTCH1 MUTATED 2 1 9
PTCH1 WILD-TYPE 54 28 85
'KIAA2018 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.75

Table S119.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
KIAA2018 MUTATED 6 4 3
KIAA2018 WILD-TYPE 68 29 74
'KIAA2018 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 0.96

Table S120.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
KIAA2018 MUTATED 4 5 0 1 2 1 0
KIAA2018 WILD-TYPE 33 37 2 40 35 16 9
'KIAA2018 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.74

Table S121.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
KIAA2018 MUTATED 4 2 0 3 0
KIAA2018 WILD-TYPE 22 26 30 31 8
'KIAA2018 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 0.71

Table S122.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
KIAA2018 MUTATED 4 1 1 0 3
KIAA2018 WILD-TYPE 19 20 21 26 31
'KIAA2018 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 0.94

Table S123.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
KIAA2018 MUTATED 9 0 2 1 0 1
KIAA2018 WILD-TYPE 65 14 40 28 9 15
'KIAA2018 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.227 (Fisher's exact test), Q value = 0.74

Table S124.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
KIAA2018 MUTATED 7 2 4
KIAA2018 WILD-TYPE 61 18 92
'KIAA2018 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.84

Table S125.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
KIAA2018 MUTATED 9 0 0 0 1 3
KIAA2018 WILD-TYPE 62 15 10 18 27 39
'KIAA2018 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.74

Table S126.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
KIAA2018 MUTATED 8 1 2 2
KIAA2018 WILD-TYPE 55 25 60 31
'KIAA2018 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 0.96

Table S127.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
KIAA2018 MUTATED 6 3 2 1
KIAA2018 WILD-TYPE 59 64 33 11
'KIAA2018 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.65

Table S128.  Gene #13: 'KIAA2018 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
KIAA2018 MUTATED 7 1 4
KIAA2018 WILD-TYPE 49 28 90
'FAM108A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 0.99

Table S129.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
FAM108A1 MUTATED 1 1 2
FAM108A1 WILD-TYPE 73 32 75
'FAM108A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 0.96

Table S130.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
FAM108A1 MUTATED 1 0 0 1 1 1 0
FAM108A1 WILD-TYPE 36 42 2 40 36 16 9
'FAM108A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 0.71

Table S131.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
FAM108A1 MUTATED 0 1 0 1 1
FAM108A1 WILD-TYPE 26 27 30 33 7
'FAM108A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 0.93

Table S132.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
FAM108A1 MUTATED 1 1 0 1 0
FAM108A1 WILD-TYPE 22 20 22 25 34
'FAM108A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 0.96

Table S133.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
FAM108A1 MUTATED 1 1 1 1 0 0
FAM108A1 WILD-TYPE 73 13 41 28 9 16
'FAM108A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.566 (Fisher's exact test), Q value = 0.95

Table S134.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
FAM108A1 MUTATED 1 1 2
FAM108A1 WILD-TYPE 67 19 94
'FAM108A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.79

Table S135.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
FAM108A1 MUTATED 1 0 0 2 0 1
FAM108A1 WILD-TYPE 70 15 10 16 28 41
'FAM108A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.748 (Fisher's exact test), Q value = 0.99

Table S136.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
FAM108A1 MUTATED 1 1 1 1
FAM108A1 WILD-TYPE 62 25 61 32
'FAM108A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 0.99

Table S137.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
FAM108A1 MUTATED 2 2 0 0
FAM108A1 WILD-TYPE 63 65 35 12
'FAM108A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.818 (Fisher's exact test), Q value = 0.99

Table S138.  Gene #14: 'FAM108A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
FAM108A1 MUTATED 1 1 2
FAM108A1 WILD-TYPE 55 28 92
'PAXIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 0.97

Table S139.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PAXIP1 MUTATED 5 2 3
PAXIP1 WILD-TYPE 69 31 74
'PAXIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.942 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
PAXIP1 MUTATED 2 2 0 3 3 0 0
PAXIP1 WILD-TYPE 35 40 2 38 34 17 9
'PAXIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.55 (Fisher's exact test), Q value = 0.94

Table S141.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PAXIP1 MUTATED 1 2 0 3 0
PAXIP1 WILD-TYPE 25 26 30 31 8
'PAXIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PAXIP1 MUTATED 1 1 0 2 2
PAXIP1 WILD-TYPE 22 20 22 24 32
'PAXIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.81

Table S143.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PAXIP1 MUTATED 3 1 5 0 0 1
PAXIP1 WILD-TYPE 71 13 37 29 9 15
'PAXIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S144.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PAXIP1 MUTATED 3 1 6
PAXIP1 WILD-TYPE 65 19 90
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.66

Table S145.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PAXIP1 MUTATED 4 0 0 0 0 6
PAXIP1 WILD-TYPE 67 15 10 18 28 36
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0578 (Fisher's exact test), Q value = 0.46

Table S146.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PAXIP1 MUTATED 3 1 1 5
PAXIP1 WILD-TYPE 60 25 61 28
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.81

Table S147.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PAXIP1 MUTATED 4 6 0 0
PAXIP1 WILD-TYPE 61 61 35 12
'PAXIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S148.  Gene #15: 'PAXIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PAXIP1 MUTATED 3 1 6
PAXIP1 WILD-TYPE 53 28 88
'MGC29506 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 0.81

Table S149.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
MGC29506 MUTATED 1 2 1
MGC29506 WILD-TYPE 73 31 76
'MGC29506 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S150.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
MGC29506 MUTATED 1 1 0 1 1 0 0
MGC29506 WILD-TYPE 36 41 2 40 36 17 9
'MGC29506 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.81

Table S151.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
MGC29506 MUTATED 1 1 1 0 0 1
MGC29506 WILD-TYPE 73 13 41 29 9 15
'MGC29506 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S152.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
MGC29506 MUTATED 2 0 2
MGC29506 WILD-TYPE 66 20 94
'MGC29506 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.411 (Fisher's exact test), Q value = 0.84

Table S153.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
MGC29506 MUTATED 1 0 1 0 1 1
MGC29506 WILD-TYPE 70 15 9 18 27 41
'MGC29506 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test), Q value = 0.73

Table S154.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
MGC29506 MUTATED 2 0 0 2
MGC29506 WILD-TYPE 61 26 62 31
'MGC29506 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 0.99

Table S155.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
MGC29506 MUTATED 2 2 0 0
MGC29506 WILD-TYPE 63 65 35 12
'MGC29506 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.96

Table S156.  Gene #16: 'MGC29506 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
MGC29506 MUTATED 2 0 2
MGC29506 WILD-TYPE 54 29 92
'C10ORF76 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0324 (Fisher's exact test), Q value = 0.37

Table S157.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
C10ORF76 MUTATED 0 3 3
C10ORF76 WILD-TYPE 74 30 74

Figure S41.  Get High-res Image Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'C10ORF76 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 0.99

Table S158.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
C10ORF76 MUTATED 0 2 0 2 1 1 0
C10ORF76 WILD-TYPE 37 40 2 39 36 16 9
'C10ORF76 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.555 (Fisher's exact test), Q value = 0.94

Table S159.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
C10ORF76 MUTATED 1 2 2 0 0
C10ORF76 WILD-TYPE 25 26 28 34 8
'C10ORF76 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.469 (Fisher's exact test), Q value = 0.88

Table S160.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
C10ORF76 MUTATED 2 1 1 1 0
C10ORF76 WILD-TYPE 21 20 21 25 34
'C10ORF76 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.89

Table S161.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
C10ORF76 MUTATED 2 0 1 2 1 0
C10ORF76 WILD-TYPE 72 14 41 27 8 16
'C10ORF76 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S162.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
C10ORF76 MUTATED 2 0 4
C10ORF76 WILD-TYPE 66 20 92
'C10ORF76 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 0.99

Table S163.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
C10ORF76 MUTATED 2 0 0 0 2 2
C10ORF76 WILD-TYPE 69 15 10 18 26 40
'C10ORF76 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.82

Table S164.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
C10ORF76 MUTATED 2 0 4 0
C10ORF76 WILD-TYPE 61 26 58 33
'C10ORF76 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.78

Table S165.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
C10ORF76 MUTATED 1 1 2 1
C10ORF76 WILD-TYPE 64 66 33 11
'C10ORF76 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.95

Table S166.  Gene #17: 'C10ORF76 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
C10ORF76 MUTATED 1 0 4
C10ORF76 WILD-TYPE 55 29 90
'IPP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S167.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
IPP MUTATED 3 1 2
IPP WILD-TYPE 71 32 75
'IPP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 0.99

Table S168.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
IPP MUTATED 3 1 0 1 1 0 0
IPP WILD-TYPE 34 41 2 40 36 17 9
'IPP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.85

Table S169.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
IPP MUTATED 0 2 0 2 0
IPP WILD-TYPE 26 26 30 32 8
'IPP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 0.9

Table S170.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
IPP MUTATED 0 2 0 1 1
IPP WILD-TYPE 23 19 22 25 33
'IPP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.83

Table S171.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
IPP MUTATED 2 2 1 1 0 0
IPP WILD-TYPE 72 12 41 28 9 16
'IPP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.85 (Fisher's exact test), Q value = 1

Table S172.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
IPP MUTATED 3 0 3
IPP WILD-TYPE 65 20 93
'IPP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.62

Table S173.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
IPP MUTATED 2 0 2 1 0 1
IPP WILD-TYPE 69 15 8 17 28 41
'IPP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 0.83

Table S174.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
IPP MUTATED 4 0 2 0
IPP WILD-TYPE 59 26 60 33
'IPP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.82

Table S175.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
IPP MUTATED 3 2 0 1
IPP WILD-TYPE 62 65 35 11
'IPP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 0.76

Table S176.  Gene #18: 'IPP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
IPP MUTATED 4 0 2
IPP WILD-TYPE 52 29 92
'DNAH10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.856 (Fisher's exact test), Q value = 1

Table S177.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
DNAH10 MUTATED 8 4 7
DNAH10 WILD-TYPE 66 29 70
'DNAH10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.85

Table S178.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
DNAH10 MUTATED 4 8 0 3 3 0 1
DNAH10 WILD-TYPE 33 34 2 38 34 17 8
'DNAH10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 0.84

Table S179.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
DNAH10 MUTATED 4 4 6 2 0
DNAH10 WILD-TYPE 22 24 24 32 8
'DNAH10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.81

Table S180.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
DNAH10 MUTATED 4 3 5 1 3
DNAH10 WILD-TYPE 19 18 17 25 31
'DNAH10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.84

Table S181.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
DNAH10 MUTATED 11 0 3 2 2 1
DNAH10 WILD-TYPE 63 14 39 27 7 15
'DNAH10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.66

Table S182.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
DNAH10 MUTATED 11 1 7
DNAH10 WILD-TYPE 57 19 89
'DNAH10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.81

Table S183.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
DNAH10 MUTATED 10 0 2 0 3 4
DNAH10 WILD-TYPE 61 15 8 18 25 38
'DNAH10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 0.96

Table S184.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
DNAH10 MUTATED 9 3 5 2
DNAH10 WILD-TYPE 54 23 57 31
'DNAH10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.96

Table S185.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
DNAH10 MUTATED 7 6 5 0
DNAH10 WILD-TYPE 58 61 30 12
'DNAH10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.84

Table S186.  Gene #19: 'DNAH10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
DNAH10 MUTATED 8 3 7
DNAH10 WILD-TYPE 48 26 87
'RIC3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.81

Table S187.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
RIC3 MUTATED 1 2 1
RIC3 WILD-TYPE 73 31 76
'RIC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.81

Table S188.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
RIC3 MUTATED 0 3 0 0 1 0 0
RIC3 WILD-TYPE 37 39 2 41 36 17 9
'RIC3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S189.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
RIC3 MUTATED 0 1 1 1 0
RIC3 WILD-TYPE 26 27 29 33 8
'RIC3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.823 (Fisher's exact test), Q value = 0.99

Table S190.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
RIC3 MUTATED 1 0 1 0 1
RIC3 WILD-TYPE 22 21 21 26 33
'RIC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S191.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
RIC3 MUTATED 3 0 1 0 0 0
RIC3 WILD-TYPE 71 14 41 29 9 16
'RIC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 0.86

Table S192.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
RIC3 MUTATED 3 0 1
RIC3 WILD-TYPE 65 20 95
'RIC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S193.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
RIC3 MUTATED 2 0 0 0 1 1
RIC3 WILD-TYPE 69 15 10 18 27 41
'RIC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 0.96

Table S194.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
RIC3 MUTATED 2 1 1 0
RIC3 WILD-TYPE 61 25 61 33
'RIC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S195.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
RIC3 MUTATED 2 1 1 0
RIC3 WILD-TYPE 63 66 34 12
'RIC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.485 (Fisher's exact test), Q value = 0.89

Table S196.  Gene #20: 'RIC3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
RIC3 MUTATED 2 1 1
RIC3 WILD-TYPE 54 28 93
'HMMR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.62

Table S197.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
HMMR MUTATED 2 2 0
HMMR WILD-TYPE 72 31 77
'HMMR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.81

Table S198.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
HMMR MUTATED 2 0 0 0 1 1 0
HMMR WILD-TYPE 35 42 2 41 36 16 9
'HMMR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.96

Table S199.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
HMMR MUTATED 2 0 1 1 0
HMMR WILD-TYPE 24 28 29 33 8
'HMMR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.519 (Fisher's exact test), Q value = 0.92

Table S200.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
HMMR MUTATED 2 0 1 0 1
HMMR WILD-TYPE 21 21 21 26 33
'HMMR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S201.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
HMMR MUTATED 2 0 2 0 0 0
HMMR WILD-TYPE 72 14 40 29 9 16
'HMMR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S202.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
HMMR MUTATED 2 0 2
HMMR WILD-TYPE 66 20 94
'HMMR MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S203.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
HMMR MUTATED 2 0 0 0 1 1
HMMR WILD-TYPE 69 15 10 18 27 41
'HMMR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S204.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
HMMR MUTATED 2 0 1 1
HMMR WILD-TYPE 61 26 61 32
'HMMR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S205.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
HMMR MUTATED 2 1 1 0
HMMR WILD-TYPE 63 66 34 12
'HMMR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.817 (Fisher's exact test), Q value = 0.99

Table S206.  Gene #21: 'HMMR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
HMMR MUTATED 1 1 2
HMMR WILD-TYPE 55 28 92
'PIAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.82

Table S207.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PIAS1 MUTATED 2 2 1
PIAS1 WILD-TYPE 72 31 76
'PIAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 0.99

Table S208.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
PIAS1 MUTATED 1 2 0 1 0 1 0
PIAS1 WILD-TYPE 36 40 2 40 37 16 9
'PIAS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 0.94

Table S209.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PIAS1 MUTATED 1 2 2 0 0
PIAS1 WILD-TYPE 25 26 28 34 8
'PIAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.66

Table S210.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PIAS1 MUTATED 2 1 2 0 0
PIAS1 WILD-TYPE 21 20 20 26 34
'PIAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.71

Table S211.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PIAS1 MUTATED 3 0 0 0 1 1
PIAS1 WILD-TYPE 71 14 42 29 8 15
'PIAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 0.99

Table S212.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PIAS1 MUTATED 3 0 2
PIAS1 WILD-TYPE 65 20 94
'PIAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 0.91

Table S213.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PIAS1 MUTATED 3 0 0 0 2 0
PIAS1 WILD-TYPE 68 15 10 18 26 42
'PIAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 0.96

Table S214.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PIAS1 MUTATED 3 0 2 0
PIAS1 WILD-TYPE 60 26 60 33
'PIAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 0.99

Table S215.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PIAS1 MUTATED 3 1 1 0
PIAS1 WILD-TYPE 62 66 34 12
'PIAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 0.97

Table S216.  Gene #22: 'PIAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PIAS1 MUTATED 2 1 2
PIAS1 WILD-TYPE 54 28 92
'ITGA6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S217.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ITGA6 MUTATED 2 1 4
ITGA6 WILD-TYPE 72 32 73
'ITGA6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.84

Table S218.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
ITGA6 MUTATED 0 3 0 1 2 0 1
ITGA6 WILD-TYPE 37 39 2 40 35 17 8
'ITGA6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 0.83

Table S219.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
ITGA6 MUTATED 0 1 1 4 0
ITGA6 WILD-TYPE 26 27 29 30 8
'ITGA6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S220.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
ITGA6 MUTATED 0 1 1 2 2
ITGA6 WILD-TYPE 23 20 21 24 32
'ITGA6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 0.93

Table S221.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ITGA6 MUTATED 2 0 3 1 1 0
ITGA6 WILD-TYPE 72 14 39 28 8 16
'ITGA6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S222.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ITGA6 MUTATED 3 0 4
ITGA6 WILD-TYPE 65 20 92
'ITGA6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S223.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ITGA6 MUTATED 3 0 0 0 1 3
ITGA6 WILD-TYPE 68 15 10 18 27 39
'ITGA6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ITGA6 MUTATED 2 1 3 1
ITGA6 WILD-TYPE 61 25 59 32
'ITGA6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.929 (Fisher's exact test), Q value = 1

Table S225.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ITGA6 MUTATED 2 3 2 0
ITGA6 WILD-TYPE 63 64 33 12
'ITGA6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S226.  Gene #23: 'ITGA6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ITGA6 MUTATED 2 1 4
ITGA6 WILD-TYPE 54 28 90
'ASTE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0828 (Fisher's exact test), Q value = 0.57

Table S227.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ASTE1 MUTATED 3 2 0
ASTE1 WILD-TYPE 71 31 77
'ASTE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0605 (Fisher's exact test), Q value = 0.47

Table S228.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
ASTE1 MUTATED 0 3 0 0 0 2 0
ASTE1 WILD-TYPE 37 39 2 41 37 15 9
'ASTE1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.753 (Fisher's exact test), Q value = 0.99

Table S229.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
ASTE1 MUTATED 1 1 1 0 0
ASTE1 WILD-TYPE 25 27 29 34 8
'ASTE1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.36 (Fisher's exact test), Q value = 0.83

Table S230.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
ASTE1 MUTATED 1 1 1 0 0
ASTE1 WILD-TYPE 22 20 21 26 34
'ASTE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.86

Table S231.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ASTE1 MUTATED 4 0 0 0 0 1
ASTE1 WILD-TYPE 70 14 42 29 9 15
'ASTE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.23

Table S232.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ASTE1 MUTATED 3 2 0
ASTE1 WILD-TYPE 65 18 96

Figure S42.  Get High-res Image Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ASTE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.609 (Fisher's exact test), Q value = 0.96

Table S233.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ASTE1 MUTATED 4 0 0 0 1 0
ASTE1 WILD-TYPE 67 15 10 18 27 42
'ASTE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00161 (Fisher's exact test), Q value = 0.057

Table S234.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ASTE1 MUTATED 1 4 0 0
ASTE1 WILD-TYPE 62 22 62 33

Figure S43.  Get High-res Image Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ASTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0828 (Fisher's exact test), Q value = 0.57

Table S235.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ASTE1 MUTATED 2 0 3 0
ASTE1 WILD-TYPE 63 67 32 12
'ASTE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00102 (Fisher's exact test), Q value = 0.041

Table S236.  Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ASTE1 MUTATED 1 4 0
ASTE1 WILD-TYPE 55 25 94

Figure S44.  Get High-res Image Gene #24: 'ASTE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KPNA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.9

Table S237.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
KPNA1 MUTATED 4 0 2
KPNA1 WILD-TYPE 70 33 75
'KPNA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.98

Table S238.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
KPNA1 MUTATED 2 1 0 2 0 1 0
KPNA1 WILD-TYPE 35 41 2 39 37 16 9
'KPNA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.87

Table S239.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
KPNA1 MUTATED 1 0 3 1 0
KPNA1 WILD-TYPE 25 28 27 33 8
'KPNA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0695 (Fisher's exact test), Q value = 0.51

Table S240.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
KPNA1 MUTATED 1 0 3 1 0
KPNA1 WILD-TYPE 22 21 19 25 34
'KPNA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.71

Table S241.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
KPNA1 MUTATED 2 1 0 1 1 1
KPNA1 WILD-TYPE 72 13 42 28 8 15
'KPNA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 1

Table S242.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
KPNA1 MUTATED 3 0 3
KPNA1 WILD-TYPE 65 20 93
'KPNA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.75

Table S243.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
KPNA1 MUTATED 1 1 1 0 2 1
KPNA1 WILD-TYPE 70 14 9 18 26 41
'KPNA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 0.99

Table S244.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
KPNA1 MUTATED 3 1 2 0
KPNA1 WILD-TYPE 60 25 60 33
'KPNA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S245.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
KPNA1 MUTATED 2 3 1 0
KPNA1 WILD-TYPE 63 64 34 12
'KPNA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 0.81

Table S246.  Gene #25: 'KPNA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
KPNA1 MUTATED 2 2 2
KPNA1 WILD-TYPE 54 27 92
'LIMA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 0.96

Table S247.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
LIMA1 MUTATED 4 2 2
LIMA1 WILD-TYPE 70 31 75
'LIMA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.96

Table S248.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
LIMA1 MUTATED 2 3 0 2 0 1 0
LIMA1 WILD-TYPE 35 39 2 39 37 16 9
'LIMA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.82

Table S249.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
LIMA1 MUTATED 2 3 2 0 0
LIMA1 WILD-TYPE 24 25 28 34 8
'LIMA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.65

Table S250.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
LIMA1 MUTATED 1 3 2 1 0
LIMA1 WILD-TYPE 22 18 20 25 34
'LIMA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.85

Table S251.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
LIMA1 MUTATED 5 1 0 1 0 1
LIMA1 WILD-TYPE 69 13 42 28 9 15
'LIMA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.101 (Fisher's exact test), Q value = 0.61

Table S252.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
LIMA1 MUTATED 6 0 2
LIMA1 WILD-TYPE 62 20 94
'LIMA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 0.81

Table S253.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
LIMA1 MUTATED 5 0 0 2 1 0
LIMA1 WILD-TYPE 66 15 10 16 27 42
'LIMA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.65

Table S254.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
LIMA1 MUTATED 6 0 2 0
LIMA1 WILD-TYPE 57 26 60 33
'LIMA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.66

Table S255.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
LIMA1 MUTATED 6 2 0 0
LIMA1 WILD-TYPE 59 65 35 12
'LIMA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.65

Table S256.  Gene #26: 'LIMA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
LIMA1 MUTATED 5 1 2
LIMA1 WILD-TYPE 51 28 92
'FAM65B MUTATION STATUS' versus 'CN_CNMF'

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

Table S257.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
FAM65B MUTATED 3 1 4
FAM65B WILD-TYPE 71 32 73
'FAM65B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.665 (Fisher's exact test), Q value = 0.96

Table S258.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
FAM65B MUTATED 2 1 0 4 1 0 0
FAM65B WILD-TYPE 35 41 2 37 36 17 9
'FAM65B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.84

Table S259.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
FAM65B MUTATED 2 1 0 2 1
FAM65B WILD-TYPE 24 27 30 32 7
'FAM65B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.81

Table S260.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
FAM65B MUTATED 1 0 0 1 4
FAM65B WILD-TYPE 22 21 22 25 30
'FAM65B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.927 (Fisher's exact test), Q value = 1

Table S261.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
FAM65B MUTATED 3 1 2 1 0 1
FAM65B WILD-TYPE 71 13 40 28 9 15
'FAM65B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S262.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
FAM65B MUTATED 3 0 5
FAM65B WILD-TYPE 65 20 91
'FAM65B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.69

Table S263.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
FAM65B MUTATED 2 2 0 2 0 2
FAM65B WILD-TYPE 69 13 10 16 28 40
'FAM65B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0425 (Fisher's exact test), Q value = 0.39

Table S264.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
FAM65B MUTATED 1 2 1 4
FAM65B WILD-TYPE 62 24 61 29

Figure S45.  Get High-res Image Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FAM65B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.97

Table S265.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
FAM65B MUTATED 2 5 1 0
FAM65B WILD-TYPE 63 62 34 12
'FAM65B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 0.84

Table S266.  Gene #27: 'FAM65B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
FAM65B MUTATED 1 2 5
FAM65B WILD-TYPE 55 27 89
'CORO7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.235 (Fisher's exact test), Q value = 0.75

Table S267.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
CORO7 MUTATED 4 2 1
CORO7 WILD-TYPE 70 31 76
'CORO7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.84

Table S268.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
CORO7 MUTATED 2 1 0 0 2 1 1
CORO7 WILD-TYPE 35 41 2 41 35 16 8
'CORO7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 0.96

Table S269.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
CORO7 MUTATED 3 2 1 1 0
CORO7 WILD-TYPE 23 26 29 33 8
'CORO7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 0.66

Table S270.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
CORO7 MUTATED 3 2 0 0 2
CORO7 WILD-TYPE 20 19 22 26 32
'CORO7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 0.9

Table S271.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
CORO7 MUTATED 5 0 0 1 0 1
CORO7 WILD-TYPE 69 14 42 28 9 15
'CORO7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.72

Table S272.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
CORO7 MUTATED 5 0 2
CORO7 WILD-TYPE 63 20 94
'CORO7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.8

Table S273.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
CORO7 MUTATED 5 0 1 0 1 0
CORO7 WILD-TYPE 66 15 9 18 27 42
'CORO7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0356 (Fisher's exact test), Q value = 0.38

Table S274.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
CORO7 MUTATED 2 3 0 2
CORO7 WILD-TYPE 61 23 62 31

Figure S46.  Get High-res Image Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CORO7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0237 (Fisher's exact test), Q value = 0.32

Table S275.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
CORO7 MUTATED 3 0 2 2
CORO7 WILD-TYPE 62 67 33 10

Figure S47.  Get High-res Image Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CORO7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.66

Table S276.  Gene #28: 'CORO7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
CORO7 MUTATED 2 3 2
CORO7 WILD-TYPE 54 26 92
'ANAPC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00016 (Fisher's exact test), Q value = 0.012

Table S277.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ANAPC1 MUTATED 0 5 0
ANAPC1 WILD-TYPE 74 28 77

Figure S48.  Get High-res Image Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ANAPC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.311 (Fisher's exact test), Q value = 0.81

Table S278.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
ANAPC1 MUTATED 0 3 0 0 2 0 0
ANAPC1 WILD-TYPE 37 39 2 41 35 17 9
'ANAPC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.96

Table S279.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
ANAPC1 MUTATED 1 2 0 1 0
ANAPC1 WILD-TYPE 25 26 30 33 8
'ANAPC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.87

Table S280.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
ANAPC1 MUTATED 2 1 0 0 1
ANAPC1 WILD-TYPE 21 20 22 26 33
'ANAPC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 0.99

Table S281.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ANAPC1 MUTATED 3 0 1 0 0 1
ANAPC1 WILD-TYPE 71 14 41 29 9 15
'ANAPC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.804 (Fisher's exact test), Q value = 0.99

Table S282.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ANAPC1 MUTATED 3 0 2
ANAPC1 WILD-TYPE 65 20 94
'ANAPC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S283.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ANAPC1 MUTATED 3 0 0 0 0 2
ANAPC1 WILD-TYPE 68 15 10 18 28 40
'ANAPC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 0.69

Table S284.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ANAPC1 MUTATED 3 0 0 2
ANAPC1 WILD-TYPE 60 26 62 31
'ANAPC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S285.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ANAPC1 MUTATED 2 1 1 0
ANAPC1 WILD-TYPE 63 66 34 12
'ANAPC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 0.96

Table S286.  Gene #29: 'ANAPC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ANAPC1 MUTATED 2 0 2
ANAPC1 WILD-TYPE 54 29 92
'IVL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00579 (Fisher's exact test), Q value = 0.12

Table S287.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
IVL MUTATED 10 4 1
IVL WILD-TYPE 64 29 76

Figure S49.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IVL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.32

Table S288.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
IVL MUTATED 7 6 0 1 0 1 0
IVL WILD-TYPE 30 36 2 40 37 16 9

Figure S50.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IVL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.66

Table S289.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
IVL MUTATED 3 2 1 0 1
IVL WILD-TYPE 23 26 29 34 7
'IVL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00388 (Fisher's exact test), Q value = 0.096

Table S290.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
IVL MUTATED 5 1 1 0 0
IVL WILD-TYPE 18 20 21 26 34

Figure S51.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'IVL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00351 (Fisher's exact test), Q value = 0.092

Table S291.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
IVL MUTATED 13 0 0 0 1 1
IVL WILD-TYPE 61 14 42 29 8 15

Figure S52.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'IVL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.013

Table S292.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
IVL MUTATED 10 4 1
IVL WILD-TYPE 58 16 95

Figure S53.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'IVL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0395 (Fisher's exact test), Q value = 0.39

Table S293.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
IVL MUTATED 11 1 0 2 1 0
IVL WILD-TYPE 60 14 10 16 27 42

Figure S54.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IVL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.035

Table S294.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
IVL MUTATED 9 5 0 1
IVL WILD-TYPE 54 21 62 32

Figure S55.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IVL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00819 (Fisher's exact test), Q value = 0.15

Table S295.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
IVL MUTATED 11 1 2 1
IVL WILD-TYPE 54 66 33 11

Figure S56.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'IVL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.019

Table S296.  Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
IVL MUTATED 9 5 1
IVL WILD-TYPE 47 24 93

Figure S57.  Get High-res Image Gene #30: 'IVL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 0.91

Table S297.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PIK3CA MUTATED 6 5 8
PIK3CA WILD-TYPE 68 28 69
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.79

Table S298.  Gene #31: '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 37 42 2 41 37 17 9
PIK3CA MUTATED 3 2 1 5 5 3 0
PIK3CA WILD-TYPE 34 40 1 36 32 14 9
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.78

Table S299.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PIK3CA MUTATED 3 1 2 7 1
PIK3CA WILD-TYPE 23 27 28 27 7
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.81

Table S300.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PIK3CA MUTATED 3 1 2 1 7
PIK3CA WILD-TYPE 20 20 20 25 27
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.66

Table S301.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PIK3CA MUTATED 3 1 6 4 2 2
PIK3CA WILD-TYPE 71 13 36 25 7 14
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.89

Table S302.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PIK3CA MUTATED 5 1 12
PIK3CA WILD-TYPE 63 19 84
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.69

Table S303.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PIK3CA MUTATED 4 1 1 1 3 9
PIK3CA WILD-TYPE 67 14 9 17 25 33
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 0.82

Table S304.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PIK3CA MUTATED 4 2 7 6
PIK3CA WILD-TYPE 59 24 55 27
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.62

Table S305.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PIK3CA MUTATED 3 11 4 0
PIK3CA WILD-TYPE 62 56 31 12
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.77

Table S306.  Gene #31: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PIK3CA MUTATED 3 2 13
PIK3CA WILD-TYPE 53 27 81
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00242 (Fisher's exact test), Q value = 0.073

Table S307.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
RB1 MUTATED 1 5 1
RB1 WILD-TYPE 73 28 76

Figure S58.  Get High-res Image Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S308.  Gene #32: '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 37 42 2 41 37 17 9
RB1 MUTATED 1 2 0 2 1 1 0
RB1 WILD-TYPE 36 40 2 39 36 16 9
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.84

Table S309.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
RB1 MUTATED 0 2 1 1 1
RB1 WILD-TYPE 26 26 29 33 7
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.408 (Fisher's exact test), Q value = 0.84

Table S310.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
RB1 MUTATED 1 1 0 0 3
RB1 WILD-TYPE 22 20 22 26 31
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 0.99

Table S311.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
RB1 MUTATED 2 1 2 1 0 1
RB1 WILD-TYPE 72 13 40 28 9 15
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S312.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
RB1 MUTATED 2 1 4
RB1 WILD-TYPE 66 19 92
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 0.96

Table S313.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
RB1 MUTATED 2 0 1 1 1 2
RB1 WILD-TYPE 69 15 9 17 27 40
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.9 (Fisher's exact test), Q value = 1

Table S314.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
RB1 MUTATED 2 1 2 2
RB1 WILD-TYPE 61 25 60 31
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 0.87

Table S315.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
RB1 MUTATED 3 3 0 1
RB1 WILD-TYPE 62 64 35 11
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S316.  Gene #32: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
RB1 MUTATED 2 1 4
RB1 WILD-TYPE 54 28 90
'EIF4EBP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.044 (Fisher's exact test), Q value = 0.39

Table S317.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
EIF4EBP2 MUTATED 1 2 0
EIF4EBP2 WILD-TYPE 73 31 77

Figure S59.  Get High-res Image Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EIF4EBP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.553 (Fisher's exact test), Q value = 0.94

Table S318.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
EIF4EBP2 MUTATED 2 1 0 0 0 0 0
EIF4EBP2 WILD-TYPE 35 41 2 41 37 17 9
'EIF4EBP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.98

Table S319.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
EIF4EBP2 MUTATED 3 0 0 0 0 0
EIF4EBP2 WILD-TYPE 71 14 42 29 9 16
'EIF4EBP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0761 (Fisher's exact test), Q value = 0.54

Table S320.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
EIF4EBP2 MUTATED 2 1 0
EIF4EBP2 WILD-TYPE 66 19 96
'EIF4EBP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 0.97

Table S321.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
EIF4EBP2 MUTATED 3 0 0 0 0 0
EIF4EBP2 WILD-TYPE 68 15 10 18 28 42
'EIF4EBP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.73

Table S322.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
EIF4EBP2 MUTATED 3 0 0 0
EIF4EBP2 WILD-TYPE 60 26 62 33
'EIF4EBP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0523 (Fisher's exact test), Q value = 0.44

Table S323.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
EIF4EBP2 MUTATED 2 0 0 1
EIF4EBP2 WILD-TYPE 63 67 35 11
'EIF4EBP2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.66

Table S324.  Gene #33: 'EIF4EBP2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
EIF4EBP2 MUTATED 2 1 0
EIF4EBP2 WILD-TYPE 54 28 94
'SCD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 0.95

Table S325.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
SCD MUTATED 1 1 1
SCD WILD-TYPE 73 32 76
'SCD MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.767 (Fisher's exact test), Q value = 0.99

Table S326.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
SCD MUTATED 0 2 0 1 0 0 0
SCD WILD-TYPE 37 40 2 40 37 17 9
'SCD MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 0.99

Table S327.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
SCD MUTATED 2 0 0 1 0 0
SCD WILD-TYPE 72 14 42 28 9 16
'SCD MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.696 (Fisher's exact test), Q value = 0.97

Table S328.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
SCD MUTATED 2 0 1
SCD WILD-TYPE 66 20 95
'SCD MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 0.95

Table S329.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
SCD MUTATED 2 0 0 1 0 0
SCD WILD-TYPE 69 15 10 17 28 42
'SCD MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 0.96

Table S330.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
SCD MUTATED 1 1 1 0
SCD WILD-TYPE 62 25 61 33
'SCD MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.97

Table S331.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
SCD MUTATED 2 1 0 0
SCD WILD-TYPE 63 66 35 12
'SCD MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 0.99

Table S332.  Gene #34: 'SCD MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
SCD MUTATED 1 1 1
SCD WILD-TYPE 55 28 93
'MKL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.62

Table S333.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
MKL2 MUTATED 2 3 1
MKL2 WILD-TYPE 72 30 76
'MKL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.81

Table S334.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
MKL2 MUTATED 1 4 0 0 1 0 0
MKL2 WILD-TYPE 36 38 2 41 36 17 9
'MKL2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 0.9

Table S335.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
MKL2 MUTATED 0 2 0 1 0
MKL2 WILD-TYPE 26 26 30 33 8
'MKL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.767 (Fisher's exact test), Q value = 0.99

Table S336.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
MKL2 MUTATED 1 1 0 0 1
MKL2 WILD-TYPE 22 20 22 26 33
'MKL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 0.96

Table S337.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
MKL2 MUTATED 5 0 1 0 0 0
MKL2 WILD-TYPE 69 14 41 29 9 16
'MKL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.66

Table S338.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
MKL2 MUTATED 4 1 1
MKL2 WILD-TYPE 64 19 95
'MKL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 0.96

Table S339.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
MKL2 MUTATED 5 0 0 0 0 1
MKL2 WILD-TYPE 66 15 10 18 28 41
'MKL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.81

Table S340.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
MKL2 MUTATED 4 1 1 0
MKL2 WILD-TYPE 59 25 61 33
'MKL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.404 (Fisher's exact test), Q value = 0.84

Table S341.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
MKL2 MUTATED 3 1 1 1
MKL2 WILD-TYPE 62 66 34 11
'MKL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.62

Table S342.  Gene #35: 'MKL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
MKL2 MUTATED 4 1 1
MKL2 WILD-TYPE 52 28 93
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0576 (Fisher's exact test), Q value = 0.46

Table S343.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
NOTCH1 MUTATED 3 3 12
NOTCH1 WILD-TYPE 71 30 65
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00426 (Fisher's exact test), Q value = 0.096

Table S344.  Gene #36: '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 37 42 2 41 37 17 9
NOTCH1 MUTATED 2 1 1 3 6 1 4
NOTCH1 WILD-TYPE 35 41 1 38 31 16 5

Figure S60.  Get High-res Image Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.66

Table S345.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
NOTCH1 MUTATED 0 2 2 6 1
NOTCH1 WILD-TYPE 26 26 28 28 7
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.092 (Fisher's exact test), Q value = 0.58

Table S346.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
NOTCH1 MUTATED 0 2 0 4 5
NOTCH1 WILD-TYPE 23 19 22 22 29
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.059 (Fisher's exact test), Q value = 0.47

Table S347.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
NOTCH1 MUTATED 3 2 8 2 0 3
NOTCH1 WILD-TYPE 71 12 34 27 9 13
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0889 (Fisher's exact test), Q value = 0.57

Table S348.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
NOTCH1 MUTATED 3 1 14
NOTCH1 WILD-TYPE 65 19 82
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0179 (Fisher's exact test), Q value = 0.28

Table S349.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
NOTCH1 MUTATED 2 4 0 1 5 5
NOTCH1 WILD-TYPE 69 11 10 17 23 37

Figure S61.  Get High-res Image Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00931 (Fisher's exact test), Q value = 0.16

Table S350.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
NOTCH1 MUTATED 2 2 12 1
NOTCH1 WILD-TYPE 61 24 50 32

Figure S62.  Get High-res Image Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0549 (Fisher's exact test), Q value = 0.46

Table S351.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
NOTCH1 MUTATED 2 7 4 3
NOTCH1 WILD-TYPE 63 60 31 9
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.062 (Fisher's exact test), Q value = 0.47

Table S352.  Gene #36: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
NOTCH1 MUTATED 2 1 13
NOTCH1 WILD-TYPE 54 28 81
'KLF3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0423 (Fisher's exact test), Q value = 0.39

Table S353.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
KLF3 MUTATED 1 2 0
KLF3 WILD-TYPE 73 31 77

Figure S63.  Get High-res Image Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KLF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.68

Table S354.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
KLF3 MUTATED 0 3 0 0 0 0 0
KLF3 WILD-TYPE 37 39 2 41 37 17 9
'KLF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.98

Table S355.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
KLF3 MUTATED 3 0 0 0 0 0
KLF3 WILD-TYPE 71 14 42 29 9 16
'KLF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.64

Table S356.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
KLF3 MUTATED 3 0 0
KLF3 WILD-TYPE 65 20 96
'KLF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 0.97

Table S357.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
KLF3 MUTATED 3 0 0 0 0 0
KLF3 WILD-TYPE 68 15 10 18 28 42
'KLF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.81

Table S358.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
KLF3 MUTATED 2 1 0 0
KLF3 WILD-TYPE 61 25 62 33
'KLF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 0.87

Table S359.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
KLF3 MUTATED 2 0 1 0
KLF3 WILD-TYPE 63 67 34 12
'KLF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.66

Table S360.  Gene #37: 'KLF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
KLF3 MUTATED 2 1 0
KLF3 WILD-TYPE 54 28 94
'IL10RA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 0.99

Table S361.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
IL10RA MUTATED 2 0 1
IL10RA WILD-TYPE 72 33 76
'IL10RA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S362.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
IL10RA MUTATED 1 1 0 1 0 0 0
IL10RA WILD-TYPE 36 41 2 40 37 17 9
'IL10RA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.754 (Fisher's exact test), Q value = 0.99

Table S363.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
IL10RA MUTATED 1 1 1 0 0
IL10RA WILD-TYPE 25 27 29 34 8
'IL10RA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.357 (Fisher's exact test), Q value = 0.83

Table S364.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
IL10RA MUTATED 1 1 1 0 0
IL10RA WILD-TYPE 22 20 21 26 34
'IL10RA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.91

Table S365.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
IL10RA MUTATED 2 0 0 0 0 1
IL10RA WILD-TYPE 72 14 42 29 9 15
'IL10RA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 0.97

Table S366.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
IL10RA MUTATED 2 0 1
IL10RA WILD-TYPE 66 20 95
'IL10RA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.815 (Fisher's exact test), Q value = 0.99

Table S367.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
IL10RA MUTATED 2 0 0 0 1 0
IL10RA WILD-TYPE 69 15 10 18 27 42
'IL10RA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S368.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
IL10RA MUTATED 2 0 1 0
IL10RA WILD-TYPE 61 26 61 33
'IL10RA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.97

Table S369.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
IL10RA MUTATED 2 1 0 0
IL10RA WILD-TYPE 63 66 35 12
'IL10RA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.741 (Fisher's exact test), Q value = 0.99

Table S370.  Gene #38: 'IL10RA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
IL10RA MUTATED 1 1 1
IL10RA WILD-TYPE 55 28 93
'RAD17 MUTATION STATUS' versus 'CN_CNMF'

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

Table S371.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
RAD17 MUTATED 2 0 2
RAD17 WILD-TYPE 72 33 75
'RAD17 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.75

Table S372.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
RAD17 MUTATED 1 0 0 0 3 0 0
RAD17 WILD-TYPE 36 42 2 41 34 17 9
'RAD17 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 0.84

Table S373.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
RAD17 MUTATED 2 0 0 2 0
RAD17 WILD-TYPE 24 28 30 32 8
'RAD17 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 0.96

Table S374.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
RAD17 MUTATED 1 0 0 2 1
RAD17 WILD-TYPE 22 21 22 24 33
'RAD17 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.633 (Fisher's exact test), Q value = 0.96

Table S375.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
RAD17 MUTATED 1 1 1 1 0 0
RAD17 WILD-TYPE 73 13 41 28 9 16
'RAD17 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 0.99

Table S376.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
RAD17 MUTATED 1 0 3
RAD17 WILD-TYPE 67 20 93
'RAD17 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.78

Table S377.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
RAD17 MUTATED 1 1 1 0 0 1
RAD17 WILD-TYPE 70 14 9 18 28 41
'RAD17 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00618 (Fisher's exact test), Q value = 0.12

Table S378.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
RAD17 MUTATED 0 1 0 3
RAD17 WILD-TYPE 63 25 62 30

Figure S64.  Get High-res Image Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'RAD17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.69

Table S379.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
RAD17 MUTATED 0 2 1 1
RAD17 WILD-TYPE 65 65 34 11
'RAD17 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.84

Table S380.  Gene #39: 'RAD17 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
RAD17 MUTATED 0 1 3
RAD17 WILD-TYPE 56 28 91
'KPNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.7

Table S381.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
KPNB1 MUTATED 1 0 5
KPNB1 WILD-TYPE 73 33 72
'KPNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0875 (Fisher's exact test), Q value = 0.57

Table S382.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
KPNB1 MUTATED 0 1 0 4 0 0 1
KPNB1 WILD-TYPE 37 41 2 37 37 17 8
'KPNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.308 (Fisher's exact test), Q value = 0.81

Table S383.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
KPNB1 MUTATED 0 0 2 3 0
KPNB1 WILD-TYPE 26 28 28 31 8
'KPNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.657 (Fisher's exact test), Q value = 0.96

Table S384.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
KPNB1 MUTATED 0 0 1 2 2
KPNB1 WILD-TYPE 23 21 21 24 32
'KPNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.82

Table S385.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
KPNB1 MUTATED 1 1 1 2 0 1
KPNB1 WILD-TYPE 73 13 41 27 9 15
'KPNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.84

Table S386.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
KPNB1 MUTATED 1 0 5
KPNB1 WILD-TYPE 67 20 91
'KPNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.69

Table S387.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
KPNB1 MUTATED 1 1 0 1 2 0
KPNB1 WILD-TYPE 70 14 10 17 26 42
'KPNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 0.97

Table S388.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
KPNB1 MUTATED 1 0 3 1
KPNB1 WILD-TYPE 62 26 59 32
'KPNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S389.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
KPNB1 MUTATED 1 3 1 0
KPNB1 WILD-TYPE 64 64 34 12
'KPNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 0.95

Table S390.  Gene #40: 'KPNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
KPNB1 MUTATED 1 0 4
KPNB1 WILD-TYPE 55 29 90
'ZBED4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 0.84

Table S391.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ZBED4 MUTATED 1 2 2
ZBED4 WILD-TYPE 73 31 75
'ZBED4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.64 (Fisher's exact test), Q value = 0.96

Table S392.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
ZBED4 MUTATED 1 0 0 2 1 1 0
ZBED4 WILD-TYPE 36 42 2 39 36 16 9
'ZBED4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.83

Table S393.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
ZBED4 MUTATED 0 0 1 3 0
ZBED4 WILD-TYPE 26 28 29 31 8
'ZBED4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.801 (Fisher's exact test), Q value = 0.99

Table S394.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
ZBED4 MUTATED 0 0 1 1 2
ZBED4 WILD-TYPE 23 21 21 25 32
'ZBED4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.38

Table S395.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ZBED4 MUTATED 0 1 4 0 0 0
ZBED4 WILD-TYPE 74 13 38 29 9 16

Figure S65.  Get High-res Image Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZBED4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.668 (Fisher's exact test), Q value = 0.96

Table S396.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ZBED4 MUTATED 1 0 4
ZBED4 WILD-TYPE 67 20 92
'ZBED4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.095 (Fisher's exact test), Q value = 0.59

Table S397.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ZBED4 MUTATED 0 1 1 0 1 2
ZBED4 WILD-TYPE 71 14 9 18 27 40
'ZBED4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 0.89

Table S398.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ZBED4 MUTATED 1 0 2 2
ZBED4 WILD-TYPE 62 26 60 31
'ZBED4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 1

Table S399.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ZBED4 MUTATED 1 3 1 0
ZBED4 WILD-TYPE 64 64 34 12
'ZBED4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 0.95

Table S400.  Gene #41: 'ZBED4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ZBED4 MUTATED 1 0 4
ZBED4 WILD-TYPE 55 29 90
'NAA16 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S401.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
NAA16 MUTATED 3 1 2
NAA16 WILD-TYPE 71 32 75
'NAA16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.89

Table S402.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
NAA16 MUTATED 1 2 0 2 0 0 1
NAA16 WILD-TYPE 36 40 2 39 37 17 8
'NAA16 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 0.96

Table S403.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
NAA16 MUTATED 2 0 1 1 0
NAA16 WILD-TYPE 24 28 29 33 8
'NAA16 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.87

Table S404.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
NAA16 MUTATED 1 0 2 0 1
NAA16 WILD-TYPE 22 21 20 26 33
'NAA16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.86

Table S405.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
NAA16 MUTATED 2 0 1 1 0 2
NAA16 WILD-TYPE 72 14 41 28 9 14
'NAA16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.231 (Fisher's exact test), Q value = 0.75

Table S406.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
NAA16 MUTATED 2 2 2
NAA16 WILD-TYPE 66 18 94
'NAA16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S407.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
NAA16 MUTATED 3 1 0 0 1 1
NAA16 WILD-TYPE 68 14 10 18 27 41
'NAA16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0924 (Fisher's exact test), Q value = 0.58

Table S408.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
NAA16 MUTATED 1 3 2 0
NAA16 WILD-TYPE 62 23 60 33
'NAA16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.79

Table S409.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
NAA16 MUTATED 1 2 3 0
NAA16 WILD-TYPE 64 65 32 12
'NAA16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.84

Table S410.  Gene #42: 'NAA16 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
NAA16 MUTATED 1 2 3
NAA16 WILD-TYPE 55 27 91
'CNNM2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 0.99

Table S411.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
CNNM2 MUTATED 4 1 2
CNNM2 WILD-TYPE 70 32 75
'CNNM2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 0.99

Table S412.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
CNNM2 MUTATED 3 2 0 1 1 0 0
CNNM2 WILD-TYPE 34 40 2 40 36 17 9
'CNNM2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.79

Table S413.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
CNNM2 MUTATED 3 2 0 1 0
CNNM2 WILD-TYPE 23 26 30 33 8
'CNNM2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.202 (Fisher's exact test), Q value = 0.71

Table S414.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
CNNM2 MUTATED 3 1 1 1 0
CNNM2 WILD-TYPE 20 20 21 25 34
'CNNM2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S415.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
CNNM2 MUTATED 5 0 1 1 0 0
CNNM2 WILD-TYPE 69 14 41 28 9 16
'CNNM2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.71

Table S416.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
CNNM2 MUTATED 5 0 2
CNNM2 WILD-TYPE 63 20 94
'CNNM2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 0.96

Table S417.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
CNNM2 MUTATED 5 0 0 1 0 1
CNNM2 WILD-TYPE 66 15 10 17 28 41
'CNNM2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.582 (Fisher's exact test), Q value = 0.95

Table S418.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
CNNM2 MUTATED 4 1 1 1
CNNM2 WILD-TYPE 59 25 61 32
'CNNM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.763 (Fisher's exact test), Q value = 0.99

Table S419.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
CNNM2 MUTATED 4 2 1 0
CNNM2 WILD-TYPE 61 65 34 12
'CNNM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.79

Table S420.  Gene #43: 'CNNM2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
CNNM2 MUTATED 4 1 2
CNNM2 WILD-TYPE 52 28 92
'HLA-B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0196 (Fisher's exact test), Q value = 0.28

Table S421.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
HLA-B MUTATED 4 3 0
HLA-B WILD-TYPE 70 30 77

Figure S66.  Get High-res Image Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HLA-B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S422.  Gene #44: '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 37 42 2 41 37 17 9
HLA-B MUTATED 1 2 0 1 2 1 0
HLA-B WILD-TYPE 36 40 2 40 35 16 9
'HLA-B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.79

Table S423.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
HLA-B MUTATED 2 2 0 1 1
HLA-B WILD-TYPE 24 26 30 33 7
'HLA-B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 0.81

Table S424.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
HLA-B MUTATED 2 2 0 0 2
HLA-B WILD-TYPE 21 19 22 26 32
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.654 (Fisher's exact test), Q value = 0.96

Table S425.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
HLA-B MUTATED 3 0 3 0 0 1
HLA-B WILD-TYPE 71 14 39 29 9 15
'HLA-B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S426.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
HLA-B MUTATED 3 0 4
HLA-B WILD-TYPE 65 20 92
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.88

Table S427.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
HLA-B MUTATED 3 0 0 0 0 4
HLA-B WILD-TYPE 68 15 10 18 28 38
'HLA-B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 0.76

Table S428.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
HLA-B MUTATED 3 0 1 3
HLA-B WILD-TYPE 60 26 61 30
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 0.99

Table S429.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
HLA-B MUTATED 3 3 0 0
HLA-B WILD-TYPE 62 64 35 12
'HLA-B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 0.96

Table S430.  Gene #44: 'HLA-B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
HLA-B MUTATED 3 0 3
HLA-B WILD-TYPE 53 29 91
'PLXNB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.531 (Fisher's exact test), Q value = 0.93

Table S431.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PLXNB2 MUTATED 3 3 6
PLXNB2 WILD-TYPE 71 30 71
'PLXNB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S432.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
PLXNB2 MUTATED 3 3 0 4 1 1 0
PLXNB2 WILD-TYPE 34 39 2 37 36 16 9
'PLXNB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.899 (Fisher's exact test), Q value = 1

Table S433.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PLXNB2 MUTATED 1 2 2 1 0
PLXNB2 WILD-TYPE 25 26 28 33 8
'PLXNB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.656 (Fisher's exact test), Q value = 0.96

Table S434.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PLXNB2 MUTATED 2 0 1 2 1
PLXNB2 WILD-TYPE 21 21 21 24 33
'PLXNB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S435.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PLXNB2 MUTATED 4 1 3 2 0 2
PLXNB2 WILD-TYPE 70 13 39 27 9 14
'PLXNB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S436.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PLXNB2 MUTATED 5 1 6
PLXNB2 WILD-TYPE 63 19 90
'PLXNB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S437.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PLXNB2 MUTATED 6 0 0 1 1 4
PLXNB2 WILD-TYPE 65 15 10 17 27 38
'PLXNB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 0.99

Table S438.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PLXNB2 MUTATED 5 1 5 1
PLXNB2 WILD-TYPE 58 25 57 32
'PLXNB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.827 (Fisher's exact test), Q value = 0.99

Table S439.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PLXNB2 MUTATED 4 5 1 0
PLXNB2 WILD-TYPE 61 62 34 12
'PLXNB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S440.  Gene #45: 'PLXNB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PLXNB2 MUTATED 3 1 6
PLXNB2 WILD-TYPE 53 28 88
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.693 (Fisher's exact test), Q value = 0.97

Table S441.  Gene #46: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PTEN MUTATED 2 2 3
PTEN WILD-TYPE 72 31 74
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 0.96

Table S442.  Gene #46: '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 37 42 2 41 37 17 9
PTEN MUTATED 0 2 0 2 3 0 0
PTEN WILD-TYPE 37 40 2 39 34 17 9
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.88

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PTEN MUTATED 0 1 1 1 1
PTEN WILD-TYPE 26 27 29 33 7
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.71

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PTEN MUTATED 0 1 0 0 3
PTEN WILD-TYPE 23 20 22 26 31
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.75 (Fisher's exact test), Q value = 0.99

Table S445.  Gene #46: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PTEN MUTATED 2 0 3 1 0 1
PTEN WILD-TYPE 72 14 39 28 9 15
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 0.86

Table S446.  Gene #46: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PTEN MUTATED 1 1 5
PTEN WILD-TYPE 67 19 91
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.84

Table S447.  Gene #46: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PTEN MUTATED 2 0 0 1 0 4
PTEN WILD-TYPE 69 15 10 17 28 38
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 0.98

Table S448.  Gene #46: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PTEN MUTATED 2 0 3 2
PTEN WILD-TYPE 61 26 59 31
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.546 (Fisher's exact test), Q value = 0.94

Table S449.  Gene #46: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PTEN MUTATED 2 4 0 0
PTEN WILD-TYPE 63 63 35 12
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 0.99

Table S450.  Gene #46: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PTEN MUTATED 2 0 4
PTEN WILD-TYPE 54 29 90
'CPT1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 0.96

Table S451.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
CPT1B MUTATED 1 1 3
CPT1B WILD-TYPE 73 32 74
'CPT1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S452.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
CPT1B MUTATED 0 2 0 2 1 0 0
CPT1B WILD-TYPE 37 40 2 39 36 17 9
'CPT1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.84

Table S453.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
CPT1B MUTATED 1 1 0 1 1
CPT1B WILD-TYPE 25 27 30 33 7
'CPT1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.559 (Fisher's exact test), Q value = 0.94

Table S454.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
CPT1B MUTATED 2 0 0 1 1
CPT1B WILD-TYPE 21 21 22 25 33
'CPT1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 0.99

Table S455.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
CPT1B MUTATED 2 0 1 2 0 0
CPT1B WILD-TYPE 72 14 41 27 9 16
'CPT1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S456.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
CPT1B MUTATED 2 0 3
CPT1B WILD-TYPE 66 20 93
'CPT1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S457.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
CPT1B MUTATED 2 0 0 1 1 1
CPT1B WILD-TYPE 69 15 10 17 27 41
'CPT1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S458.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
CPT1B MUTATED 2 0 2 1
CPT1B WILD-TYPE 61 26 60 32
'CPT1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.87

Table S459.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
CPT1B MUTATED 2 1 1 1
CPT1B WILD-TYPE 63 66 34 11
'CPT1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S460.  Gene #47: 'CPT1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
CPT1B MUTATED 2 0 3
CPT1B WILD-TYPE 54 29 91
'CAMTA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.93

Table S461.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
CAMTA1 MUTATED 3 3 3
CAMTA1 WILD-TYPE 71 30 74
'CAMTA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.62

Table S462.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
CAMTA1 MUTATED 0 6 0 1 2 0 0
CAMTA1 WILD-TYPE 37 36 2 40 35 17 9
'CAMTA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.62

Table S463.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
CAMTA1 MUTATED 4 1 0 1 0
CAMTA1 WILD-TYPE 22 27 30 33 8
'CAMTA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0474 (Fisher's exact test), Q value = 0.41

Table S464.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
CAMTA1 MUTATED 4 0 0 1 1
CAMTA1 WILD-TYPE 19 21 22 25 33

Figure S67.  Get High-res Image Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CAMTA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S465.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
CAMTA1 MUTATED 5 0 1 2 0 1
CAMTA1 WILD-TYPE 69 14 41 27 9 15
'CAMTA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.84

Table S466.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
CAMTA1 MUTATED 5 1 3
CAMTA1 WILD-TYPE 63 19 93
'CAMTA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.66

Table S467.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
CAMTA1 MUTATED 6 1 1 1 0 0
CAMTA1 WILD-TYPE 65 14 9 17 28 42
'CAMTA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.762 (Fisher's exact test), Q value = 0.99

Table S468.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
CAMTA1 MUTATED 4 2 2 1
CAMTA1 WILD-TYPE 59 24 60 32
'CAMTA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.96

Table S469.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
CAMTA1 MUTATED 3 2 2 1
CAMTA1 WILD-TYPE 62 65 33 11
'CAMTA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 0.96

Table S470.  Gene #48: 'CAMTA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
CAMTA1 MUTATED 3 2 3
CAMTA1 WILD-TYPE 53 27 91
'OTUD7B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.62

Table S471.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
OTUD7B MUTATED 3 3 1
OTUD7B WILD-TYPE 71 30 76
'OTUD7B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.84

Table S472.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
OTUD7B MUTATED 0 4 0 1 1 1 0
OTUD7B WILD-TYPE 37 38 2 40 36 16 9
'OTUD7B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S473.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
OTUD7B MUTATED 1 1 1 1 0
OTUD7B WILD-TYPE 25 27 29 33 8
'OTUD7B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.871 (Fisher's exact test), Q value = 1

Table S474.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
OTUD7B MUTATED 1 1 1 0 1
OTUD7B WILD-TYPE 22 20 21 26 33
'OTUD7B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.82

Table S475.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
OTUD7B MUTATED 4 0 0 1 1 1
OTUD7B WILD-TYPE 70 14 42 28 8 15
'OTUD7B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.525 (Fisher's exact test), Q value = 0.93

Table S476.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
OTUD7B MUTATED 4 0 3
OTUD7B WILD-TYPE 64 20 93
'OTUD7B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 0.84

Table S477.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
OTUD7B MUTATED 4 1 0 0 2 0
OTUD7B WILD-TYPE 67 14 10 18 26 42
'OTUD7B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S478.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
OTUD7B MUTATED 3 1 2 1
OTUD7B WILD-TYPE 60 25 60 32
'OTUD7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.477 (Fisher's exact test), Q value = 0.89

Table S479.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
OTUD7B MUTATED 4 1 2 0
OTUD7B WILD-TYPE 61 66 33 12
'OTUD7B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S480.  Gene #49: 'OTUD7B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
OTUD7B MUTATED 3 1 3
OTUD7B WILD-TYPE 53 28 91
'ARRB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 0.98

Table S481.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
ARRB1 MUTATED 3 0 2
ARRB1 WILD-TYPE 71 33 75
'ARRB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.84

Table S482.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
ARRB1 MUTATED 0 3 0 2 0 0 0
ARRB1 WILD-TYPE 37 39 2 39 37 17 9
'ARRB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 0.94

Table S483.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
ARRB1 MUTATED 1 2 1 0 0
ARRB1 WILD-TYPE 25 26 29 34 8
'ARRB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.71

Table S484.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
ARRB1 MUTATED 1 2 0 1 0
ARRB1 WILD-TYPE 22 19 22 25 34
'ARRB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.413 (Fisher's exact test), Q value = 0.84

Table S485.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
ARRB1 MUTATED 2 1 0 1 0 1
ARRB1 WILD-TYPE 72 13 42 28 9 15
'ARRB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.109 (Fisher's exact test), Q value = 0.62

Table S486.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
ARRB1 MUTATED 1 2 2
ARRB1 WILD-TYPE 67 18 94
'ARRB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.662 (Fisher's exact test), Q value = 0.96

Table S487.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
ARRB1 MUTATED 3 0 0 1 1 0
ARRB1 WILD-TYPE 68 15 10 17 27 42
'ARRB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.747 (Fisher's exact test), Q value = 0.99

Table S488.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
ARRB1 MUTATED 3 0 1 1
ARRB1 WILD-TYPE 60 26 61 32
'ARRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 0.99

Table S489.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
ARRB1 MUTATED 3 1 1 0
ARRB1 WILD-TYPE 62 66 34 12
'ARRB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.87

Table S490.  Gene #50: 'ARRB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
ARRB1 MUTATED 3 0 2
ARRB1 WILD-TYPE 53 29 92
'KIAA1704 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0844 (Fisher's exact test), Q value = 0.57

Table S491.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
KIAA1704 MUTATED 0 2 1
KIAA1704 WILD-TYPE 74 31 76
'KIAA1704 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 0.99

Table S492.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
KIAA1704 MUTATED 0 2 0 1 0 0 0
KIAA1704 WILD-TYPE 37 40 2 40 37 17 9
'KIAA1704 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 0.99

Table S493.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
KIAA1704 MUTATED 2 0 0 1 0 0
KIAA1704 WILD-TYPE 72 14 42 28 9 16
'KIAA1704 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S494.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
KIAA1704 MUTATED 2 0 1
KIAA1704 WILD-TYPE 66 20 95
'KIAA1704 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S495.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
KIAA1704 MUTATED 2 0 0 0 0 1
KIAA1704 WILD-TYPE 69 15 10 18 28 41
'KIAA1704 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S496.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
KIAA1704 MUTATED 2 0 1 0
KIAA1704 WILD-TYPE 61 26 61 33
'KIAA1704 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.97

Table S497.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
KIAA1704 MUTATED 2 1 0 0
KIAA1704 WILD-TYPE 63 66 35 12
'KIAA1704 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 0.95

Table S498.  Gene #51: 'KIAA1704 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
KIAA1704 MUTATED 2 0 1
KIAA1704 WILD-TYPE 54 29 93
'RNF169 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.9

Table S499.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
RNF169 MUTATED 4 0 2
RNF169 WILD-TYPE 70 33 75
'RNF169 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.981 (Fisher's exact test), Q value = 1

Table S500.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
RNF169 MUTATED 2 2 0 1 1 0 0
RNF169 WILD-TYPE 35 40 2 40 36 17 9
'RNF169 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.715 (Fisher's exact test), Q value = 0.98

Table S501.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
RNF169 MUTATED 1 0 2 1 0
RNF169 WILD-TYPE 25 28 28 33 8
'RNF169 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.406 (Fisher's exact test), Q value = 0.84

Table S502.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
RNF169 MUTATED 1 0 1 2 0
RNF169 WILD-TYPE 22 21 21 24 34
'RNF169 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.967 (Fisher's exact test), Q value = 1

Table S503.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
RNF169 MUTATED 4 0 1 1 0 0
RNF169 WILD-TYPE 70 14 41 28 9 16
'RNF169 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.81

Table S504.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
RNF169 MUTATED 4 0 2
RNF169 WILD-TYPE 64 20 94
'RNF169 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S505.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
RNF169 MUTATED 3 0 0 0 1 2
RNF169 WILD-TYPE 68 15 10 18 27 40
'RNF169 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.516 (Fisher's exact test), Q value = 0.92

Table S506.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
RNF169 MUTATED 2 2 1 1
RNF169 WILD-TYPE 61 24 61 32
'RNF169 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S507.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
RNF169 MUTATED 2 2 2 0
RNF169 WILD-TYPE 63 65 33 12
'RNF169 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.311 (Fisher's exact test), Q value = 0.81

Table S508.  Gene #52: 'RNF169 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
RNF169 MUTATED 2 2 2
RNF169 WILD-TYPE 54 27 92
'RBPJL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 0.96

Table S509.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
RBPJL MUTATED 2 2 2
RBPJL WILD-TYPE 72 31 75
'RBPJL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.194 (Fisher's exact test), Q value = 0.71

Table S510.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
RBPJL MUTATED 0 2 0 0 2 2 0
RBPJL WILD-TYPE 37 40 2 41 35 15 9
'RBPJL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.69

Table S511.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
RBPJL MUTATED 0 3 0 1 0
RBPJL WILD-TYPE 26 25 30 33 8
'RBPJL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.68

Table S512.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
RBPJL MUTATED 0 2 0 0 2
RBPJL WILD-TYPE 23 19 22 26 32
'RBPJL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.82

Table S513.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
RBPJL MUTATED 2 0 3 0 1 0
RBPJL WILD-TYPE 72 14 39 29 8 16
'RBPJL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S514.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
RBPJL MUTATED 2 0 4
RBPJL WILD-TYPE 66 20 92
'RBPJL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 0.99

Table S515.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
RBPJL MUTATED 2 0 0 0 1 3
RBPJL WILD-TYPE 69 15 10 18 27 39
'RBPJL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.715 (Fisher's exact test), Q value = 0.98

Table S516.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
RBPJL MUTATED 2 0 2 2
RBPJL WILD-TYPE 61 26 60 31
'RBPJL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S517.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
RBPJL MUTATED 2 3 1 0
RBPJL WILD-TYPE 63 64 34 12
'RBPJL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 0.99

Table S518.  Gene #53: 'RBPJL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
RBPJL MUTATED 2 0 4
RBPJL WILD-TYPE 54 29 90
'MGAT5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.707 (Fisher's exact test), Q value = 0.98

Table S519.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
MGAT5B MUTATED 2 2 4
MGAT5B WILD-TYPE 72 31 73
'MGAT5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.78

Table S520.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
MGAT5B MUTATED 1 3 0 0 4 0 0
MGAT5B WILD-TYPE 36 39 2 41 33 17 9
'MGAT5B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S521.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
MGAT5B MUTATED 0 1 1 2 0
MGAT5B WILD-TYPE 26 27 29 32 8
'MGAT5B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.631 (Fisher's exact test), Q value = 0.96

Table S522.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
MGAT5B MUTATED 1 0 0 2 1
MGAT5B WILD-TYPE 22 21 22 24 33
'MGAT5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 0.92

Table S523.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
MGAT5B MUTATED 4 0 4 0 0 0
MGAT5B WILD-TYPE 70 14 38 29 9 16
'MGAT5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S524.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
MGAT5B MUTATED 3 1 4
MGAT5B WILD-TYPE 65 19 92
'MGAT5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.986 (Fisher's exact test), Q value = 1

Table S525.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
MGAT5B MUTATED 3 1 0 1 1 2
MGAT5B WILD-TYPE 68 14 10 17 27 40
'MGAT5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 0.96

Table S526.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
MGAT5B MUTATED 4 0 2 2
MGAT5B WILD-TYPE 59 26 60 31
'MGAT5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.65

Table S527.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
MGAT5B MUTATED 3 3 0 2
MGAT5B WILD-TYPE 62 64 35 10
'MGAT5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 0.81

Table S528.  Gene #54: 'MGAT5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
MGAT5B MUTATED 4 0 4
MGAT5B WILD-TYPE 52 29 90
'LRRC32 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.71

Table S529.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
LRRC32 MUTATED 6 0 3
LRRC32 WILD-TYPE 68 33 74
'LRRC32 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.84

Table S530.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
LRRC32 MUTATED 1 4 0 0 3 1 0
LRRC32 WILD-TYPE 36 38 2 41 34 16 9
'LRRC32 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.578 (Fisher's exact test), Q value = 0.95

Table S531.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
LRRC32 MUTATED 3 1 3 1 0
LRRC32 WILD-TYPE 23 27 27 33 8
'LRRC32 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S532.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
LRRC32 MUTATED 2 1 2 1 2
LRRC32 WILD-TYPE 21 20 20 25 32
'LRRC32 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S533.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
LRRC32 MUTATED 4 0 2 2 0 1
LRRC32 WILD-TYPE 70 14 40 27 9 15
'LRRC32 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.88

Table S534.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
LRRC32 MUTATED 3 2 4
LRRC32 WILD-TYPE 65 18 92
'LRRC32 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.98

Table S535.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
LRRC32 MUTATED 3 1 1 0 2 2
LRRC32 WILD-TYPE 68 14 9 18 26 40
'LRRC32 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.806 (Fisher's exact test), Q value = 0.99

Table S536.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
LRRC32 MUTATED 3 2 2 2
LRRC32 WILD-TYPE 60 24 60 31
'LRRC32 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.87

Table S537.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
LRRC32 MUTATED 3 2 3 1
LRRC32 WILD-TYPE 62 65 32 11
'LRRC32 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 0.99

Table S538.  Gene #55: 'LRRC32 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
LRRC32 MUTATED 3 2 4
LRRC32 WILD-TYPE 53 27 90
'TCHH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.86

Table S539.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
TCHH MUTATED 4 4 6
TCHH WILD-TYPE 70 29 71
'TCHH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0146 (Fisher's exact test), Q value = 0.23

Table S540.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
TCHH MUTATED 1 5 1 6 0 0 1
TCHH WILD-TYPE 36 37 1 35 37 17 8

Figure S68.  Get High-res Image Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TCHH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 0.93

Table S541.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
TCHH MUTATED 0 2 2 2 1
TCHH WILD-TYPE 26 26 28 32 7
'TCHH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.773 (Fisher's exact test), Q value = 0.99

Table S542.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
TCHH MUTATED 1 1 1 3 1
TCHH WILD-TYPE 22 20 21 23 33
'TCHH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.81

Table S543.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
TCHH MUTATED 6 1 1 5 0 1
TCHH WILD-TYPE 68 13 41 24 9 15
'TCHH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.554 (Fisher's exact test), Q value = 0.94

Table S544.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
TCHH MUTATED 6 0 8
TCHH WILD-TYPE 62 20 88
'TCHH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 0.96

Table S545.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
TCHH MUTATED 5 3 0 1 2 3
TCHH WILD-TYPE 66 12 10 17 26 39
'TCHH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.81

Table S546.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
TCHH MUTATED 3 3 7 1
TCHH WILD-TYPE 60 23 55 32
'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S547.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
TCHH MUTATED 5 6 2 0
TCHH WILD-TYPE 60 61 33 12
'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 0.96

Table S548.  Gene #56: 'TCHH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
TCHH MUTATED 3 3 7
TCHH WILD-TYPE 53 26 87
'SLC22A2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.7

Table S549.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
SLC22A2 MUTATED 3 1 0
SLC22A2 WILD-TYPE 71 32 77
'SLC22A2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.84

Table S550.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
SLC22A2 MUTATED 2 1 0 0 0 1 0
SLC22A2 WILD-TYPE 35 41 2 41 37 16 9
'SLC22A2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.81

Table S551.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
SLC22A2 MUTATED 3 0 0 0 1 0
SLC22A2 WILD-TYPE 71 14 42 29 8 16
'SLC22A2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 0.86

Table S552.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
SLC22A2 MUTATED 3 0 1
SLC22A2 WILD-TYPE 65 20 95
'SLC22A2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 0.99

Table S553.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
SLC22A2 MUTATED 3 0 0 0 1 0
SLC22A2 WILD-TYPE 68 15 10 18 27 42
'SLC22A2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.542 (Fisher's exact test), Q value = 0.93

Table S554.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
SLC22A2 MUTATED 3 0 1 0
SLC22A2 WILD-TYPE 60 26 61 33
'SLC22A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.79

Table S555.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
SLC22A2 MUTATED 3 0 1 0
SLC22A2 WILD-TYPE 62 67 34 12
'SLC22A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.73

Table S556.  Gene #57: 'SLC22A2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
SLC22A2 MUTATED 3 0 1
SLC22A2 WILD-TYPE 53 29 93
'PCDH15 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.98

Table S557.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
PCDH15 MUTATED 10 4 7
PCDH15 WILD-TYPE 64 29 70
'PCDH15 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 0.99

Table S558.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
PCDH15 MUTATED 5 7 0 5 3 1 0
PCDH15 WILD-TYPE 32 35 2 36 34 16 9
'PCDH15 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.96

Table S559.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
PCDH15 MUTATED 4 4 4 2 0
PCDH15 WILD-TYPE 22 24 26 32 8
'PCDH15 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.84

Table S560.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
PCDH15 MUTATED 5 2 3 1 3
PCDH15 WILD-TYPE 18 19 19 25 31
'PCDH15 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.84

Table S561.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
PCDH15 MUTATED 11 2 3 1 1 3
PCDH15 WILD-TYPE 63 12 39 28 8 13
'PCDH15 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.66

Table S562.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
PCDH15 MUTATED 12 1 8
PCDH15 WILD-TYPE 56 19 88
'PCDH15 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S563.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
PCDH15 MUTATED 10 2 1 2 3 3
PCDH15 WILD-TYPE 61 13 9 16 25 39
'PCDH15 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.71

Table S564.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
PCDH15 MUTATED 10 3 3 5
PCDH15 WILD-TYPE 53 23 59 28
'PCDH15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.606 (Fisher's exact test), Q value = 0.96

Table S565.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
PCDH15 MUTATED 10 8 2 1
PCDH15 WILD-TYPE 55 59 33 11
'PCDH15 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.82

Table S566.  Gene #58: 'PCDH15 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
PCDH15 MUTATED 9 4 8
PCDH15 WILD-TYPE 47 25 86
'KIAA1549 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0571 (Fisher's exact test), Q value = 0.46

Table S567.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
KIAA1549 MUTATED 1 4 3
KIAA1549 WILD-TYPE 73 29 74
'KIAA1549 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 0.99

Table S568.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
KIAA1549 MUTATED 1 2 0 1 3 1 0
KIAA1549 WILD-TYPE 36 40 2 40 34 16 9
'KIAA1549 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.238 (Fisher's exact test), Q value = 0.75

Table S569.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
KIAA1549 MUTATED 0 2 0 3 0
KIAA1549 WILD-TYPE 26 26 30 31 8
'KIAA1549 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 0.99

Table S570.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
KIAA1549 MUTATED 1 1 0 2 1
KIAA1549 WILD-TYPE 22 20 22 24 33
'KIAA1549 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.96

Table S571.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
KIAA1549 MUTATED 3 0 3 1 1 0
KIAA1549 WILD-TYPE 71 14 39 28 8 16
'KIAA1549 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.671 (Fisher's exact test), Q value = 0.96

Table S572.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
KIAA1549 MUTATED 4 0 4
KIAA1549 WILD-TYPE 64 20 92
'KIAA1549 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.985 (Fisher's exact test), Q value = 1

Table S573.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
KIAA1549 MUTATED 3 1 0 1 1 2
KIAA1549 WILD-TYPE 68 14 10 17 27 40
'KIAA1549 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.954 (Fisher's exact test), Q value = 1

Table S574.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
KIAA1549 MUTATED 3 1 2 2
KIAA1549 WILD-TYPE 60 25 60 31
'KIAA1549 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.716 (Fisher's exact test), Q value = 0.98

Table S575.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
KIAA1549 MUTATED 2 3 1 1
KIAA1549 WILD-TYPE 63 64 34 11
'KIAA1549 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S576.  Gene #59: 'KIAA1549 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
KIAA1549 MUTATED 3 1 3
KIAA1549 WILD-TYPE 53 28 91
'SETBP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 0.95

Table S577.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 74 33 77
SETBP1 MUTATED 7 3 4
SETBP1 WILD-TYPE 67 30 73
'SETBP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.71

Table S578.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 37 42 2 41 37 17 9
SETBP1 MUTATED 3 7 0 1 1 2 0
SETBP1 WILD-TYPE 34 35 2 40 36 15 9
'SETBP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.88

Table S579.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 28 30 34 8
SETBP1 MUTATED 1 3 4 1 0
SETBP1 WILD-TYPE 25 25 26 33 8
'SETBP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.41

Table S580.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 23 21 22 26 34
SETBP1 MUTATED 1 3 4 0 1
SETBP1 WILD-TYPE 22 18 18 26 33

Figure S69.  Get High-res Image Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SETBP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0717 (Fisher's exact test), Q value = 0.52

Table S581.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 74 14 42 29 9 16
SETBP1 MUTATED 9 1 1 0 0 3
SETBP1 WILD-TYPE 65 13 41 29 9 13
'SETBP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0865 (Fisher's exact test), Q value = 0.57

Table S582.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 20 96
SETBP1 MUTATED 9 1 4
SETBP1 WILD-TYPE 59 19 92
'SETBP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.79

Table S583.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 71 15 10 18 28 42
SETBP1 MUTATED 8 2 0 0 3 1
SETBP1 WILD-TYPE 63 13 10 18 25 41
'SETBP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.69

Table S584.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 63 26 62 33
SETBP1 MUTATED 7 3 4 0
SETBP1 WILD-TYPE 56 23 58 33
'SETBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.41

Table S585.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 67 35 12
SETBP1 MUTATED 8 1 4 1
SETBP1 WILD-TYPE 57 66 31 11

Figure S70.  Get High-res Image Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SETBP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.66

Table S586.  Gene #60: 'SETBP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 56 29 94
SETBP1 MUTATED 7 3 4
SETBP1 WILD-TYPE 49 26 90
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/ESCA-TP/22588513/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/ESCA-TP/22541001/ESCA-TP.transferedmergedcluster.txt

  • Number of patients = 185

  • Number of significantly mutated genes = 60

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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