Correlation between gene mutation status and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
28 January 2016  |  analyses__2016_01_28
Maintainer Information
Citation Information
doi:10.7908/C1FJ2G6V
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1FJ2G6V
Overview
Introduction

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

Summary

Testing the association between mutation status of 99 genes and 8 molecular subtypes across 373 patients, 51 significant findings detected with P value < 0.05 and Q value < 0.25.

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

  • CTNNB1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • AXIN1 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • RB1 mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

  • BAP1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • APOB mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • TSC2 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • TCHH mutation correlated to 'CN_CNMF'.

  • GPR110 mutation correlated to 'MIRSEQ_CHIERARCHICAL' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • KRTAP5-7 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • PLA2G3 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • NUCB2 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • C1ORF125 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • SPHK1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • PBRM1 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • SGK269 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • CBX4 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • CRIP3 mutation correlated to 'CN_CNMF'.

  • FOXK2 mutation correlated to 'MRNASEQ_CNMF'.

  • C10ORF28 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 99 genes and 8 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 51 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		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
CTNNB1 97 (26%) 276 0.00025
(0.011) 		1e-05
(0.000609) 		1e-05
(0.000609) 		1e-05
(0.000609) 		1e-05
(0.000609) 		1e-05
(0.000609) 		1e-05
(0.000609) 		1e-05
(0.000609)
TP53 114 (31%) 259 1e-05
(0.000609) 		0.157
(0.679) 		1e-05
(0.000609) 		3e-05
(0.00158) 		0.0002
(0.00932) 		0.00018
(0.00891) 		0.00391
(0.102) 		0.00047
(0.0186)
BAP1 21 (6%) 352 0.714
(0.919) 		1e-05
(0.000609) 		3e-05
(0.00158) 		1e-05
(0.000609) 		0.00116
(0.0399) 		0.00174
(0.0551) 		0.00359
(0.0989) 		0.00052
(0.0196)
AXIN1 24 (6%) 349 0.00362
(0.0989) 		0.0299
(0.382) 		1e-05
(0.000609) 		0.00947
(0.198) 		1e-05
(0.000609) 		0.035
(0.403) 		0.00521
(0.125) 		0.843
(0.959)
APOB 39 (10%) 334 0.226
(0.725) 		0.544
(0.851) 		0.0142
(0.242) 		0.0119
(0.219) 		0.9
(0.981) 		0.215
(0.721) 		0.0231
(0.327) 		0.0157
(0.244)
PBRM1 9 (2%) 364 0.431
(0.819) 		0.205
(0.717) 		0.00951
(0.198) 		0.0077
(0.174) 		0.279
(0.766) 		0.0113
(0.218) 		0.519
(0.849) 		0.166
(0.692)
RB1 21 (6%) 352 0.0537
(0.512) 		0.0145
(0.242) 		0.0387
(0.415) 		0.533
(0.851) 		0.0117
(0.219) 		0.518
(0.849) 		0.407
(0.81) 		0.445
(0.819)
TSC2 12 (3%) 361 0.0549
(0.512) 		0.0356
(0.403) 		0.00027
(0.0113) 		0.00062
(0.0223) 		0.481
(0.819) 		0.83
(0.958) 		0.491
(0.82) 		0.579
(0.883)
GPR110 6 (2%) 367 0.77
(0.937) 		0.442
(0.819) 		0.0364
(0.403) 		0.0548
(0.512) 		0.0652
(0.552) 		0.00672
(0.157) 		0.726
(0.919) 		0.0052
(0.125)
CBX4 6 (2%) 367 0.144
(0.677) 		0.336
(0.788) 		0.00226
(0.0688) 		0.00398
(0.102) 		0.333
(0.788) 		0.487
(0.82) 		0.0538
(0.512) 		0.32
(0.784)
TCHH 17 (5%) 356 0.00974
(0.198) 		0.0771
(0.578) 		0.697
(0.919) 		0.971
(1.00) 		0.769
(0.937) 		0.802
(0.95) 		0.332
(0.788) 		0.947
(1.00)
KRTAP5-7 4 (1%) 369 0.463
(0.819) 		0.467
(0.819) 		0.918
(0.986) 		0.0779
(0.578) 		0.17
(0.692) 		0.528
(0.851) 		0.00323
(0.0947) 		0.256
(0.764)
PLA2G3 6 (2%) 367 0.391
(0.801) 		0.0974
(0.616) 		0.164
(0.692) 		0.126
(0.663) 		0.372
(0.795) 		0.0133
(0.234) 		0.723
(0.919) 		0.0366
(0.403)
NUCB2 3 (1%) 370 0.617
(0.898) 		0.472
(0.819) 		0.397
(0.802) 		0.445
(0.819) 		0.0147
(0.242) 		0.843
(0.959)
C1ORF125 11 (3%) 362 0.336
(0.788) 		0.0673
(0.552) 		0.677
(0.918) 		0.813
(0.95) 		0.185
(0.711) 		0.0155
(0.244) 		0.0799
(0.586) 		0.226
(0.725)
SPHK1 6 (2%) 367 0.395
(0.801) 		0.77
(0.937) 		0.0365
(0.403) 		0.0107
(0.211) 		0.524
(0.851) 		0.0937
(0.612) 		0.116
(0.662) 		0.105
(0.633)
SGK269 8 (2%) 365 1
(1.00) 		0.0897
(0.606) 		0.274
(0.766) 		0.643
(0.91) 		0.584
(0.886) 		0.33
(0.788) 		0.224
(0.725) 		0.0156
(0.244)
CRIP3 6 (2%) 367 0.00148
(0.0488) 		0.15
(0.677) 		0.38
(0.795) 		0.771
(0.937) 		0.394
(0.801) 		0.394
(0.801) 		0.255
(0.764) 		0.123
(0.662)
FOXK2 6 (2%) 367 1
(1.00) 		0.147
(0.677) 		0.00814
(0.179) 		0.742
(0.923) 		0.455
(0.819) 		0.339
(0.788) 		0.229
(0.728) 		0.367
(0.795)
C10ORF28 4 (1%) 369 0.684
(0.918) 		0.47
(0.819) 		1
(1.00) 		0.166
(0.692) 		0.0362
(0.403) 		0.849
(0.959) 		0.0133
(0.234) 		0.16
(0.679)
ARID1A 32 (9%) 341 0.365
(0.795) 		0.593
(0.894) 		0.285
(0.766) 		0.217
(0.724) 		0.638
(0.91) 		0.724
(0.919) 		0.282
(0.766) 		0.966
(1.00)
CDC27 15 (4%) 358 0.796
(0.949) 		0.229
(0.728) 		0.315
(0.784) 		0.39
(0.801) 		0.472
(0.819) 		0.506
(0.836) 		0.157
(0.679) 		0.121
(0.662)
CDKN2A 11 (3%) 362 0.861
(0.961) 		0.182
(0.711) 		0.206
(0.717) 		0.666
(0.918) 		0.627
(0.901) 		0.577
(0.883) 		0.468
(0.819) 		0.201
(0.717)
KRT2 12 (3%) 361 0.526
(0.851) 		0.292
(0.766) 		0.0885
(0.604) 		0.224
(0.725) 		0.452
(0.819) 		0.42
(0.819) 		0.0662
(0.552) 		0.481
(0.819)
NFE2L2 13 (3%) 360 0.0313
(0.388) 		0.674
(0.918) 		0.15
(0.677) 		0.0974
(0.616) 		0.16
(0.679) 		0.0755
(0.578) 		0.136
(0.677) 		0.0212
(0.314)
PTEN 11 (3%) 362 0.849
(0.959) 		0.0676
(0.552) 		0.0698
(0.559) 		0.0375
(0.407) 		0.355
(0.795) 		0.0393
(0.416) 		0.472
(0.819) 		0.148
(0.677)
ARID2 22 (6%) 351 0.844
(0.959) 		0.479
(0.819) 		0.482
(0.819) 		0.747
(0.927) 		0.488
(0.82) 		0.492
(0.82) 		0.946
(1.00) 		0.313
(0.784)
RBM10 8 (2%) 365 0.71
(0.919) 		0.197
(0.717) 		0.442
(0.819) 		0.771
(0.937) 		0.817
(0.951) 		0.754
(0.933) 		0.727
(0.919) 		0.247
(0.76)
ZNF512B 8 (2%) 365 0.344
(0.788) 		0.811
(0.95) 		0.143
(0.677) 		0.583
(0.886) 		0.197
(0.717) 		0.861
(0.961) 		0.452
(0.819) 		1
(1.00)
KCNN3 12 (3%) 361 0.0769
(0.578) 		0.291
(0.766) 		0.378
(0.795) 		0.605
(0.898) 		0.84
(0.959) 		0.409
(0.812) 		0.278
(0.766) 		0.0642
(0.552)
KRT10 9 (2%) 364 1
(1.00) 		0.125
(0.662) 		0.251
(0.76) 		0.613
(0.898) 		0.515
(0.848) 		0.436
(0.819) 		0.125
(0.662) 		0.449
(0.819)
MLL4 19 (5%) 354 0.256
(0.764) 		0.234
(0.735) 		0.642
(0.91) 		0.46
(0.819) 		0.737
(0.919) 		0.695
(0.919) 		0.678
(0.918) 		0.838
(0.959)
ALB 43 (12%) 330 0.0492
(0.488) 		0.0487
(0.488) 		0.537
(0.851) 		0.523
(0.851) 		0.272
(0.766) 		0.885
(0.974) 		0.414
(0.817) 		0.034
(0.403)
IL6ST 12 (3%) 361 0.0231
(0.327) 		0.371
(0.795) 		0.686
(0.918) 		0.552
(0.86) 		0.0673
(0.552) 		0.0214
(0.314) 		0.762
(0.937) 		0.518
(0.849)
C19ORF55 6 (2%) 367 0.393
(0.801) 		0.672
(0.918) 		0.727
(0.919) 		0.157
(0.679) 		0.785
(0.946) 		0.869
(0.966) 		0.0781
(0.578) 		0.674
(0.918)
PIK3CA 13 (3%) 360 1
(1.00) 		1
(1.00) 		0.528
(0.851) 		0.628
(0.901) 		0.374
(0.795) 		0.206
(0.717) 		0.468
(0.819) 		0.591
(0.893)
CELA1 6 (2%) 367 0.769
(0.937) 		0.443
(0.819) 		0.887
(0.974) 		0.948
(1.00) 		0.214
(0.721) 		0.536
(0.851) 		1
(1.00) 		0.893
(0.976)
RPS6KA3 14 (4%) 359 0.289
(0.766) 		0.205
(0.717) 		0.323
(0.787) 		0.342
(0.788) 		0.543
(0.851) 		0.899
(0.981) 		0.295
(0.768) 		0.947
(1.00)
NRD1 13 (3%) 360 0.878
(0.97) 		0.825
(0.955) 		0.291
(0.766) 		0.454
(0.819) 		0.721
(0.919) 		0.379
(0.795) 		0.185
(0.711) 		0.803
(0.95)
EEF1A1 9 (2%) 364 0.0279
(0.369) 		0.393
(0.801) 		0.4
(0.804) 		0.333
(0.788) 		0.683
(0.918) 		0.0606
(0.552) 		0.325
(0.788) 		0.724
(0.919)
COG2 4 (1%) 369 0.686
(0.918) 		0.366
(0.795) 		0.116
(0.662) 		0.168
(0.692) 		0.884
(0.974) 		0.374
(0.795) 		1
(1.00) 		0.363
(0.795)
ATXN1 10 (3%) 363 0.661
(0.918) 		0.658
(0.918) 		0.285
(0.766) 		0.837
(0.959) 		0.198
(0.717) 		0.709
(0.919) 		0.0313
(0.388) 		0.208
(0.717)
KCTD20 5 (1%) 368 1
(1.00) 		0.319
(0.784) 		0.0506
(0.495) 		0.0699
(0.559) 		0.474
(0.819) 		0.185
(0.711) 		0.832
(0.959) 		0.729
(0.919)
CEP164 9 (2%) 364 0.573
(0.882) 		1
(1.00) 		0.807
(0.95) 		0.679
(0.918) 		0.858
(0.961) 		0.983
(1.00) 		1
(1.00) 		0.779
(0.942)
TCEAL6 4 (1%) 369 0.684
(0.918) 		0.367
(0.795) 		0.116
(0.662) 		0.167
(0.692) 		0.888
(0.974) 		0.374
(0.795) 		1
(1.00) 		0.363
(0.795)
DNAJC28 4 (1%) 369 0.46
(0.819) 		0.821
(0.953) 		0.206
(0.717) 		0.187
(0.711) 		0.886
(0.974) 		0.104
(0.631) 		0.372
(0.795) 		0.89
(0.974)
FOXI1 5 (1%) 368 0.376
(0.795) 		0.616
(0.898) 		0.142
(0.677) 		0.0918
(0.606) 		0.551
(0.86) 		0.243
(0.755) 		0.871
(0.966) 		0.704
(0.919)
JAK1 14 (4%) 359 0.697
(0.919) 		1
(1.00) 		0.29
(0.766) 		0.146
(0.677) 		0.964
(1.00) 		0.821
(0.953) 		0.202
(0.717) 		0.344
(0.788)
DENND4B 12 (3%) 361 0.293
(0.766) 		0.268
(0.766) 		0.143
(0.677) 		0.615
(0.898) 		0.0467
(0.474) 		0.537
(0.851) 		1
(1.00) 		0.347
(0.791)
BRD7 10 (3%) 363 0.659
(0.918) 		0.511
(0.844) 		0.35
(0.795) 		0.598
(0.894) 		0.57
(0.882) 		0.173
(0.692) 		0.801
(0.95) 		0.129
(0.67)
IDH1 8 (2%) 365 0.482
(0.819) 		0.25
(0.76) 		0.141
(0.677) 		0.235
(0.737) 		0.21
(0.72) 		0.39
(0.801) 		0.388
(0.801) 		0.174
(0.692)
CNGA3 11 (3%) 362 0.142
(0.677) 		0.928
(0.992) 		0.595
(0.894) 		0.215
(0.721) 		0.652
(0.918) 		0.33
(0.788) 		0.675
(0.918) 		0.439
(0.819)
HLA-DPB1 5 (1%) 368 1
(1.00) 		0.317
(0.784) 		0.48
(0.819) 		0.281
(0.766) 		0.171
(0.692) 		0.776
(0.939) 		0.685
(0.918) 		0.404
(0.808)
ALMS1 24 (6%) 349 0.492
(0.82) 		0.179
(0.703) 		0.789
(0.948) 		0.981
(1.00) 		0.439
(0.819) 		0.7
(0.919) 		0.485
(0.82) 		0.702
(0.919)
BAZ2A 11 (3%) 362 0.466
(0.819) 		0.354
(0.795) 		0.973
(1.00) 		0.683
(0.918) 		0.423
(0.819) 		0.579
(0.883) 		0.0766
(0.578) 		0.596
(0.894)
TAF1B 6 (2%) 367 0.205
(0.717) 		0.0952
(0.613) 		0.0838
(0.59) 		0.658
(0.918) 		0.808
(0.95) 		0.805
(0.95) 		0.463
(0.819) 		0.27
(0.766)
AR 10 (3%) 363 0.473
(0.819) 		1
(1.00) 		0.712
(0.919) 		0.726
(0.919) 		0.474
(0.819) 		0.171
(0.692) 		0.205
(0.717) 		0.661
(0.918)
CREB3L3 5 (1%) 368 0.0913
(0.606) 		0.449
(0.819) 		0.134
(0.677) 		0.619
(0.898) 		0.366
(0.795) 		0.0816
(0.59) 		1
(1.00) 		0.16
(0.679)
LFNG 7 (2%) 366 0.496
(0.823) 		0.623
(0.9) 		0.7
(0.919) 		0.905
(0.982) 		0.441
(0.819) 		0.464
(0.819) 		0.759
(0.937) 		0.535
(0.851)
FZR1 6 (2%) 367 0.579
(0.883) 		1
(1.00) 		0.318
(0.784) 		0.466
(0.819) 		0.791
(0.948) 		0.0293
(0.38) 		0.2
(0.717) 		0.0877
(0.604)
TRIOBP 11 (3%) 362 1
(1.00) 		0.121
(0.662) 		0.339
(0.788) 		0.376
(0.795) 		0.377
(0.795) 		0.466
(0.819) 		0.0981
(0.616) 		0.402
(0.805)
GJB1 3 (1%) 370 1
(1.00) 		0.794
(0.948) 		0.262
(0.766) 		0.73
(0.919) 		0.225
(0.725) 		0.91
(0.982) 		0.153
(0.679) 		1
(1.00)
DYRK1A 7 (2%) 366 0.0325
(0.396) 		0.891
(0.974) 		0.838
(0.959) 		0.634
(0.907) 		0.261
(0.766) 		0.482
(0.819) 		0.768
(0.937) 		0.293
(0.766)
TNPO1 9 (2%) 364 0.434
(0.819) 		0.908
(0.982) 		0.343
(0.788) 		0.505
(0.836) 		0.611
(0.898) 		0.466
(0.819) 		0.186
(0.711) 		0.629
(0.902)
PDZD4 4 (1%) 369 0.304
(0.779) 		1
(1.00) 		0.729
(0.919) 		0.249
(0.76) 		0.496
(0.823) 		0.286
(0.766)
CCNA2 5 (1%) 368 0.456
(0.819) 		0.73
(0.919) 		0.0943
(0.612) 		0.789
(0.948) 		0.237
(0.739) 		0.212
(0.721) 		0.399
(0.804) 		0.257
(0.764)
AHCTF1 8 (2%) 365 0.541
(0.851) 		0.812
(0.95) 		0.6
(0.895) 		0.736
(0.919) 		0.54
(0.851) 		0.978
(1.00) 		0.909
(0.982) 		0.978
(1.00)
RXRB 8 (2%) 365 0.816
(0.951) 		0.66
(0.918) 		0.428
(0.819) 		0.761
(0.937) 		0.49
(0.82) 		0.811
(0.95) 		0.921
(0.987) 		0.876
(0.969)
PARP1 5 (1%) 368 0.539
(0.851) 		0.857
(0.961) 		0.272
(0.766) 		0.659
(0.918) 		0.341
(0.788) 		0.598
(0.894) 		0.618
(0.898) 		0.533
(0.851)
NBEA 21 (6%) 352 0.685
(0.918) 		0.406
(0.81) 		0.859
(0.961) 		0.911
(0.982) 		0.279
(0.766) 		0.15
(0.677) 		0.733
(0.919) 		0.705
(0.919)
H6PD 5 (1%) 368 0.538
(0.851) 		0.615
(0.898) 		0.268
(0.766) 		0.152
(0.679) 		0.429
(0.819) 		0.12
(0.662) 		0.871
(0.966) 		0.312
(0.784)
VPS4B 5 (1%) 368 0.738
(0.919) 		0.0445
(0.458) 		0.0876
(0.604) 		0.29
(0.766) 		0.76
(0.937) 		0.302
(0.778) 		0.201
(0.717) 		0.0721
(0.571)
HNRNPL 8 (2%) 365 0.54
(0.851) 		0.307
(0.784) 		0.0264
(0.368) 		0.297
(0.768) 		0.283
(0.766) 		0.764
(0.937) 		0.702
(0.919) 		0.597
(0.894)
FILIP1 13 (3%) 360 0.82
(0.953) 		0.366
(0.795) 		0.297
(0.768) 		0.446
(0.819) 		0.722
(0.919) 		0.377
(0.795) 		0.487
(0.82) 		0.572
(0.882)
FAM22F 4 (1%) 369 0.131
(0.673) 		0.0908
(0.606) 		0.0277
(0.369) 		0.32
(0.784) 		0.737
(0.919) 		0.395
(0.801) 		0.0842
(0.59) 		0.279
(0.766)
GPSM2 4 (1%) 369 0.457
(0.819) 		0.689
(0.918) 		0.678
(0.918) 		0.872
(0.966) 		0.969
(1.00) 		0.641
(0.91) 		0.0833
(0.59) 		0.845
(0.959)
RCCD1 5 (1%) 368 0.312
(0.784) 		0.857
(0.961) 		0.783
(0.945) 		0.465
(0.819) 		0.714
(0.919) 		0.456
(0.819) 		0.348
(0.791) 		0.625
(0.9)
PTGR1 5 (1%) 368 0.22
(0.725) 		0.617
(0.898) 		0.84
(0.959) 		0.445
(0.819) 		0.929
(0.992) 		0.321
(0.784) 		0.812
(0.95) 		0.192
(0.717)
SAMM50 3 (1%) 370 0.617
(0.898) 		0.611
(0.898) 		0.115
(0.662) 		0.169
(0.692) 		0.532
(0.851) 		0.1
(0.619) 		0.864
(0.962) 		0.144
(0.677)
LEO1 5 (1%) 368 0.143
(0.677) 		0.381
(0.795) 		0.803
(0.95) 		0.175
(0.694) 		0.431
(0.819) 		0.334
(0.788) 		0.265
(0.766) 		0.705
(0.919)
CD97 5 (1%) 368 0.457
(0.819) 		0.854
(0.961) 		0.368
(0.795) 		0.146
(0.677) 		0.735
(0.919) 		0.185
(0.711) 		0.328
(0.788) 		0.521
(0.851)
SKA3 4 (1%) 369 0.685
(0.918) 		0.219
(0.725) 		0.42
(0.819) 		0.716
(0.919) 		0.281
(0.766) 		0.942
(1.00) 		0.375
(0.795) 		0.847
(0.959)
MTA1 6 (2%) 367 1
(1.00) 		0.12
(0.662) 		0.04
(0.417) 		0.289
(0.766) 		0.0573
(0.528) 		0.0666
(0.552) 		0.463
(0.819) 		0.16
(0.679)
NR4A2 6 (2%) 367 1
(1.00) 		0.579
(0.883) 		0.271
(0.766) 		0.111
(0.658) 		0.684
(0.918) 		0.114
(0.662) 		0.809
(0.95) 		0.149
(0.677)
HNF1A 8 (2%) 365 0.0189
(0.288) 		1
(1.00) 		0.0673
(0.552) 		0.317
(0.784) 		0.0641
(0.552) 		0.207
(0.717) 		0.125
(0.662) 		0.287
(0.766)
KRAS 6 (2%) 367 0.29
(0.766) 		0.673
(0.918) 		0.543
(0.851) 		0.19
(0.717) 		0.691
(0.919) 		0.122
(0.662) 		0.174
(0.692) 		0.607
(0.898)
PGBD1 3 (1%) 370 0.79
(0.948) 		0.793
(0.948) 		1
(1.00) 		0.411
(0.815) 		0.561
(0.872) 		0.827
(0.956) 		0.462
(0.819) 		0.909
(0.982)
LATS1 7 (2%) 366 0.708
(0.919) 		0.624
(0.9) 		0.573
(0.882) 		0.145
(0.677) 		0.857
(0.961) 		0.672
(0.918) 		1
(1.00) 		0.614
(0.898)
KEAP1 17 (5%) 356 0.231
(0.728) 		0.14
(0.677) 		0.273
(0.766) 		0.94
(1.00) 		0.101
(0.621) 		0.251
(0.76) 		0.724
(0.919) 		0.23
(0.728)
SENP6 11 (3%) 362 0.395
(0.801) 		0.0744
(0.578) 		0.793
(0.948) 		0.223
(0.725) 		0.467
(0.819) 		0.43
(0.819) 		0.104
(0.631) 		0.93
(0.992)
FKBP4 4 (1%) 369 0.461
(0.819) 		0.57
(0.882) 		0.838
(0.959) 		0.675
(0.918) 		0.839
(0.959) 		0.641
(0.91) 		1
(1.00) 		0.312
(0.784)
DSPP 21 (6%) 352 0.359
(0.795) 		0.92
(0.987) 		0.737
(0.919) 		0.212
(0.721) 		0.913
(0.982) 		0.442
(0.819) 		0.772
(0.937) 		0.223
(0.725)
PRAMEF4 4 (1%) 369 0.682
(0.918) 		0.363
(0.795) 		0.334
(0.788) 		0.561
(0.872) 		0.19
(0.717) 		0.159
(0.679) 		0.689
(0.918) 		0.25
(0.76)
RPS6KA5 5 (1%) 368 1
(1.00) 		0.318
(0.784) 		0.619
(0.898) 		0.331
(0.788) 		0.313
(0.784) 		0.426
(0.819) 		0.285
(0.766) 		0.523
(0.851)
DDX42 6 (2%) 367 0.202
(0.717) 		0.208
(0.717) 		0.155
(0.679) 		0.0278
(0.369) 		0.251
(0.76) 		0.0626
(0.552) 		0.341
(0.788) 		0.222
(0.725)
RHCG 4 (1%) 369 0.129
(0.67) 		0.365
(0.795) 		0.275
(0.766) 		0.26
(0.766) 		0.685
(0.918) 		0.0837
(0.59) 		0.912
(0.982) 		0.123
(0.662)
SWAP70 5 (1%) 368 0.854
(0.961) 		1
(1.00) 		0.286
(0.766) 		0.749
(0.929) 		0.62
(0.898) 		0.694
(0.919) 		0.111
(0.658) 		0.388
(0.801)
BIN1 4 (1%) 369 0.302
(0.778) 		0.687
(0.918) 		0.591
(0.893) 		0.484
(0.82) 		0.681
(0.918) 		0.0997
(0.619) 		0.912
(0.982) 		0.125
(0.662)
SMARCA4 11 (3%) 362 0.135
(0.677) 		0.427
(0.819) 		0.34
(0.788) 		0.476
(0.819) 		0.736
(0.919) 		0.197
(0.717) 		0.146
(0.677) 		0.372
(0.795)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
TP53 MUTATED 12 82 19
TP53 WILD-TYPE 80 67 106

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
TP53 MUTATED 35 48 31
TP53 WILD-TYPE 57 113 89
'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
TP53 MUTATED 44 27 14 12 14
TP53 WILD-TYPE 24 61 60 56 55

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0016

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
TP53 MUTATED 30 16 38 17 10
TP53 WILD-TYPE 23 39 78 70 46

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-04 (Fisher's exact test), Q value = 0.0093

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
TP53 MUTATED 23 25 17 18 17 13
TP53 WILD-TYPE 17 39 74 66 31 28

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0089

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
TP53 MUTATED 22 37 18 30 6
TP53 WILD-TYPE 21 58 39 96 41

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00391 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
TP53 MUTATED 45 18 25 22
TP53 WILD-TYPE 65 62 78 28

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
TP53 MUTATED 29 35 23 15 8
TP53 WILD-TYPE 44 48 77 18 46

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00025 (Fisher's exact test), Q value = 0.011

Table S9.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CTNNB1 MUTATED 31 23 43
CTNNB1 WILD-TYPE 61 126 82

Figure S8.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S10.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CTNNB1 MUTATED 12 66 19
CTNNB1 WILD-TYPE 80 95 101

Figure S9.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S11.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CTNNB1 MUTATED 7 14 7 6 62
CTNNB1 WILD-TYPE 61 74 67 62 7

Figure S10.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S12.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CTNNB1 MUTATED 2 12 16 16 50
CTNNB1 WILD-TYPE 51 43 100 71 6

Figure S11.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S13.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CTNNB1 MUTATED 12 13 10 49 9 3
CTNNB1 WILD-TYPE 28 51 81 35 39 38

Figure S12.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S14.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CTNNB1 MUTATED 13 15 10 18 40
CTNNB1 WILD-TYPE 30 80 47 108 7

Figure S13.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S15.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CTNNB1 MUTATED 17 7 52 8
CTNNB1 WILD-TYPE 93 73 51 42

Figure S14.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S16.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CTNNB1 MUTATED 10 13 9 10 42
CTNNB1 WILD-TYPE 63 70 91 23 12

Figure S15.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00362 (Fisher's exact test), Q value = 0.099

Table S17.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
AXIN1 MUTATED 1 7 15
AXIN1 WILD-TYPE 91 142 110

Figure S16.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'AXIN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0299 (Fisher's exact test), Q value = 0.38

Table S18.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
AXIN1 MUTATED 1 12 11
AXIN1 WILD-TYPE 91 149 109

Figure S17.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S19.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
AXIN1 MUTATED 2 5 15 0 2
AXIN1 WILD-TYPE 66 83 59 68 67

Figure S18.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00947 (Fisher's exact test), Q value = 0.2

Table S20.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
AXIN1 MUTATED 2 0 10 11 1
AXIN1 WILD-TYPE 51 55 106 76 55

Figure S19.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S21.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
AXIN1 MUTATED 1 0 0 9 10 3
AXIN1 WILD-TYPE 39 64 91 75 38 38

Figure S20.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.035 (Fisher's exact test), Q value = 0.4

Table S22.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
AXIN1 MUTATED 2 2 8 10 1
AXIN1 WILD-TYPE 41 93 49 116 46

Figure S21.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00521 (Fisher's exact test), Q value = 0.13

Table S23.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
AXIN1 MUTATED 7 0 6 7
AXIN1 WILD-TYPE 103 80 97 43

Figure S22.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 0.96

Table S24.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
AXIN1 MUTATED 5 3 6 2 4
AXIN1 WILD-TYPE 68 80 94 31 50
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0537 (Fisher's exact test), Q value = 0.51

Table S25.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
RB1 MUTATED 1 12 7
RB1 WILD-TYPE 91 137 118
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0145 (Fisher's exact test), Q value = 0.24

Table S26.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
RB1 MUTATED 2 6 13
RB1 WILD-TYPE 90 155 107

Figure S23.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0387 (Fisher's exact test), Q value = 0.41

Table S27.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
RB1 MUTATED 2 7 9 2 1
RB1 WILD-TYPE 66 81 65 66 68

Figure S24.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 0.85

Table S28.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
RB1 MUTATED 4 2 9 5 1
RB1 WILD-TYPE 49 53 107 82 55
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.22

Table S29.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
RB1 MUTATED 1 5 5 1 1 7
RB1 WILD-TYPE 39 59 86 83 47 34

Figure S25.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.85

Table S30.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
RB1 MUTATED 1 4 4 10 1
RB1 WILD-TYPE 42 91 53 116 46
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.81

Table S31.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
RB1 MUTATED 9 4 4 1
RB1 WILD-TYPE 101 76 99 49
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 0.82

Table S32.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
RB1 MUTATED 7 4 5 1 1
RB1 WILD-TYPE 66 79 95 32 53
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.8

Table S33.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
ARID1A MUTATED 9 9 13
ARID1A WILD-TYPE 83 140 112
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S34.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
ARID1A MUTATED 7 12 13
ARID1A WILD-TYPE 85 149 107
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.77

Table S35.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
ARID1A MUTATED 7 3 7 7 8
ARID1A WILD-TYPE 61 85 67 61 61
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.217 (Fisher's exact test), Q value = 0.72

Table S36.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
ARID1A MUTATED 4 6 5 10 7
ARID1A WILD-TYPE 49 49 111 77 49
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.638 (Fisher's exact test), Q value = 0.91

Table S37.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
ARID1A MUTATED 4 4 7 8 7 2
ARID1A WILD-TYPE 36 60 84 76 41 39
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 0.92

Table S38.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
ARID1A MUTATED 4 6 7 12 3
ARID1A WILD-TYPE 39 89 50 114 44
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.77

Table S39.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
ARID1A MUTATED 8 9 6 7
ARID1A WILD-TYPE 102 71 97 43
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
ARID1A MUTATED 7 6 10 3 4
ARID1A WILD-TYPE 66 77 90 30 50
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.92

Table S41.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
BAP1 MUTATED 4 8 9
BAP1 WILD-TYPE 88 141 116
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S42.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
BAP1 MUTATED 6 0 15
BAP1 WILD-TYPE 86 161 105

Figure S26.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0016

Table S43.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
BAP1 MUTATED 1 0 8 11 1
BAP1 WILD-TYPE 67 88 66 57 68

Figure S27.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00061

Table S44.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
BAP1 MUTATED 9 0 0 11 1
BAP1 WILD-TYPE 44 55 116 76 55

Figure S28.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00116 (Fisher's exact test), Q value = 0.04

Table S45.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
BAP1 MUTATED 0 1 8 2 2 8
BAP1 WILD-TYPE 40 63 83 82 46 33

Figure S29.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.055

Table S46.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
BAP1 MUTATED 0 1 4 15 1
BAP1 WILD-TYPE 43 94 53 111 46

Figure S30.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00359 (Fisher's exact test), Q value = 0.099

Table S47.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
BAP1 MUTATED 5 10 1 5
BAP1 WILD-TYPE 105 70 102 45

Figure S31.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.02

Table S48.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
BAP1 MUTATED 4 1 15 0 1
BAP1 WILD-TYPE 69 82 85 33 53

Figure S32.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 0.95

Table S49.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CDC27 MUTATED 4 5 6
CDC27 WILD-TYPE 88 144 119
'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.73

Table S50.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CDC27 MUTATED 2 10 3
CDC27 WILD-TYPE 90 151 117
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.78

Table S51.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CDC27 MUTATED 2 4 2 1 6
CDC27 WILD-TYPE 66 84 72 67 63
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.8

Table S52.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CDC27 MUTATED 2 1 5 2 5
CDC27 WILD-TYPE 51 54 111 85 51
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.82

Table S53.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CDC27 MUTATED 2 4 1 5 2 1
CDC27 WILD-TYPE 38 60 90 79 46 40
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 0.84

Table S54.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CDC27 MUTATED 2 4 1 4 4
CDC27 WILD-TYPE 41 91 56 122 43
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.68

Table S55.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CDC27 MUTATED 4 1 8 1
CDC27 WILD-TYPE 106 79 95 49
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.66

Table S56.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CDC27 MUTATED 1 3 3 1 6
CDC27 WILD-TYPE 72 80 97 32 48
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 0.96

Table S57.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CDKN2A MUTATED 3 5 3
CDKN2A WILD-TYPE 89 144 122
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.71

Table S58.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CDKN2A MUTATED 1 8 2
CDKN2A WILD-TYPE 91 153 118
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.72

Table S59.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CDKN2A MUTATED 2 4 0 1 4
CDKN2A WILD-TYPE 66 84 74 67 65
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.666 (Fisher's exact test), Q value = 0.92

Table S60.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CDKN2A MUTATED 1 2 4 1 3
CDKN2A WILD-TYPE 52 53 112 86 53
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CDKN2A MUTATED 1 4 3 2 0 1
CDKN2A WILD-TYPE 39 60 88 82 48 40
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.577 (Fisher's exact test), Q value = 0.88

Table S62.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CDKN2A MUTATED 2 4 1 2 2
CDKN2A WILD-TYPE 41 91 56 124 45
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.82

Table S63.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CDKN2A MUTATED 4 2 5 0
CDKN2A WILD-TYPE 106 78 98 50
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.72

Table S64.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CDKN2A MUTATED 1 5 1 1 3
CDKN2A WILD-TYPE 72 78 99 32 51
'KRT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 0.85

Table S65.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
KRT2 MUTATED 4 3 5
KRT2 WILD-TYPE 88 146 120
'KRT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.77

Table S66.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
KRT2 MUTATED 1 5 6
KRT2 WILD-TYPE 91 156 114
'KRT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0885 (Fisher's exact test), Q value = 0.6

Table S67.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
KRT2 MUTATED 0 1 3 3 5
KRT2 WILD-TYPE 68 87 71 65 64
'KRT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.224 (Fisher's exact test), Q value = 0.72

Table S68.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
KRT2 MUTATED 1 2 1 5 3
KRT2 WILD-TYPE 52 53 115 82 53
'KRT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.82

Table S69.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
KRT2 MUTATED 1 1 2 2 4 1
KRT2 WILD-TYPE 39 63 89 82 44 40
'KRT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 0.82

Table S70.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
KRT2 MUTATED 1 1 1 7 1
KRT2 WILD-TYPE 42 94 56 119 46
'KRT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0662 (Fisher's exact test), Q value = 0.55

Table S71.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
KRT2 MUTATED 2 2 2 5
KRT2 WILD-TYPE 108 78 101 45
'KRT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.82

Table S72.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
KRT2 MUTATED 2 1 6 1 1
KRT2 WILD-TYPE 71 82 94 32 53
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.39

Table S73.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
NFE2L2 MUTATED 2 2 9
NFE2L2 WILD-TYPE 90 147 116

Figure S33.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 0.92

Table S74.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
NFE2L2 MUTATED 2 7 4
NFE2L2 WILD-TYPE 90 154 116
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.68

Table S75.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
NFE2L2 MUTATED 1 4 3 0 5
NFE2L2 WILD-TYPE 67 84 71 68 64
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0974 (Fisher's exact test), Q value = 0.62

Table S76.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
NFE2L2 MUTATED 0 3 3 2 5
NFE2L2 WILD-TYPE 53 52 113 85 51
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.16 (Fisher's exact test), Q value = 0.68

Table S77.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
NFE2L2 MUTATED 2 0 3 6 2 0
NFE2L2 WILD-TYPE 38 64 88 78 46 41
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0755 (Fisher's exact test), Q value = 0.58

Table S78.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
NFE2L2 MUTATED 1 1 1 5 5
NFE2L2 WILD-TYPE 42 94 56 121 42
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.68

Table S79.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
NFE2L2 MUTATED 4 0 6 2
NFE2L2 WILD-TYPE 106 80 97 48
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.31

Table S80.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
NFE2L2 MUTATED 0 2 3 1 6
NFE2L2 WILD-TYPE 73 81 97 32 48

Figure S34.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 0.96

Table S81.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PTEN MUTATED 2 5 3
PTEN WILD-TYPE 90 144 122
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0676 (Fisher's exact test), Q value = 0.55

Table S82.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PTEN MUTATED 0 8 3
PTEN WILD-TYPE 92 153 117
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0698 (Fisher's exact test), Q value = 0.56

Table S83.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PTEN MUTATED 2 4 0 0 4
PTEN WILD-TYPE 66 84 74 68 65
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0375 (Fisher's exact test), Q value = 0.41

Table S84.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PTEN MUTATED 1 0 5 0 4
PTEN WILD-TYPE 52 55 111 87 52

Figure S35.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.8

Table S85.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PTEN MUTATED 0 3 2 5 0 1
PTEN WILD-TYPE 40 61 89 79 48 40
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0393 (Fisher's exact test), Q value = 0.42

Table S86.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PTEN MUTATED 0 5 0 2 4
PTEN WILD-TYPE 43 90 57 124 43

Figure S36.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.82

Table S87.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PTEN MUTATED 3 2 5 0
PTEN WILD-TYPE 107 78 98 50
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.68

Table S88.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PTEN MUTATED 1 5 1 0 3
PTEN WILD-TYPE 72 78 99 33 51
'ARID2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.844 (Fisher's exact test), Q value = 0.96

Table S89.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
ARID2 MUTATED 4 9 8
ARID2 WILD-TYPE 88 140 117
'ARID2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.82

Table S90.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
ARID2 MUTATED 3 11 8
ARID2 WILD-TYPE 89 150 112
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.82

Table S91.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
ARID2 MUTATED 2 5 3 4 7
ARID2 WILD-TYPE 66 83 71 64 62
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.747 (Fisher's exact test), Q value = 0.93

Table S92.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
ARID2 MUTATED 3 3 7 3 5
ARID2 WILD-TYPE 50 52 109 84 51
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 0.82

Table S93.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
ARID2 MUTATED 1 2 5 9 3 2
ARID2 WILD-TYPE 39 62 86 75 45 39
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.492 (Fisher's exact test), Q value = 0.82

Table S94.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
ARID2 MUTATED 1 4 4 8 5
ARID2 WILD-TYPE 42 91 53 118 42
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.946 (Fisher's exact test), Q value = 1

Table S95.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
ARID2 MUTATED 6 6 6 3
ARID2 WILD-TYPE 104 74 97 47
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.313 (Fisher's exact test), Q value = 0.78

Table S96.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
ARID2 MUTATED 3 4 6 1 7
ARID2 WILD-TYPE 70 79 94 32 47
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 0.92

Table S97.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
RBM10 MUTATED 1 4 2
RBM10 WILD-TYPE 91 145 123
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.72

Table S98.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
RBM10 MUTATED 0 4 4
RBM10 WILD-TYPE 92 157 116
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.82

Table S99.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
RBM10 MUTATED 1 4 2 1 0
RBM10 WILD-TYPE 67 84 72 67 69
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 0.94

Table S100.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
RBM10 MUTATED 1 2 3 2 0
RBM10 WILD-TYPE 52 53 113 85 56
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 0.95

Table S101.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
RBM10 MUTATED 0 2 2 2 2 0
RBM10 WILD-TYPE 40 62 89 82 46 41
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 0.93

Table S102.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
RBM10 MUTATED 0 3 1 4 0
RBM10 WILD-TYPE 43 92 56 122 47
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.92

Table S103.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
RBM10 MUTATED 2 1 3 0
RBM10 WILD-TYPE 108 79 100 50
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.247 (Fisher's exact test), Q value = 0.76

Table S104.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
RBM10 MUTATED 3 2 0 0 1
RBM10 WILD-TYPE 70 81 100 33 53
'ZNF512B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.79

Table S105.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
ZNF512B MUTATED 0 4 3
ZNF512B WILD-TYPE 92 145 122
'ZNF512B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 0.95

Table S106.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
ZNF512B MUTATED 1 4 3
ZNF512B WILD-TYPE 91 157 117
'ZNF512B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.68

Table S107.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
ZNF512B MUTATED 4 1 0 1 2
ZNF512B WILD-TYPE 64 87 74 67 67
'ZNF512B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.583 (Fisher's exact test), Q value = 0.89

Table S108.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
ZNF512B MUTATED 1 2 4 1 0
ZNF512B WILD-TYPE 52 53 112 86 56
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.72

Table S109.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
ZNF512B MUTATED 1 2 0 1 2 2
ZNF512B WILD-TYPE 39 62 91 83 46 39
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.861 (Fisher's exact test), Q value = 0.96

Table S110.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
ZNF512B MUTATED 1 2 2 3 0
ZNF512B WILD-TYPE 42 93 55 123 47
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.82

Table S111.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
ZNF512B MUTATED 4 1 1 2
ZNF512B WILD-TYPE 106 79 102 48
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S112.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
ZNF512B MUTATED 2 2 2 1 1
ZNF512B WILD-TYPE 71 81 98 32 53
'KCNN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0769 (Fisher's exact test), Q value = 0.58

Table S113.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
KCNN3 MUTATED 1 3 8
KCNN3 WILD-TYPE 91 146 117
'KCNN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.77

Table S114.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
KCNN3 MUTATED 1 5 6
KCNN3 WILD-TYPE 91 156 114
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.8

Table S115.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
KCNN3 MUTATED 2 1 2 2 5
KCNN3 WILD-TYPE 66 87 72 66 64
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.605 (Fisher's exact test), Q value = 0.9

Table S116.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
KCNN3 MUTATED 2 0 4 3 3
KCNN3 WILD-TYPE 51 55 112 84 53
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 0.96

Table S117.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
KCNN3 MUTATED 1 1 3 5 1 1
KCNN3 WILD-TYPE 39 63 88 79 47 40
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
KCNN3 MUTATED 1 3 3 2 3
KCNN3 WILD-TYPE 42 92 54 124 44
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.77

Table S119.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
KCNN3 MUTATED 2 4 5 0
KCNN3 WILD-TYPE 108 76 98 50
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0642 (Fisher's exact test), Q value = 0.55

Table S120.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
KCNN3 MUTATED 4 0 2 1 4
KCNN3 WILD-TYPE 69 83 98 32 50
'KRT10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S121.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
KRT10 MUTATED 2 4 3
KRT10 WILD-TYPE 90 145 122
'KRT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.66

Table S122.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
KRT10 MUTATED 1 2 6
KRT10 WILD-TYPE 91 159 114
'KRT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.76

Table S123.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
KRT10 MUTATED 1 0 3 3 2
KRT10 WILD-TYPE 67 88 71 65 67
'KRT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.613 (Fisher's exact test), Q value = 0.9

Table S124.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
KRT10 MUTATED 1 0 3 4 1
KRT10 WILD-TYPE 52 55 113 83 55
'KRT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 0.85

Table S125.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
KRT10 MUTATED 0 1 4 2 0 2
KRT10 WILD-TYPE 40 63 87 82 48 39
'KRT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.436 (Fisher's exact test), Q value = 0.82

Table S126.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
KRT10 MUTATED 0 2 1 6 0
KRT10 WILD-TYPE 43 93 56 120 47
'KRT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.66

Table S127.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
KRT10 MUTATED 3 5 1 0
KRT10 WILD-TYPE 107 75 102 50
'KRT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 0.82

Table S128.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
KRT10 MUTATED 1 1 5 0 2
KRT10 WILD-TYPE 72 82 95 33 52
'APOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.72

Table S129.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
APOB MUTATED 13 11 14
APOB WILD-TYPE 79 138 111
'APOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 0.85

Table S130.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
APOB MUTATED 9 20 10
APOB WILD-TYPE 83 141 110
'APOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0142 (Fisher's exact test), Q value = 0.24

Table S131.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
APOB MUTATED 6 8 3 5 15
APOB WILD-TYPE 62 80 71 63 54

Figure S37.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'APOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0119 (Fisher's exact test), Q value = 0.22

Table S132.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
APOB MUTATED 6 5 9 4 13
APOB WILD-TYPE 47 50 107 83 43

Figure S38.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'APOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.9 (Fisher's exact test), Q value = 0.98

Table S133.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
APOB MUTATED 5 8 9 9 3 5
APOB WILD-TYPE 35 56 82 75 45 36
'APOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.72

Table S134.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
APOB MUTATED 5 11 3 11 9
APOB WILD-TYPE 38 84 54 115 38
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.33

Table S135.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
APOB MUTATED 9 6 19 2
APOB WILD-TYPE 101 74 84 48

Figure S39.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0157 (Fisher's exact test), Q value = 0.24

Table S136.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
APOB MUTATED 4 9 6 5 12
APOB WILD-TYPE 69 74 94 28 42

Figure S40.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.76

Table S137.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
MLL4 MUTATED 3 6 10
MLL4 WILD-TYPE 89 143 115
'MLL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.234 (Fisher's exact test), Q value = 0.73

Table S138.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
MLL4 MUTATED 3 12 4
MLL4 WILD-TYPE 89 149 116
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.91

Table S139.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
MLL4 MUTATED 4 4 3 2 6
MLL4 WILD-TYPE 64 84 71 66 63
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.46 (Fisher's exact test), Q value = 0.82

Table S140.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
MLL4 MUTATED 3 4 4 3 5
MLL4 WILD-TYPE 50 51 112 84 51
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.92

Table S141.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
MLL4 MUTATED 3 5 3 5 2 1
MLL4 WILD-TYPE 37 59 88 79 46 40
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S142.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
MLL4 MUTATED 3 4 3 5 4
MLL4 WILD-TYPE 40 91 54 121 43
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 0.92

Table S143.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
MLL4 MUTATED 4 4 6 4
MLL4 WILD-TYPE 106 76 97 46
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S144.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
MLL4 MUTATED 3 4 5 3 3
MLL4 WILD-TYPE 70 79 95 30 51
'ALB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.49

Table S145.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
ALB MUTATED 8 13 22
ALB WILD-TYPE 84 136 103

Figure S41.  Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ALB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.49

Table S146.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
ALB MUTATED 6 26 11
ALB WILD-TYPE 86 135 109

Figure S42.  Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ALB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 0.85

Table S147.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
ALB MUTATED 10 11 5 6 9
ALB WILD-TYPE 58 77 69 62 60
'ALB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S148.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
ALB MUTATED 5 8 14 6 8
ALB WILD-TYPE 48 47 102 81 48
'ALB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.77

Table S149.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
ALB MUTATED 4 8 10 14 4 1
ALB WILD-TYPE 36 56 81 70 44 40
'ALB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.885 (Fisher's exact test), Q value = 0.97

Table S150.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
ALB MUTATED 5 11 5 13 7
ALB WILD-TYPE 38 84 52 113 40
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.414 (Fisher's exact test), Q value = 0.82

Table S151.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
ALB MUTATED 13 7 15 3
ALB WILD-TYPE 97 73 88 47
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.034 (Fisher's exact test), Q value = 0.4

Table S152.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
ALB MUTATED 4 13 7 3 11
ALB WILD-TYPE 69 70 93 30 43

Figure S43.  Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TSC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0549 (Fisher's exact test), Q value = 0.51

Table S153.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
TSC2 MUTATED 0 8 4
TSC2 WILD-TYPE 92 141 121
'TSC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.4

Table S154.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
TSC2 MUTATED 7 3 2
TSC2 WILD-TYPE 85 158 118

Figure S44.  Get High-res Image Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TSC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00027 (Fisher's exact test), Q value = 0.011

Table S155.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
TSC2 MUTATED 8 0 3 0 1
TSC2 WILD-TYPE 60 88 71 68 68

Figure S45.  Get High-res Image Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'TSC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.022

Table S156.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
TSC2 MUTATED 7 0 4 0 1
TSC2 WILD-TYPE 46 55 112 87 55

Figure S46.  Get High-res Image Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'TSC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.481 (Fisher's exact test), Q value = 0.82

Table S157.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
TSC2 MUTATED 1 3 1 3 1 3
TSC2 WILD-TYPE 39 61 90 81 47 38
'TSC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 0.96

Table S158.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
TSC2 MUTATED 1 5 2 3 1
TSC2 WILD-TYPE 42 90 55 123 46
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.491 (Fisher's exact test), Q value = 0.82

Table S159.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
TSC2 MUTATED 6 1 4 1
TSC2 WILD-TYPE 104 79 99 49
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S160.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
TSC2 MUTATED 4 4 2 0 2
TSC2 WILD-TYPE 69 79 98 33 52
'IL6ST MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.33

Table S161.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
IL6ST MUTATED 7 2 2
IL6ST WILD-TYPE 85 147 123

Figure S47.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IL6ST MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.8

Table S162.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
IL6ST MUTATED 4 3 5
IL6ST WILD-TYPE 88 158 115
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.92

Table S163.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
IL6ST MUTATED 2 2 2 1 4
IL6ST WILD-TYPE 66 86 72 67 65
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 0.86

Table S164.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
IL6ST MUTATED 0 2 3 3 3
IL6ST WILD-TYPE 53 53 113 84 53
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 0.55

Table S165.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
IL6ST MUTATED 0 1 2 4 5 0
IL6ST WILD-TYPE 40 63 89 80 43 41
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.31

Table S166.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
IL6ST MUTATED 0 0 1 8 3
IL6ST WILD-TYPE 43 95 56 118 44

Figure S48.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 0.94

Table S167.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
IL6ST MUTATED 4 1 4 1
IL6ST WILD-TYPE 106 79 99 49
'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 0.85

Table S168.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
IL6ST MUTATED 3 1 3 0 3
IL6ST WILD-TYPE 70 82 97 33 51
'C19ORF55 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.8

Table S169.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
C19ORF55 MUTATED 0 3 3
C19ORF55 WILD-TYPE 92 146 122
'C19ORF55 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.672 (Fisher's exact test), Q value = 0.92

Table S170.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
C19ORF55 MUTATED 1 2 3
C19ORF55 WILD-TYPE 91 159 117
'C19ORF55 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 0.92

Table S171.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
C19ORF55 MUTATED 1 1 1 2 0
C19ORF55 WILD-TYPE 67 87 73 66 69
'C19ORF55 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.68

Table S172.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
C19ORF55 MUTATED 1 1 0 3 0
C19ORF55 WILD-TYPE 52 54 116 84 56
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 0.95

Table S173.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
C19ORF55 MUTATED 1 0 2 1 1 1
C19ORF55 WILD-TYPE 39 64 89 83 47 40
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.869 (Fisher's exact test), Q value = 0.97

Table S174.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
C19ORF55 MUTATED 1 1 1 3 0
C19ORF55 WILD-TYPE 42 94 56 123 47
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0781 (Fisher's exact test), Q value = 0.58

Table S175.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
C19ORF55 MUTATED 1 3 0 2
C19ORF55 WILD-TYPE 109 77 103 48
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 0.92

Table S176.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
C19ORF55 MUTATED 1 1 3 1 0
C19ORF55 WILD-TYPE 72 82 97 32 54
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

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

Table S177.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PIK3CA MUTATED 3 5 4
PIK3CA WILD-TYPE 89 144 121
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S178.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PIK3CA MUTATED 3 6 4
PIK3CA WILD-TYPE 89 155 116
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.85

Table S179.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PIK3CA MUTATED 3 5 1 1 2
PIK3CA WILD-TYPE 65 83 73 67 67
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 0.9

Table S180.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PIK3CA MUTATED 2 1 6 1 2
PIK3CA WILD-TYPE 51 54 110 86 54
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.8

Table S181.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PIK3CA MUTATED 0 3 5 2 3 0
PIK3CA WILD-TYPE 40 61 86 82 45 41
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.72

Table S182.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PIK3CA MUTATED 0 6 0 5 2
PIK3CA WILD-TYPE 43 89 57 121 45
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.82

Table S183.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PIK3CA MUTATED 2 3 6 1
PIK3CA WILD-TYPE 108 77 97 49
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 0.89

Table S184.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PIK3CA MUTATED 1 4 5 0 2
PIK3CA WILD-TYPE 72 79 95 33 52
'CELA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 0.94

Table S185.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CELA1 MUTATED 1 2 3
CELA1 WILD-TYPE 91 147 122
'CELA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 0.82

Table S186.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CELA1 MUTATED 0 4 2
CELA1 WILD-TYPE 92 157 118
'CELA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.887 (Fisher's exact test), Q value = 0.97

Table S187.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CELA1 MUTATED 1 2 2 0 1
CELA1 WILD-TYPE 67 86 72 68 68
'CELA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.948 (Fisher's exact test), Q value = 1

Table S188.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CELA1 MUTATED 1 0 2 2 1
CELA1 WILD-TYPE 52 55 114 85 55
'CELA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.72

Table S189.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CELA1 MUTATED 0 3 0 1 1 1
CELA1 WILD-TYPE 40 61 91 83 47 40
'CELA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.536 (Fisher's exact test), Q value = 0.85

Table S190.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CELA1 MUTATED 0 2 2 1 1
CELA1 WILD-TYPE 43 93 55 125 46
'CELA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S191.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CELA1 MUTATED 2 1 2 1
CELA1 WILD-TYPE 108 79 101 49
'CELA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.893 (Fisher's exact test), Q value = 0.98

Table S192.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CELA1 MUTATED 2 2 1 0 1
CELA1 WILD-TYPE 71 81 99 33 53
'RPS6KA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.77

Table S193.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
RPS6KA3 MUTATED 4 3 7
RPS6KA3 WILD-TYPE 88 146 118
'RPS6KA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.72

Table S194.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
RPS6KA3 MUTATED 1 9 4
RPS6KA3 WILD-TYPE 91 152 116
'RPS6KA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.79

Table S195.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
RPS6KA3 MUTATED 2 2 6 1 3
RPS6KA3 WILD-TYPE 66 86 68 67 66
'RPS6KA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 0.79

Table S196.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
RPS6KA3 MUTATED 1 2 2 6 3
RPS6KA3 WILD-TYPE 52 53 114 81 53
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 0.85

Table S197.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
RPS6KA3 MUTATED 2 3 1 3 3 2
RPS6KA3 WILD-TYPE 38 61 90 81 45 39
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.899 (Fisher's exact test), Q value = 0.98

Table S198.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
RPS6KA3 MUTATED 2 3 3 4 2
RPS6KA3 WILD-TYPE 41 92 54 122 45
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.77

Table S199.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
RPS6KA3 MUTATED 7 2 2 3
RPS6KA3 WILD-TYPE 103 78 101 47
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S200.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
RPS6KA3 MUTATED 4 4 3 1 2
RPS6KA3 WILD-TYPE 69 79 97 32 52
'NRD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 0.97

Table S201.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
NRD1 MUTATED 4 5 4
NRD1 WILD-TYPE 88 144 121
'NRD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 0.96

Table S202.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
NRD1 MUTATED 2 6 5
NRD1 WILD-TYPE 90 155 115
'NRD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.77

Table S203.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
NRD1 MUTATED 3 3 0 4 3
NRD1 WILD-TYPE 65 85 74 64 66
'NRD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.82

Table S204.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
NRD1 MUTATED 3 1 2 5 2
NRD1 WILD-TYPE 50 54 114 82 54
'NRD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 0.92

Table S205.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
NRD1 MUTATED 2 3 3 3 0 2
NRD1 WILD-TYPE 38 61 88 81 48 39
'NRD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.379 (Fisher's exact test), Q value = 0.8

Table S206.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
NRD1 MUTATED 2 4 0 4 3
NRD1 WILD-TYPE 41 91 57 122 44
'NRD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.71

Table S207.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
NRD1 MUTATED 3 6 4 0
NRD1 WILD-TYPE 107 74 99 50
'NRD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 0.95

Table S208.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
NRD1 MUTATED 2 3 3 2 3
NRD1 WILD-TYPE 71 80 97 31 51
'EEF1A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.37

Table S209.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
EEF1A1 MUTATED 6 2 1
EEF1A1 WILD-TYPE 86 147 124

Figure S49.  Get High-res Image Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EEF1A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.8

Table S210.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
EEF1A1 MUTATED 3 5 1
EEF1A1 WILD-TYPE 89 156 119
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S211.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
EEF1A1 MUTATED 2 4 0 1 2
EEF1A1 WILD-TYPE 66 84 74 67 67
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.333 (Fisher's exact test), Q value = 0.79

Table S212.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
EEF1A1 MUTATED 1 2 4 0 2
EEF1A1 WILD-TYPE 52 53 112 87 54
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.683 (Fisher's exact test), Q value = 0.92

Table S213.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
EEF1A1 MUTATED 1 2 4 1 0 1
EEF1A1 WILD-TYPE 39 62 87 83 48 40
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0606 (Fisher's exact test), Q value = 0.55

Table S214.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
EEF1A1 MUTATED 1 5 2 0 1
EEF1A1 WILD-TYPE 42 90 55 126 46
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.325 (Fisher's exact test), Q value = 0.79

Table S215.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
EEF1A1 MUTATED 3 1 5 0
EEF1A1 WILD-TYPE 107 79 98 50
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 0.92

Table S216.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
EEF1A1 MUTATED 1 4 2 1 1
EEF1A1 WILD-TYPE 72 79 98 32 53
'TCHH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.2

Table S217.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
TCHH MUTATED 3 2 11
TCHH WILD-TYPE 89 147 114

Figure S50.  Get High-res Image Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TCHH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0771 (Fisher's exact test), Q value = 0.58

Table S218.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
TCHH MUTATED 1 7 9
TCHH WILD-TYPE 91 154 111
'TCHH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.92

Table S219.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
TCHH MUTATED 4 2 5 3 3
TCHH WILD-TYPE 64 86 69 65 66
'TCHH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.971 (Fisher's exact test), Q value = 1

Table S220.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
TCHH MUTATED 3 3 5 4 2
TCHH WILD-TYPE 50 52 111 83 54
'TCHH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 0.94

Table S221.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
TCHH MUTATED 1 1 5 5 3 2
TCHH WILD-TYPE 39 63 86 79 45 39
'TCHH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.802 (Fisher's exact test), Q value = 0.95

Table S222.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
TCHH MUTATED 1 3 3 8 2
TCHH WILD-TYPE 42 92 54 118 45
'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.79

Table S223.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
TCHH MUTATED 6 5 4 0
TCHH WILD-TYPE 104 75 99 50
'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.947 (Fisher's exact test), Q value = 1

Table S224.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
TCHH MUTATED 4 3 4 1 3
TCHH WILD-TYPE 69 80 96 32 51
'COG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 0.92

Table S225.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
COG2 MUTATED 0 2 2
COG2 WILD-TYPE 92 147 123
'COG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.8

Table S226.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
COG2 MUTATED 1 3 0
COG2 WILD-TYPE 91 158 120
'COG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.66

Table S227.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
COG2 MUTATED 2 0 0 0 1
COG2 WILD-TYPE 66 88 74 68 68
'COG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.69

Table S228.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
COG2 MUTATED 1 1 0 0 1
COG2 WILD-TYPE 52 54 116 87 55
'COG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 0.97

Table S229.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
COG2 MUTATED 1 1 1 1 0 0
COG2 WILD-TYPE 39 63 90 83 48 41
'COG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.8

Table S230.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
COG2 MUTATED 1 0 1 1 1
COG2 WILD-TYPE 42 95 56 125 46
'COG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S231.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
COG2 MUTATED 2 1 1 0
COG2 WILD-TYPE 108 79 102 50
'COG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.8

Table S232.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
COG2 MUTATED 1 1 0 1 1
COG2 WILD-TYPE 72 82 100 32 53
'ATXN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 0.92

Table S233.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
ATXN1 MUTATED 2 3 5
ATXN1 WILD-TYPE 90 146 120
'ATXN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 0.92

Table S234.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
ATXN1 MUTATED 2 6 2
ATXN1 WILD-TYPE 90 155 118
'ATXN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.77

Table S235.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
ATXN1 MUTATED 2 3 1 0 4
ATXN1 WILD-TYPE 66 85 73 68 65
'ATXN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.837 (Fisher's exact test), Q value = 0.96

Table S236.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
ATXN1 MUTATED 1 2 4 1 2
ATXN1 WILD-TYPE 52 53 112 86 54
'ATXN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.72

Table S237.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
ATXN1 MUTATED 1 1 1 6 1 0
ATXN1 WILD-TYPE 39 63 90 78 47 41
'ATXN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.709 (Fisher's exact test), Q value = 0.92

Table S238.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
ATXN1 MUTATED 1 4 1 2 2
ATXN1 WILD-TYPE 42 91 56 124 45
'ATXN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.39

Table S239.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
ATXN1 MUTATED 3 0 7 0
ATXN1 WILD-TYPE 107 80 96 50

Figure S51.  Get High-res Image Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'ATXN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.208 (Fisher's exact test), Q value = 0.72

Table S240.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
ATXN1 MUTATED 0 4 2 1 3
ATXN1 WILD-TYPE 73 79 98 32 51
'KCTD20 MUTATION STATUS' versus 'CN_CNMF'

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

Table S241.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
KCTD20 MUTATED 1 2 2
KCTD20 WILD-TYPE 91 147 123
'KCTD20 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.78

Table S242.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
KCTD20 MUTATED 0 4 1
KCTD20 WILD-TYPE 92 157 119
'KCTD20 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0506 (Fisher's exact test), Q value = 0.5

Table S243.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
KCTD20 MUTATED 0 0 3 0 2
KCTD20 WILD-TYPE 68 88 71 68 67
'KCTD20 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0699 (Fisher's exact test), Q value = 0.56

Table S244.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
KCTD20 MUTATED 0 0 0 3 2
KCTD20 WILD-TYPE 53 55 116 84 54
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.82

Table S245.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
KCTD20 MUTATED 0 0 1 2 2 0
KCTD20 WILD-TYPE 40 64 90 82 46 41
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.71

Table S246.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
KCTD20 MUTATED 0 0 0 3 2
KCTD20 WILD-TYPE 43 95 57 123 45
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 0.96

Table S247.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
KCTD20 MUTATED 1 1 1 1
KCTD20 WILD-TYPE 109 79 102 49
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.729 (Fisher's exact test), Q value = 0.92

Table S248.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
KCTD20 MUTATED 1 0 2 0 1
KCTD20 WILD-TYPE 72 83 98 33 53
'GPR110 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 0.94

Table S249.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
GPR110 MUTATED 1 2 3
GPR110 WILD-TYPE 91 147 122
'GPR110 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.82

Table S250.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
GPR110 MUTATED 0 4 2
GPR110 WILD-TYPE 92 157 118
'GPR110 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.4

Table S251.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
GPR110 MUTATED 0 0 1 1 4
GPR110 WILD-TYPE 68 88 73 67 65

Figure S52.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'GPR110 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0548 (Fisher's exact test), Q value = 0.51

Table S252.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
GPR110 MUTATED 0 1 0 2 3
GPR110 WILD-TYPE 53 54 116 85 53
'GPR110 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0652 (Fisher's exact test), Q value = 0.55

Table S253.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
GPR110 MUTATED 0 0 1 5 0 0
GPR110 WILD-TYPE 40 64 90 79 48 41
'GPR110 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00672 (Fisher's exact test), Q value = 0.16

Table S254.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
GPR110 MUTATED 0 0 1 1 4
GPR110 WILD-TYPE 43 95 56 125 43

Figure S53.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'GPR110 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.92

Table S255.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
GPR110 MUTATED 2 1 3 0
GPR110 WILD-TYPE 108 79 100 50
'GPR110 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0052 (Fisher's exact test), Q value = 0.13

Table S256.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
GPR110 MUTATED 2 0 0 0 4
GPR110 WILD-TYPE 71 83 100 33 50

Figure S54.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CEP164 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.88

Table S257.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CEP164 MUTATED 1 5 3
CEP164 WILD-TYPE 91 144 122
'CEP164 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S258.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CEP164 MUTATED 2 4 3
CEP164 WILD-TYPE 90 157 117
'CEP164 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.807 (Fisher's exact test), Q value = 0.95

Table S259.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CEP164 MUTATED 3 2 1 1 2
CEP164 WILD-TYPE 65 86 73 67 67
'CEP164 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.92

Table S260.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CEP164 MUTATED 2 0 3 2 2
CEP164 WILD-TYPE 51 55 113 85 54
'CEP164 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.858 (Fisher's exact test), Q value = 0.96

Table S261.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CEP164 MUTATED 1 3 2 1 1 1
CEP164 WILD-TYPE 39 61 89 83 47 40
'CEP164 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S262.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CEP164 MUTATED 1 2 1 4 1
CEP164 WILD-TYPE 42 93 56 122 46
'CEP164 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S263.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CEP164 MUTATED 3 2 3 1
CEP164 WILD-TYPE 107 78 100 49
'CEP164 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.779 (Fisher's exact test), Q value = 0.94

Table S264.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CEP164 MUTATED 1 2 4 0 2
CEP164 WILD-TYPE 72 81 96 33 52
'TCEAL6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 0.92

Table S265.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
TCEAL6 MUTATED 0 2 2
TCEAL6 WILD-TYPE 92 147 123
'TCEAL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.8

Table S266.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
TCEAL6 MUTATED 1 3 0
TCEAL6 WILD-TYPE 91 158 120
'TCEAL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.66

Table S267.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
TCEAL6 MUTATED 2 0 0 0 1
TCEAL6 WILD-TYPE 66 88 74 68 68
'TCEAL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.167 (Fisher's exact test), Q value = 0.69

Table S268.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
TCEAL6 MUTATED 1 1 0 0 1
TCEAL6 WILD-TYPE 52 54 116 87 55
'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.888 (Fisher's exact test), Q value = 0.97

Table S269.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
TCEAL6 MUTATED 1 1 1 1 0 0
TCEAL6 WILD-TYPE 39 63 90 83 48 41
'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.8

Table S270.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
TCEAL6 MUTATED 1 0 1 1 1
TCEAL6 WILD-TYPE 42 95 56 125 46
'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S271.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
TCEAL6 MUTATED 2 1 1 0
TCEAL6 WILD-TYPE 108 79 102 50
'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.8

Table S272.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
TCEAL6 MUTATED 1 1 0 1 1
TCEAL6 WILD-TYPE 72 82 100 32 53
'DNAJC28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.82

Table S273.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
DNAJC28 MUTATED 0 3 1
DNAJC28 WILD-TYPE 92 146 124
'DNAJC28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 0.95

Table S274.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
DNAJC28 MUTATED 1 1 2
DNAJC28 WILD-TYPE 91 160 118
'DNAJC28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.72

Table S275.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
DNAJC28 MUTATED 2 2 0 0 0
DNAJC28 WILD-TYPE 66 86 74 68 69
'DNAJC28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S276.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
DNAJC28 MUTATED 2 1 1 0 0
DNAJC28 WILD-TYPE 51 54 115 87 56
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 0.97

Table S277.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
DNAJC28 MUTATED 1 1 1 1 0 0
DNAJC28 WILD-TYPE 39 63 90 83 48 41
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.63

Table S278.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
DNAJC28 MUTATED 1 3 0 0 0
DNAJC28 WILD-TYPE 42 92 57 126 47
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.8

Table S279.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
DNAJC28 MUTATED 2 2 0 0
DNAJC28 WILD-TYPE 108 78 103 50
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.89 (Fisher's exact test), Q value = 0.97

Table S280.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
DNAJC28 MUTATED 1 2 1 0 0
DNAJC28 WILD-TYPE 72 81 99 33 54
'FOXI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.8

Table S281.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
FOXI1 MUTATED 0 2 3
FOXI1 WILD-TYPE 92 147 122
'FOXI1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 0.9

Table S282.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
FOXI1 MUTATED 0 3 2
FOXI1 WILD-TYPE 92 158 118
'FOXI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.68

Table S283.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
FOXI1 MUTATED 0 0 2 0 2
FOXI1 WILD-TYPE 68 88 72 68 67
'FOXI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0918 (Fisher's exact test), Q value = 0.61

Table S284.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
FOXI1 MUTATED 0 0 0 2 2
FOXI1 WILD-TYPE 53 55 116 85 54
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 0.86

Table S285.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
FOXI1 MUTATED 0 0 1 3 1 0
FOXI1 WILD-TYPE 40 64 90 81 47 41
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 0.75

Table S286.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
FOXI1 MUTATED 0 0 1 2 2
FOXI1 WILD-TYPE 43 95 56 124 45
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 0.97

Table S287.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
FOXI1 MUTATED 1 1 2 1
FOXI1 WILD-TYPE 109 79 101 49
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 0.92

Table S288.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
FOXI1 MUTATED 1 1 1 0 2
FOXI1 WILD-TYPE 72 82 99 33 52
'KRTAP5-7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.82

Table S289.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
KRTAP5-7 MUTATED 0 3 1
KRTAP5-7 WILD-TYPE 92 146 124
'KRTAP5-7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.82

Table S290.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
KRTAP5-7 MUTATED 2 1 1
KRTAP5-7 WILD-TYPE 90 160 119
'KRTAP5-7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S291.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
KRTAP5-7 MUTATED 1 1 1 1 0
KRTAP5-7 WILD-TYPE 67 87 73 67 69
'KRTAP5-7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0779 (Fisher's exact test), Q value = 0.58

Table S292.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
KRTAP5-7 MUTATED 0 2 0 2 0
KRTAP5-7 WILD-TYPE 53 53 116 85 56
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.69

Table S293.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
KRTAP5-7 MUTATED 0 0 1 0 2 0
KRTAP5-7 WILD-TYPE 40 64 90 84 46 41
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 0.85

Table S294.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
KRTAP5-7 MUTATED 1 0 0 2 0
KRTAP5-7 WILD-TYPE 42 95 57 124 47
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.095

Table S295.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
KRTAP5-7 MUTATED 0 0 0 3
KRTAP5-7 WILD-TYPE 110 80 103 47

Figure S55.  Get High-res Image Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.76

Table S296.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
KRTAP5-7 MUTATED 0 0 2 1 0
KRTAP5-7 WILD-TYPE 73 83 98 32 54
'JAK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.92

Table S297.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
JAK1 MUTATED 5 5 4
JAK1 WILD-TYPE 87 144 121
'JAK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S298.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
JAK1 MUTATED 3 6 5
JAK1 WILD-TYPE 89 155 115
'JAK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.77

Table S299.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
JAK1 MUTATED 3 4 0 3 4
JAK1 WILD-TYPE 65 84 74 65 65
'JAK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.68

Table S300.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
JAK1 MUTATED 2 5 3 1 3
JAK1 WILD-TYPE 51 50 113 86 53
'JAK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S301.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
JAK1 MUTATED 2 2 4 4 1 1
JAK1 WILD-TYPE 38 62 87 80 47 40
'JAK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.821 (Fisher's exact test), Q value = 0.95

Table S302.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
JAK1 MUTATED 2 2 3 5 2
JAK1 WILD-TYPE 41 93 54 121 45
'JAK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.72

Table S303.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
JAK1 MUTATED 3 4 7 0
JAK1 WILD-TYPE 107 76 96 50
'JAK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.79

Table S304.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
JAK1 MUTATED 4 2 2 2 4
JAK1 WILD-TYPE 69 81 98 31 50
'DENND4B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.77

Table S305.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
DENND4B MUTATED 1 5 6
DENND4B WILD-TYPE 91 144 119
'DENND4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.77

Table S306.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
DENND4B MUTATED 2 8 2
DENND4B WILD-TYPE 90 153 118
'DENND4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.68

Table S307.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
DENND4B MUTATED 3 6 2 0 1
DENND4B WILD-TYPE 65 82 72 68 68
'DENND4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S308.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
DENND4B MUTATED 2 2 6 1 1
DENND4B WILD-TYPE 51 53 110 86 55
'DENND4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.47

Table S309.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
DENND4B MUTATED 2 4 0 5 0 1
DENND4B WILD-TYPE 38 60 91 79 48 40

Figure S56.  Get High-res Image Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'DENND4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 0.85

Table S310.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
DENND4B MUTATED 2 4 3 2 1
DENND4B WILD-TYPE 41 91 54 124 46
'DENND4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S311.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
DENND4B MUTATED 4 3 3 1
DENND4B WILD-TYPE 106 77 100 49
'DENND4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.347 (Fisher's exact test), Q value = 0.79

Table S312.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
DENND4B MUTATED 2 3 1 2 3
DENND4B WILD-TYPE 71 80 99 31 51
'BRD7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.659 (Fisher's exact test), Q value = 0.92

Table S313.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
BRD7 MUTATED 2 3 5
BRD7 WILD-TYPE 90 146 120
'BRD7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.84

Table S314.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
BRD7 MUTATED 2 3 5
BRD7 WILD-TYPE 90 158 115
'BRD7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.35 (Fisher's exact test), Q value = 0.8

Table S315.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
BRD7 MUTATED 1 2 5 1 1
BRD7 WILD-TYPE 67 86 69 67 68
'BRD7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.598 (Fisher's exact test), Q value = 0.89

Table S316.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
BRD7 MUTATED 1 0 4 4 1
BRD7 WILD-TYPE 52 55 112 83 55
'BRD7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.88

Table S317.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
BRD7 MUTATED 1 0 3 2 2 2
BRD7 WILD-TYPE 39 64 88 82 46 39
'BRD7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.69

Table S318.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
BRD7 MUTATED 1 0 3 5 1
BRD7 WILD-TYPE 42 95 54 121 46
'BRD7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 0.95

Table S319.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
BRD7 MUTATED 2 3 3 2
BRD7 WILD-TYPE 108 77 100 48
'BRD7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 0.67

Table S320.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
BRD7 MUTATED 1 0 5 1 3
BRD7 WILD-TYPE 72 83 95 32 51
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.82

Table S321.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
IDH1 MUTATED 1 5 2
IDH1 WILD-TYPE 91 144 123
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.25 (Fisher's exact test), Q value = 0.76

Table S322.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
IDH1 MUTATED 4 3 1
IDH1 WILD-TYPE 88 158 119
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.68

Table S323.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
IDH1 MUTATED 2 1 0 4 1
IDH1 WILD-TYPE 66 87 74 64 68
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.74

Table S324.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
IDH1 MUTATED 3 2 1 1 1
IDH1 WILD-TYPE 50 53 115 86 55
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.72

Table S325.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
IDH1 MUTATED 2 0 3 1 0 2
IDH1 WILD-TYPE 38 64 88 83 48 39
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.39 (Fisher's exact test), Q value = 0.8

Table S326.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
IDH1 MUTATED 2 1 0 4 1
IDH1 WILD-TYPE 41 94 57 122 46
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.8

Table S327.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
IDH1 MUTATED 2 4 2 0
IDH1 WILD-TYPE 108 76 101 50
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.174 (Fisher's exact test), Q value = 0.69

Table S328.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
IDH1 MUTATED 1 0 4 2 1
IDH1 WILD-TYPE 72 83 96 31 53
'CNGA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.68

Table S329.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CNGA3 MUTATED 0 5 5
CNGA3 WILD-TYPE 92 144 120
'CNGA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 0.99

Table S330.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CNGA3 MUTATED 2 5 4
CNGA3 WILD-TYPE 90 156 116
'CNGA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S331.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CNGA3 MUTATED 1 2 1 2 4
CNGA3 WILD-TYPE 67 86 73 66 65
'CNGA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.215 (Fisher's exact test), Q value = 0.72

Table S332.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CNGA3 MUTATED 2 1 4 0 3
CNGA3 WILD-TYPE 51 54 112 87 53
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.652 (Fisher's exact test), Q value = 0.92

Table S333.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CNGA3 MUTATED 1 1 3 4 0 2
CNGA3 WILD-TYPE 39 63 88 80 48 39
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

Table S334.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CNGA3 MUTATED 1 4 0 3 3
CNGA3 WILD-TYPE 42 91 57 123 44
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 0.92

Table S335.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CNGA3 MUTATED 5 1 3 1
CNGA3 WILD-TYPE 105 79 100 49
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 0.82

Table S336.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CNGA3 MUTATED 3 2 1 1 3
CNGA3 WILD-TYPE 70 81 99 32 51
'PLA2G3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.8

Table S337.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PLA2G3 MUTATED 0 3 3
PLA2G3 WILD-TYPE 92 146 122
'PLA2G3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0974 (Fisher's exact test), Q value = 0.62

Table S338.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PLA2G3 MUTATED 1 5 0
PLA2G3 WILD-TYPE 91 156 120
'PLA2G3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.69

Table S339.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PLA2G3 MUTATED 2 1 0 0 3
PLA2G3 WILD-TYPE 66 87 74 68 66
'PLA2G3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.66

Table S340.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PLA2G3 MUTATED 1 0 2 0 3
PLA2G3 WILD-TYPE 52 55 114 87 53
'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.8

Table S341.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PLA2G3 MUTATED 0 1 1 4 0 0
PLA2G3 WILD-TYPE 40 63 90 80 48 41
'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0133 (Fisher's exact test), Q value = 0.23

Table S342.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PLA2G3 MUTATED 0 1 0 1 4
PLA2G3 WILD-TYPE 43 94 57 125 43

Figure S57.  Get High-res Image Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 0.92

Table S343.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PLA2G3 MUTATED 2 1 3 0
PLA2G3 WILD-TYPE 108 79 100 50
'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0366 (Fisher's exact test), Q value = 0.4

Table S344.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PLA2G3 MUTATED 0 1 1 0 4
PLA2G3 WILD-TYPE 73 82 99 33 50

Figure S58.  Get High-res Image Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-DPB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S345.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
HLA-DPB1 MUTATED 1 2 1
HLA-DPB1 WILD-TYPE 91 147 124
'HLA-DPB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.78

Table S346.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
HLA-DPB1 MUTATED 0 4 1
HLA-DPB1 WILD-TYPE 92 157 119
'HLA-DPB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.82

Table S347.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
HLA-DPB1 MUTATED 2 2 0 0 1
HLA-DPB1 WILD-TYPE 66 86 74 68 68
'HLA-DPB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.77

Table S348.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
HLA-DPB1 MUTATED 2 0 2 0 1
HLA-DPB1 WILD-TYPE 51 55 114 87 55
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 0.69

Table S349.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
HLA-DPB1 MUTATED 0 3 0 1 1 0
HLA-DPB1 WILD-TYPE 40 61 91 83 47 41
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.776 (Fisher's exact test), Q value = 0.94

Table S350.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
HLA-DPB1 MUTATED 0 2 1 1 1
HLA-DPB1 WILD-TYPE 43 93 56 125 46
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S351.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
HLA-DPB1 MUTATED 2 0 2 0
HLA-DPB1 WILD-TYPE 108 80 101 50
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.81

Table S352.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
HLA-DPB1 MUTATED 2 1 0 0 1
HLA-DPB1 WILD-TYPE 71 82 100 33 53
'ALMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.82

Table S353.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
ALMS1 MUTATED 5 8 11
ALMS1 WILD-TYPE 87 141 114
'ALMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.7

Table S354.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
ALMS1 MUTATED 5 7 12
ALMS1 WILD-TYPE 87 154 108
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 0.95

Table S355.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
ALMS1 MUTATED 6 4 5 3 5
ALMS1 WILD-TYPE 62 84 69 65 64
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.981 (Fisher's exact test), Q value = 1

Table S356.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
ALMS1 MUTATED 4 3 8 5 3
ALMS1 WILD-TYPE 49 52 108 82 53
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 0.82

Table S357.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
ALMS1 MUTATED 2 4 7 9 1 1
ALMS1 WILD-TYPE 38 60 84 75 47 40
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.7 (Fisher's exact test), Q value = 0.92

Table S358.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
ALMS1 MUTATED 2 9 4 6 3
ALMS1 WILD-TYPE 41 86 53 120 44
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.82

Table S359.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
ALMS1 MUTATED 8 7 8 1
ALMS1 WILD-TYPE 102 73 95 49
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.702 (Fisher's exact test), Q value = 0.92

Table S360.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
ALMS1 MUTATED 6 7 5 1 5
ALMS1 WILD-TYPE 67 76 95 32 49
'NUCB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S361.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
NUCB2 MUTATED 0 1 2
NUCB2 WILD-TYPE 92 148 123
'NUCB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.82

Table S362.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
NUCB2 MUTATED 0 1 2
NUCB2 WILD-TYPE 92 160 118
'NUCB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.397 (Fisher's exact test), Q value = 0.8

Table S363.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
NUCB2 MUTATED 0 0 2 0 0 1
NUCB2 WILD-TYPE 40 64 89 84 48 40
'NUCB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 0.82

Table S364.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
NUCB2 MUTATED 0 0 0 3 0
NUCB2 WILD-TYPE 43 95 57 123 47
'NUCB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0147 (Fisher's exact test), Q value = 0.24

Table S365.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
NUCB2 MUTATED 0 3 0 0
NUCB2 WILD-TYPE 110 77 103 50

Figure S59.  Get High-res Image Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'NUCB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 0.96

Table S366.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
NUCB2 MUTATED 0 1 2 0 0
NUCB2 WILD-TYPE 73 82 98 33 54
'BAZ2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.82

Table S367.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
BAZ2A MUTATED 1 5 5
BAZ2A WILD-TYPE 91 144 120
'BAZ2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.8

Table S368.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
BAZ2A MUTATED 1 7 3
BAZ2A WILD-TYPE 91 154 117
'BAZ2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.973 (Fisher's exact test), Q value = 1

Table S369.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
BAZ2A MUTATED 2 2 2 3 2
BAZ2A WILD-TYPE 66 86 72 65 67
'BAZ2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.683 (Fisher's exact test), Q value = 0.92

Table S370.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
BAZ2A MUTATED 2 3 2 2 2
BAZ2A WILD-TYPE 51 52 114 85 54
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.82

Table S371.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
BAZ2A MUTATED 0 3 2 4 0 2
BAZ2A WILD-TYPE 40 61 89 80 48 39
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S372.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
BAZ2A MUTATED 0 2 3 4 2
BAZ2A WILD-TYPE 43 93 54 122 45
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 0.58

Table S373.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
BAZ2A MUTATED 2 6 2 0
BAZ2A WILD-TYPE 108 74 101 50
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 0.89

Table S374.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
BAZ2A MUTATED 4 2 2 0 2
BAZ2A WILD-TYPE 69 81 98 33 52
'TAF1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.72

Table S375.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
TAF1B MUTATED 0 2 4
TAF1B WILD-TYPE 92 147 121
'TAF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0952 (Fisher's exact test), Q value = 0.61

Table S376.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
TAF1B MUTATED 1 5 0
TAF1B WILD-TYPE 91 156 120
'TAF1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0838 (Fisher's exact test), Q value = 0.59

Table S377.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
TAF1B MUTATED 3 0 0 1 1
TAF1B WILD-TYPE 65 88 74 67 68
'TAF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 0.92

Table S378.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
TAF1B MUTATED 1 1 2 0 1
TAF1B WILD-TYPE 52 54 114 87 55
'TAF1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 0.95

Table S379.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
TAF1B MUTATED 1 2 2 1 0 0
TAF1B WILD-TYPE 39 62 89 83 48 41
'TAF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.805 (Fisher's exact test), Q value = 0.95

Table S380.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
TAF1B MUTATED 1 2 1 1 1
TAF1B WILD-TYPE 42 93 56 125 46
'TAF1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.82

Table S381.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
TAF1B MUTATED 4 1 1 0
TAF1B WILD-TYPE 106 79 102 50
'TAF1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 0.77

Table S382.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
TAF1B MUTATED 1 3 0 1 1
TAF1B WILD-TYPE 72 80 100 32 53
'C1ORF125 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.79

Table S383.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
C1ORF125 MUTATED 1 4 6
C1ORF125 WILD-TYPE 91 145 119
'C1ORF125 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 0.55

Table S384.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
C1ORF125 MUTATED 0 8 3
C1ORF125 WILD-TYPE 92 153 117
'C1ORF125 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S385.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
C1ORF125 MUTATED 1 4 1 3 2
C1ORF125 WILD-TYPE 67 84 73 65 67
'C1ORF125 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.813 (Fisher's exact test), Q value = 0.95

Table S386.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
C1ORF125 MUTATED 1 3 3 2 2
C1ORF125 WILD-TYPE 52 52 113 85 54
'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.71

Table S387.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
C1ORF125 MUTATED 0 4 5 1 0 1
C1ORF125 WILD-TYPE 40 60 86 83 48 40
'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.24

Table S388.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
C1ORF125 MUTATED 1 8 1 1 0
C1ORF125 WILD-TYPE 42 87 56 125 47

Figure S60.  Get High-res Image Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0799 (Fisher's exact test), Q value = 0.59

Table S389.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
C1ORF125 MUTATED 1 5 5 0
C1ORF125 WILD-TYPE 109 75 98 50
'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.226 (Fisher's exact test), Q value = 0.72

Table S390.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
C1ORF125 MUTATED 1 6 2 0 2
C1ORF125 WILD-TYPE 72 77 98 33 52
'AR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.473 (Fisher's exact test), Q value = 0.82

Table S391.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
AR MUTATED 4 4 2
AR WILD-TYPE 88 145 123
'AR MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S392.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
AR MUTATED 2 5 3
AR WILD-TYPE 90 156 117
'AR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.712 (Fisher's exact test), Q value = 0.92

Table S393.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
AR MUTATED 3 2 3 1 1
AR WILD-TYPE 65 86 71 67 68
'AR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 0.92

Table S394.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
AR MUTATED 2 0 4 3 1
AR WILD-TYPE 51 55 112 84 55
'AR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.474 (Fisher's exact test), Q value = 0.82

Table S395.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
AR MUTATED 1 2 2 2 0 3
AR WILD-TYPE 39 62 89 82 48 38
'AR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.171 (Fisher's exact test), Q value = 0.69

Table S396.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
AR MUTATED 1 3 4 1 1
AR WILD-TYPE 42 92 53 125 46
'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.72

Table S397.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
AR MUTATED 6 1 2 0
AR WILD-TYPE 104 79 101 50
'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.661 (Fisher's exact test), Q value = 0.92

Table S398.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
AR MUTATED 3 3 1 1 1
AR WILD-TYPE 70 80 99 32 53
'SPHK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.8

Table S399.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
SPHK1 MUTATED 0 3 3
SPHK1 WILD-TYPE 92 146 122
'SPHK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 0.94

Table S400.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
SPHK1 MUTATED 2 3 1
SPHK1 WILD-TYPE 90 158 119
'SPHK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0365 (Fisher's exact test), Q value = 0.4

Table S401.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
SPHK1 MUTATED 1 0 0 0 3
SPHK1 WILD-TYPE 67 88 74 68 66

Figure S61.  Get High-res Image Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'SPHK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0107 (Fisher's exact test), Q value = 0.21

Table S402.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
SPHK1 MUTATED 1 0 0 0 3
SPHK1 WILD-TYPE 52 55 116 87 53

Figure S62.  Get High-res Image Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'SPHK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.524 (Fisher's exact test), Q value = 0.85

Table S403.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
SPHK1 MUTATED 1 0 2 3 0 0
SPHK1 WILD-TYPE 39 64 89 81 48 41
'SPHK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0937 (Fisher's exact test), Q value = 0.61

Table S404.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
SPHK1 MUTATED 1 1 0 1 3
SPHK1 WILD-TYPE 42 94 57 125 44
'SPHK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.116 (Fisher's exact test), Q value = 0.66

Table S405.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
SPHK1 MUTATED 0 1 3 2
SPHK1 WILD-TYPE 110 79 100 48
'SPHK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.105 (Fisher's exact test), Q value = 0.63

Table S406.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
SPHK1 MUTATED 1 2 0 0 3
SPHK1 WILD-TYPE 72 81 100 33 51
'CREB3L3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0913 (Fisher's exact test), Q value = 0.61

Table S407.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CREB3L3 MUTATED 2 0 3
CREB3L3 WILD-TYPE 90 149 122
'CREB3L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.82

Table S408.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CREB3L3 MUTATED 1 1 3
CREB3L3 WILD-TYPE 91 160 117
'CREB3L3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.68

Table S409.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CREB3L3 MUTATED 1 0 1 0 3
CREB3L3 WILD-TYPE 67 88 73 68 66
'CREB3L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.619 (Fisher's exact test), Q value = 0.9

Table S410.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CREB3L3 MUTATED 0 0 2 1 2
CREB3L3 WILD-TYPE 53 55 114 86 54
'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.8

Table S411.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CREB3L3 MUTATED 0 1 0 3 1 0
CREB3L3 WILD-TYPE 40 63 91 81 47 41
'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0816 (Fisher's exact test), Q value = 0.59

Table S412.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CREB3L3 MUTATED 0 1 0 1 3
CREB3L3 WILD-TYPE 43 94 57 125 44
'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S413.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CREB3L3 MUTATED 1 1 1 0
CREB3L3 WILD-TYPE 109 79 102 50
'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.68

Table S414.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CREB3L3 MUTATED 2 0 0 0 1
CREB3L3 WILD-TYPE 71 83 100 33 53
'LFNG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.82

Table S415.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
LFNG MUTATED 1 2 4
LFNG WILD-TYPE 91 147 121
'LFNG MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S416.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
LFNG MUTATED 2 4 1
LFNG WILD-TYPE 90 157 119
'LFNG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.7 (Fisher's exact test), Q value = 0.92

Table S417.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
LFNG MUTATED 1 2 0 2 2
LFNG WILD-TYPE 67 86 74 66 67
'LFNG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.905 (Fisher's exact test), Q value = 0.98

Table S418.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
LFNG MUTATED 1 1 2 1 2
LFNG WILD-TYPE 52 54 114 86 54
'LFNG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.82

Table S419.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
LFNG MUTATED 2 0 2 2 0 1
LFNG WILD-TYPE 38 64 89 82 48 40
'LFNG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 0.82

Table S420.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
LFNG MUTATED 2 1 0 3 1
LFNG WILD-TYPE 41 94 57 123 46
'LFNG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 0.94

Table S421.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
LFNG MUTATED 1 2 2 0
LFNG WILD-TYPE 109 78 101 50
'LFNG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 0.85

Table S422.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
LFNG MUTATED 0 2 1 1 1
LFNG WILD-TYPE 73 81 99 32 53
'FZR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S423.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
FZR1 MUTATED 1 4 1
FZR1 WILD-TYPE 91 145 124
'FZR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S424.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
FZR1 MUTATED 1 3 2
FZR1 WILD-TYPE 91 158 118
'FZR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.78

Table S425.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
FZR1 MUTATED 0 3 0 1 2
FZR1 WILD-TYPE 68 85 74 67 67
'FZR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 0.82

Table S426.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
FZR1 MUTATED 0 0 3 1 2
FZR1 WILD-TYPE 53 55 113 86 54
'FZR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 0.95

Table S427.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
FZR1 MUTATED 0 1 3 2 0 0
FZR1 WILD-TYPE 40 63 88 82 48 41
'FZR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.38

Table S428.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
FZR1 MUTATED 0 4 0 0 2
FZR1 WILD-TYPE 43 91 57 126 45

Figure S63.  Get High-res Image Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'FZR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.72

Table S429.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
FZR1 MUTATED 0 2 3 0
FZR1 WILD-TYPE 110 78 100 50
'FZR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0877 (Fisher's exact test), Q value = 0.6

Table S430.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
FZR1 MUTATED 1 1 0 0 3
FZR1 WILD-TYPE 72 82 100 33 51
'TRIOBP MUTATION STATUS' versus 'CN_CNMF'

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

Table S431.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
TRIOBP MUTATED 3 4 4
TRIOBP WILD-TYPE 89 145 121
'TRIOBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.66

Table S432.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
TRIOBP MUTATED 0 6 5
TRIOBP WILD-TYPE 92 155 115
'TRIOBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.79

Table S433.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
TRIOBP MUTATED 0 2 3 2 4
TRIOBP WILD-TYPE 68 86 71 66 65
'TRIOBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.376 (Fisher's exact test), Q value = 0.8

Table S434.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
TRIOBP MUTATED 2 1 2 2 4
TRIOBP WILD-TYPE 51 54 114 85 52
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.8

Table S435.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
TRIOBP MUTATED 1 1 1 4 1 3
TRIOBP WILD-TYPE 39 63 90 80 47 38
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 0.82

Table S436.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
TRIOBP MUTATED 1 1 2 4 3
TRIOBP WILD-TYPE 42 94 55 122 44
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0981 (Fisher's exact test), Q value = 0.62

Table S437.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
TRIOBP MUTATED 0 3 4 2
TRIOBP WILD-TYPE 110 77 99 48
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.81

Table S438.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
TRIOBP MUTATED 1 1 4 0 3
TRIOBP WILD-TYPE 72 82 96 33 51
'GJB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S439.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
GJB1 MUTATED 1 1 1
GJB1 WILD-TYPE 91 148 124
'GJB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 0.95

Table S440.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
GJB1 MUTATED 0 2 1
GJB1 WILD-TYPE 92 159 119
'GJB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 0.77

Table S441.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
GJB1 MUTATED 1 0 2 0 0
GJB1 WILD-TYPE 67 88 72 68 69
'GJB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 0.92

Table S442.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
GJB1 MUTATED 0 0 1 2 0
GJB1 WILD-TYPE 53 55 115 85 56
'GJB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.72

Table S443.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
GJB1 MUTATED 0 1 0 0 1 1
GJB1 WILD-TYPE 40 63 91 84 47 40
'GJB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.91 (Fisher's exact test), Q value = 0.98

Table S444.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
GJB1 MUTATED 0 1 1 1 0
GJB1 WILD-TYPE 43 94 56 125 47
'GJB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.68

Table S445.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
GJB1 MUTATED 3 0 0 0
GJB1 WILD-TYPE 107 80 103 50
'GJB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S446.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
GJB1 MUTATED 1 1 1 0 0
GJB1 WILD-TYPE 72 82 99 33 54
'DYRK1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0325 (Fisher's exact test), Q value = 0.4

Table S447.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
DYRK1A MUTATED 2 0 5
DYRK1A WILD-TYPE 90 149 120

Figure S64.  Get High-res Image Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DYRK1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 0.97

Table S448.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
DYRK1A MUTATED 1 4 2
DYRK1A WILD-TYPE 91 157 118
'DYRK1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S449.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
DYRK1A MUTATED 2 1 1 2 1
DYRK1A WILD-TYPE 66 87 73 66 68
'DYRK1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 0.91

Table S450.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
DYRK1A MUTATED 1 2 3 1 0
DYRK1A WILD-TYPE 52 53 113 86 56
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.77

Table S451.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
DYRK1A MUTATED 2 2 0 2 1 0
DYRK1A WILD-TYPE 38 62 91 82 47 41
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.82

Table S452.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
DYRK1A MUTATED 2 2 1 1 1
DYRK1A WILD-TYPE 41 93 56 125 46
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 0.94

Table S453.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
DYRK1A MUTATED 3 1 1 1
DYRK1A WILD-TYPE 107 79 102 49
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 0.77

Table S454.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
DYRK1A MUTATED 1 2 1 2 0
DYRK1A WILD-TYPE 72 81 99 31 54
'TNPO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.82

Table S455.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
TNPO1 MUTATED 1 3 5
TNPO1 WILD-TYPE 91 146 120
'TNPO1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 0.98

Table S456.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
TNPO1 MUTATED 2 5 2
TNPO1 WILD-TYPE 90 156 118
'TNPO1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.79

Table S457.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
TNPO1 MUTATED 1 2 0 3 3
TNPO1 WILD-TYPE 67 86 74 65 66
'TNPO1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.505 (Fisher's exact test), Q value = 0.84

Table S458.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
TNPO1 MUTATED 2 1 2 1 3
TNPO1 WILD-TYPE 51 54 114 86 53
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S459.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
TNPO1 MUTATED 0 2 2 3 0 2
TNPO1 WILD-TYPE 40 62 89 81 48 39
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.466 (Fisher's exact test), Q value = 0.82

Table S460.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
TNPO1 MUTATED 0 2 1 3 3
TNPO1 WILD-TYPE 43 93 56 123 44
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.186 (Fisher's exact test), Q value = 0.71

Table S461.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
TNPO1 MUTATED 1 4 4 0
TNPO1 WILD-TYPE 109 76 99 50
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.629 (Fisher's exact test), Q value = 0.9

Table S462.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
TNPO1 MUTATED 1 2 3 0 3
TNPO1 WILD-TYPE 72 81 97 33 51
'PDZD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.78

Table S463.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PDZD4 MUTATED 0 1 3
PDZD4 WILD-TYPE 92 148 122
'PDZD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S464.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PDZD4 MUTATED 1 2 1
PDZD4 WILD-TYPE 91 159 119
'PDZD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 0.92

Table S465.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PDZD4 MUTATED 1 2 0 0 1
PDZD4 WILD-TYPE 67 86 74 68 68
'PDZD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.76

Table S466.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PDZD4 MUTATED 0 2 1 0 1
PDZD4 WILD-TYPE 53 53 115 87 55
'PDZD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.82

Table S467.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PDZD4 MUTATED 1 1 0 2 0 0
PDZD4 WILD-TYPE 39 63 91 82 48 41
'PDZD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.77

Table S468.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PDZD4 MUTATED 1 1 1 0 1
PDZD4 WILD-TYPE 42 94 56 126 46
'CCNA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 0.82

Table S469.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CCNA2 MUTATED 0 3 2
CCNA2 WILD-TYPE 92 146 123
'CCNA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.73 (Fisher's exact test), Q value = 0.92

Table S470.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CCNA2 MUTATED 2 2 1
CCNA2 WILD-TYPE 90 159 119
'CCNA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0943 (Fisher's exact test), Q value = 0.61

Table S471.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CCNA2 MUTATED 2 0 0 2 0
CCNA2 WILD-TYPE 66 88 74 66 69
'CCNA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.789 (Fisher's exact test), Q value = 0.95

Table S472.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CCNA2 MUTATED 1 1 1 1 0
CCNA2 WILD-TYPE 52 54 115 86 56
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.74

Table S473.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CCNA2 MUTATED 2 1 2 0 0 0
CCNA2 WILD-TYPE 38 63 89 84 48 41
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.72

Table S474.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CCNA2 MUTATED 2 0 1 2 0
CCNA2 WILD-TYPE 41 95 56 124 47
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.8

Table S475.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CCNA2 MUTATED 2 2 0 1
CCNA2 WILD-TYPE 108 78 103 49
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.257 (Fisher's exact test), Q value = 0.76

Table S476.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CCNA2 MUTATED 1 1 1 2 0
CCNA2 WILD-TYPE 72 82 99 31 54
'AHCTF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 0.85

Table S477.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
AHCTF1 MUTATED 3 2 3
AHCTF1 WILD-TYPE 89 147 122
'AHCTF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 0.95

Table S478.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
AHCTF1 MUTATED 1 4 3
AHCTF1 WILD-TYPE 91 157 117
'AHCTF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.6 (Fisher's exact test), Q value = 0.9

Table S479.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
AHCTF1 MUTATED 1 2 3 0 2
AHCTF1 WILD-TYPE 67 86 71 68 67
'AHCTF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 0.92

Table S480.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
AHCTF1 MUTATED 2 1 2 1 2
AHCTF1 WILD-TYPE 51 54 114 86 54
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.85

Table S481.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
AHCTF1 MUTATED 1 1 1 3 0 2
AHCTF1 WILD-TYPE 39 63 90 81 48 39
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S482.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
AHCTF1 MUTATED 1 3 1 2 1
AHCTF1 WILD-TYPE 42 92 56 124 46
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 0.98

Table S483.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
AHCTF1 MUTATED 2 1 3 1
AHCTF1 WILD-TYPE 108 79 100 49
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S484.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
AHCTF1 MUTATED 1 2 2 1 1
AHCTF1 WILD-TYPE 72 81 98 32 53
'RXRB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.816 (Fisher's exact test), Q value = 0.95

Table S485.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
RXRB MUTATED 1 4 3
RXRB WILD-TYPE 91 145 122
'RXRB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.66 (Fisher's exact test), Q value = 0.92

Table S486.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
RXRB MUTATED 1 5 2
RXRB WILD-TYPE 91 156 118
'RXRB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.82

Table S487.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
RXRB MUTATED 1 1 2 0 3
RXRB WILD-TYPE 67 87 72 68 66
'RXRB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 0.94

Table S488.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
RXRB MUTATED 1 1 1 2 2
RXRB WILD-TYPE 52 54 115 85 54
'RXRB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.82

Table S489.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
RXRB MUTATED 1 0 1 3 2 1
RXRB WILD-TYPE 39 64 90 81 46 40
'RXRB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.811 (Fisher's exact test), Q value = 0.95

Table S490.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
RXRB MUTATED 1 2 0 4 1
RXRB WILD-TYPE 42 93 57 122 46
'RXRB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.921 (Fisher's exact test), Q value = 0.99

Table S491.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
RXRB MUTATED 3 1 3 1
RXRB WILD-TYPE 107 79 100 49
'RXRB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 0.97

Table S492.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
RXRB MUTATED 1 2 2 1 2
RXRB WILD-TYPE 72 81 98 32 52
'PARP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 0.85

Table S493.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PARP1 MUTATED 1 1 3
PARP1 WILD-TYPE 91 148 122
'PARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 0.96

Table S494.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PARP1 MUTATED 1 3 1
PARP1 WILD-TYPE 91 158 119
'PARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.77

Table S495.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PARP1 MUTATED 2 0 1 0 2
PARP1 WILD-TYPE 66 88 73 68 67
'PARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.659 (Fisher's exact test), Q value = 0.92

Table S496.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PARP1 MUTATED 1 1 2 0 1
PARP1 WILD-TYPE 52 54 114 87 55
'PARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.79

Table S497.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PARP1 MUTATED 1 2 0 1 0 1
PARP1 WILD-TYPE 39 62 91 83 48 40
'PARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.598 (Fisher's exact test), Q value = 0.89

Table S498.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PARP1 MUTATED 1 2 0 1 1
PARP1 WILD-TYPE 42 93 57 125 46
'PARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 0.9

Table S499.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PARP1 MUTATED 2 0 2 1
PARP1 WILD-TYPE 108 80 101 49
'PARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 0.85

Table S500.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PARP1 MUTATED 0 2 1 1 1
PARP1 WILD-TYPE 73 81 99 32 53
'NBEA MUTATION STATUS' versus 'CN_CNMF'

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

Table S501.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
NBEA MUTATED 5 7 9
NBEA WILD-TYPE 87 142 116
'NBEA MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S502.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
NBEA MUTATED 3 12 6
NBEA WILD-TYPE 89 149 114
'NBEA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 0.96

Table S503.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
NBEA MUTATED 4 6 5 2 4
NBEA WILD-TYPE 64 82 69 66 65
'NBEA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 0.98

Table S504.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
NBEA MUTATED 2 2 8 6 3
NBEA WILD-TYPE 51 53 108 81 53
'NBEA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.77

Table S505.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
NBEA MUTATED 2 6 3 8 1 1
NBEA WILD-TYPE 38 58 88 76 47 40
'NBEA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.68

Table S506.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
NBEA MUTATED 2 9 5 3 2
NBEA WILD-TYPE 41 86 52 123 45
'NBEA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.733 (Fisher's exact test), Q value = 0.92

Table S507.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
NBEA MUTATED 8 3 7 2
NBEA WILD-TYPE 102 77 96 48
'NBEA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 0.92

Table S508.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
NBEA MUTATED 5 7 4 2 2
NBEA WILD-TYPE 68 76 96 31 52
'H6PD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 0.85

Table S509.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
H6PD MUTATED 1 1 3
H6PD WILD-TYPE 91 148 122
'H6PD MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S510.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
H6PD MUTATED 0 3 2
H6PD WILD-TYPE 92 158 118
'H6PD MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.77

Table S511.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
H6PD MUTATED 2 0 1 0 2
H6PD WILD-TYPE 66 88 73 68 67
'H6PD MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.152 (Fisher's exact test), Q value = 0.68

Table S512.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
H6PD MUTATED 1 0 0 2 2
H6PD WILD-TYPE 52 55 116 85 54
'H6PD MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.82

Table S513.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
H6PD MUTATED 0 2 0 2 1 0
H6PD WILD-TYPE 40 62 91 82 47 41
'H6PD MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.12 (Fisher's exact test), Q value = 0.66

Table S514.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
H6PD MUTATED 0 2 1 0 2
H6PD WILD-TYPE 43 93 56 126 45
'H6PD MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.871 (Fisher's exact test), Q value = 0.97

Table S515.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
H6PD MUTATED 1 1 2 1
H6PD WILD-TYPE 109 79 101 49
'H6PD MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.78

Table S516.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
H6PD MUTATED 2 0 1 0 2
H6PD WILD-TYPE 71 83 99 33 52
'VPS4B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 0.92

Table S517.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
VPS4B MUTATED 2 2 1
VPS4B WILD-TYPE 90 147 124
'VPS4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0445 (Fisher's exact test), Q value = 0.46

Table S518.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
VPS4B MUTATED 0 5 0
VPS4B WILD-TYPE 92 156 120

Figure S65.  Get High-res Image Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'VPS4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0876 (Fisher's exact test), Q value = 0.6

Table S519.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
VPS4B MUTATED 0 1 0 0 3
VPS4B WILD-TYPE 68 87 74 68 66
'VPS4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.77

Table S520.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
VPS4B MUTATED 0 0 2 0 2
VPS4B WILD-TYPE 53 55 114 87 54
'VPS4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.76 (Fisher's exact test), Q value = 0.94

Table S521.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
VPS4B MUTATED 0 2 1 2 0 0
VPS4B WILD-TYPE 40 62 90 82 48 41
'VPS4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.302 (Fisher's exact test), Q value = 0.78

Table S522.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
VPS4B MUTATED 1 1 0 1 2
VPS4B WILD-TYPE 42 94 57 125 45
'VPS4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.72

Table S523.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
VPS4B MUTATED 0 2 3 0
VPS4B WILD-TYPE 110 78 100 50
'VPS4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0721 (Fisher's exact test), Q value = 0.57

Table S524.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
VPS4B MUTATED 0 3 0 0 2
VPS4B WILD-TYPE 73 80 100 33 52
'HNRNPL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.85

Table S525.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
HNRNPL MUTATED 3 2 3
HNRNPL WILD-TYPE 89 147 122
'HNRNPL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.78

Table S526.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
HNRNPL MUTATED 1 6 1
HNRNPL WILD-TYPE 91 155 119
'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0264 (Fisher's exact test), Q value = 0.37

Table S527.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
HNRNPL MUTATED 4 0 0 1 2
HNRNPL WILD-TYPE 64 88 74 67 67

Figure S66.  Get High-res Image Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.77

Table S528.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
HNRNPL MUTATED 3 0 2 1 1
HNRNPL WILD-TYPE 50 55 114 86 55
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.77

Table S529.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
HNRNPL MUTATED 1 4 2 1 0 0
HNRNPL WILD-TYPE 39 60 89 83 48 41
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 0.94

Table S530.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
HNRNPL MUTATED 0 3 2 2 1
HNRNPL WILD-TYPE 43 92 55 124 46
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 0.92

Table S531.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
HNRNPL MUTATED 4 2 2 0
HNRNPL WILD-TYPE 106 78 101 50
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S532.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
HNRNPL MUTATED 3 3 1 0 1
HNRNPL WILD-TYPE 70 80 99 33 53
'FILIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.82 (Fisher's exact test), Q value = 0.95

Table S533.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
FILIP1 MUTATED 2 6 5
FILIP1 WILD-TYPE 90 143 120
'FILIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.8

Table S534.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
FILIP1 MUTATED 3 8 2
FILIP1 WILD-TYPE 89 153 118
'FILIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.77

Table S535.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
FILIP1 MUTATED 4 3 0 2 3
FILIP1 WILD-TYPE 64 85 74 66 66
'FILIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.446 (Fisher's exact test), Q value = 0.82

Table S536.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
FILIP1 MUTATED 3 2 3 1 3
FILIP1 WILD-TYPE 50 53 113 86 53
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.92

Table S537.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
FILIP1 MUTATED 2 3 3 4 0 1
FILIP1 WILD-TYPE 38 61 88 80 48 40
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.8

Table S538.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
FILIP1 MUTATED 3 2 2 3 3
FILIP1 WILD-TYPE 40 93 55 123 44
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.487 (Fisher's exact test), Q value = 0.82

Table S539.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
FILIP1 MUTATED 4 4 3 0
FILIP1 WILD-TYPE 106 76 100 50
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 0.88

Table S540.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
FILIP1 MUTATED 2 4 2 0 3
FILIP1 WILD-TYPE 71 79 98 33 51
'FAM22F MUTATION STATUS' versus 'CN_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.67

Table S541.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
FAM22F MUTATED 1 0 3
FAM22F WILD-TYPE 91 149 122
'FAM22F MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0908 (Fisher's exact test), Q value = 0.61

Table S542.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
FAM22F MUTATED 1 0 3
FAM22F WILD-TYPE 91 161 117
'FAM22F MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0277 (Fisher's exact test), Q value = 0.37

Table S543.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
FAM22F MUTATED 0 0 0 3 1
FAM22F WILD-TYPE 68 88 74 65 68

Figure S67.  Get High-res Image Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FAM22F MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.78

Table S544.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
FAM22F MUTATED 1 0 0 2 1
FAM22F WILD-TYPE 52 55 116 85 55
'FAM22F MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.92

Table S545.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
FAM22F MUTATED 0 0 2 1 0 1
FAM22F WILD-TYPE 40 64 89 83 48 40
'FAM22F MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.8

Table S546.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
FAM22F MUTATED 0 0 0 3 1
FAM22F WILD-TYPE 43 95 57 123 46
'FAM22F MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0842 (Fisher's exact test), Q value = 0.59

Table S547.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
FAM22F MUTATED 0 3 1 0
FAM22F WILD-TYPE 110 77 102 50
'FAM22F MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.77

Table S548.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
FAM22F MUTATED 0 0 3 0 1
FAM22F WILD-TYPE 73 83 97 33 53
'GPSM2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.82

Table S549.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
GPSM2 MUTATED 0 3 1
GPSM2 WILD-TYPE 92 146 124
'GPSM2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 0.92

Table S550.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
GPSM2 MUTATED 0 2 2
GPSM2 WILD-TYPE 92 159 118
'GPSM2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 0.92

Table S551.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
GPSM2 MUTATED 1 2 0 1 0
GPSM2 WILD-TYPE 67 86 74 67 69
'GPSM2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.872 (Fisher's exact test), Q value = 0.97

Table S552.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
GPSM2 MUTATED 1 0 2 1 0
GPSM2 WILD-TYPE 52 55 114 86 56
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S553.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
GPSM2 MUTATED 0 1 2 1 0 0
GPSM2 WILD-TYPE 40 63 89 83 48 41
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.91

Table S554.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
GPSM2 MUTATED 0 2 0 1 1
GPSM2 WILD-TYPE 43 93 57 125 46
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0833 (Fisher's exact test), Q value = 0.59

Table S555.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
GPSM2 MUTATED 0 3 1 0
GPSM2 WILD-TYPE 110 77 102 50
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.845 (Fisher's exact test), Q value = 0.96

Table S556.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
GPSM2 MUTATED 0 1 2 0 1
GPSM2 WILD-TYPE 73 82 98 33 53
'RCCD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.78

Table S557.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
RCCD1 MUTATED 0 4 1
RCCD1 WILD-TYPE 92 145 124
'RCCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 0.96

Table S558.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
RCCD1 MUTATED 1 3 1
RCCD1 WILD-TYPE 91 158 119
'RCCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 0.95

Table S559.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
RCCD1 MUTATED 1 2 1 0 0
RCCD1 WILD-TYPE 67 86 73 68 69
'RCCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.465 (Fisher's exact test), Q value = 0.82

Table S560.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
RCCD1 MUTATED 0 2 1 1 0
RCCD1 WILD-TYPE 53 53 115 86 56
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 0.92

Table S561.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
RCCD1 MUTATED 1 0 1 2 1 0
RCCD1 WILD-TYPE 39 64 90 82 47 41
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.82

Table S562.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
RCCD1 MUTATED 1 1 2 1 0
RCCD1 WILD-TYPE 42 94 55 125 47
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.79

Table S563.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
RCCD1 MUTATED 3 1 0 1
RCCD1 WILD-TYPE 107 79 103 49
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.625 (Fisher's exact test), Q value = 0.9

Table S564.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
RCCD1 MUTATED 2 1 1 1 0
RCCD1 WILD-TYPE 71 82 99 32 54
'PTGR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.72

Table S565.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PTGR1 MUTATED 2 3 0
PTGR1 WILD-TYPE 90 146 125
'PTGR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S566.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PTGR1 MUTATED 0 3 2
PTGR1 WILD-TYPE 92 158 118
'PTGR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 0.96

Table S567.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PTGR1 MUTATED 1 0 1 1 1
PTGR1 WILD-TYPE 67 88 73 67 68
'PTGR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.445 (Fisher's exact test), Q value = 0.82

Table S568.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PTGR1 MUTATED 1 1 0 1 1
PTGR1 WILD-TYPE 52 54 116 86 55
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.929 (Fisher's exact test), Q value = 0.99

Table S569.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PTGR1 MUTATED 0 1 2 2 0 0
PTGR1 WILD-TYPE 40 63 89 82 48 41
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.78

Table S570.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PTGR1 MUTATED 0 0 2 2 1
PTGR1 WILD-TYPE 43 95 55 124 46
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.812 (Fisher's exact test), Q value = 0.95

Table S571.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PTGR1 MUTATED 2 2 1 0
PTGR1 WILD-TYPE 108 78 102 50
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.72

Table S572.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PTGR1 MUTATED 3 1 0 0 1
PTGR1 WILD-TYPE 70 82 100 33 53
'SAMM50 MUTATION STATUS' versus 'CN_CNMF'

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

Table S573.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
SAMM50 MUTATED 0 1 2
SAMM50 WILD-TYPE 92 148 123
'SAMM50 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S574.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
SAMM50 MUTATED 1 2 0
SAMM50 WILD-TYPE 91 159 120
'SAMM50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.115 (Fisher's exact test), Q value = 0.66

Table S575.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
SAMM50 MUTATED 2 0 0 0 1
SAMM50 WILD-TYPE 66 88 74 68 68
'SAMM50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.69

Table S576.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
SAMM50 MUTATED 1 1 0 0 1
SAMM50 WILD-TYPE 52 54 116 87 55
'SAMM50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.532 (Fisher's exact test), Q value = 0.85

Table S577.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
SAMM50 MUTATED 1 1 0 1 0 0
SAMM50 WILD-TYPE 39 63 91 83 48 41
'SAMM50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.62

Table S578.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
SAMM50 MUTATED 1 0 1 0 1
SAMM50 WILD-TYPE 42 95 56 126 46
'SAMM50 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 0.96

Table S579.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
SAMM50 MUTATED 2 0 1 0
SAMM50 WILD-TYPE 108 80 102 50
'SAMM50 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.68

Table S580.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
SAMM50 MUTATED 1 0 0 1 1
SAMM50 WILD-TYPE 72 83 100 32 53
'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 0.82

Table S581.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PBRM1 MUTATED 1 3 5
PBRM1 WILD-TYPE 91 146 120
'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.72

Table S582.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PBRM1 MUTATED 0 5 4
PBRM1 WILD-TYPE 92 156 116
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00951 (Fisher's exact test), Q value = 0.2

Table S583.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PBRM1 MUTATED 0 0 1 2 5
PBRM1 WILD-TYPE 68 88 73 66 64

Figure S68.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0077 (Fisher's exact test), Q value = 0.17

Table S584.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PBRM1 MUTATED 1 1 1 0 5
PBRM1 WILD-TYPE 52 54 115 87 51

Figure S69.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 0.77

Table S585.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PBRM1 MUTATED 0 0 2 5 1 1
PBRM1 WILD-TYPE 40 64 89 79 47 40
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0113 (Fisher's exact test), Q value = 0.22

Table S586.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PBRM1 MUTATED 0 1 0 3 5
PBRM1 WILD-TYPE 43 94 57 123 42

Figure S70.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 0.85

Table S587.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PBRM1 MUTATED 1 2 4 1
PBRM1 WILD-TYPE 109 78 99 49
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.69

Table S588.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PBRM1 MUTATED 1 2 1 0 4
PBRM1 WILD-TYPE 72 81 99 33 50
'SGK269 MUTATION STATUS' versus 'CN_CNMF'

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

Table S589.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
SGK269 MUTATED 2 3 3
SGK269 WILD-TYPE 90 146 122
'SGK269 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 0.61

Table S590.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
SGK269 MUTATED 3 5 0
SGK269 WILD-TYPE 89 156 120
'SGK269 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.77

Table S591.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
SGK269 MUTATED 3 1 1 0 3
SGK269 WILD-TYPE 65 87 73 68 66
'SGK269 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.643 (Fisher's exact test), Q value = 0.91

Table S592.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
SGK269 MUTATED 0 1 4 1 2
SGK269 WILD-TYPE 53 54 112 86 54
'SGK269 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 0.89

Table S593.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
SGK269 MUTATED 2 2 1 2 0 1
SGK269 WILD-TYPE 38 62 90 82 48 40
'SGK269 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 0.79

Table S594.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
SGK269 MUTATED 2 2 1 1 2
SGK269 WILD-TYPE 41 93 56 125 45
'SGK269 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.72

Table S595.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
SGK269 MUTATED 2 0 4 2
SGK269 WILD-TYPE 108 80 99 48
'SGK269 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0156 (Fisher's exact test), Q value = 0.24

Table S596.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
SGK269 MUTATED 0 3 0 2 3
SGK269 WILD-TYPE 73 80 100 31 51

Figure S71.  Get High-res Image Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

'LEO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.68

Table S597.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
LEO1 MUTATED 0 1 4
LEO1 WILD-TYPE 92 148 121
'LEO1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 0.8

Table S598.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
LEO1 MUTATED 0 2 3
LEO1 WILD-TYPE 92 159 117
'LEO1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.803 (Fisher's exact test), Q value = 0.95

Table S599.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
LEO1 MUTATED 1 1 1 0 2
LEO1 WILD-TYPE 67 87 73 68 67
'LEO1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.175 (Fisher's exact test), Q value = 0.69

Table S600.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
LEO1 MUTATED 0 1 0 2 2
LEO1 WILD-TYPE 53 54 116 85 54
'LEO1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 0.82

Table S601.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
LEO1 MUTATED 0 2 0 2 1 0
LEO1 WILD-TYPE 40 62 91 82 47 41
'LEO1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.79

Table S602.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
LEO1 MUTATED 0 2 0 1 2
LEO1 WILD-TYPE 43 93 57 125 45
'LEO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.77

Table S603.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
LEO1 MUTATED 0 1 3 1
LEO1 WILD-TYPE 110 79 100 49
'LEO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 0.92

Table S604.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
LEO1 MUTATED 1 1 1 0 2
LEO1 WILD-TYPE 72 82 99 33 52
'CD97 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.82

Table S605.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CD97 MUTATED 0 3 2
CD97 WILD-TYPE 92 146 123
'CD97 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 0.96

Table S606.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CD97 MUTATED 1 3 1
CD97 WILD-TYPE 91 158 119
'CD97 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.8

Table S607.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CD97 MUTATED 1 0 1 0 2
CD97 WILD-TYPE 67 88 73 68 67
'CD97 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.68

Table S608.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CD97 MUTATED 1 0 0 1 2
CD97 WILD-TYPE 52 55 116 86 54
'CD97 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.735 (Fisher's exact test), Q value = 0.92

Table S609.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CD97 MUTATED 0 0 1 2 1 1
CD97 WILD-TYPE 40 64 90 82 47 40
'CD97 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.185 (Fisher's exact test), Q value = 0.71

Table S610.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CD97 MUTATED 0 0 0 3 2
CD97 WILD-TYPE 43 95 57 123 45
'CD97 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.79

Table S611.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CD97 MUTATED 0 2 2 1
CD97 WILD-TYPE 110 78 101 49
'CD97 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.521 (Fisher's exact test), Q value = 0.85

Table S612.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CD97 MUTATED 0 1 2 0 2
CD97 WILD-TYPE 73 82 98 33 52
'SKA3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S613.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
SKA3 MUTATED 0 2 2
SKA3 WILD-TYPE 92 147 123
'SKA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.72

Table S614.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
SKA3 MUTATED 0 1 3
SKA3 WILD-TYPE 92 160 117
'SKA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.82

Table S615.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
SKA3 MUTATED 0 0 2 1 1
SKA3 WILD-TYPE 68 88 72 67 68
'SKA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 0.92

Table S616.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
SKA3 MUTATED 0 0 1 2 1
SKA3 WILD-TYPE 53 55 115 85 55
'SKA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.77

Table S617.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
SKA3 MUTATED 0 0 1 1 0 2
SKA3 WILD-TYPE 40 64 90 83 48 39
'SKA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S618.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
SKA3 MUTATED 0 1 0 2 1
SKA3 WILD-TYPE 43 94 57 124 46
'SKA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.8

Table S619.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
SKA3 MUTATED 2 2 0 0
SKA3 WILD-TYPE 108 78 103 50
'SKA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.847 (Fisher's exact test), Q value = 0.96

Table S620.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
SKA3 MUTATED 0 1 2 0 1
SKA3 WILD-TYPE 73 82 98 33 53
'CBX4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.68

Table S621.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CBX4 MUTATED 0 5 1
CBX4 WILD-TYPE 92 144 124
'CBX4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.79

Table S622.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CBX4 MUTATED 2 1 3
CBX4 WILD-TYPE 90 160 117
'CBX4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00226 (Fisher's exact test), Q value = 0.069

Table S623.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CBX4 MUTATED 5 0 1 0 0
CBX4 WILD-TYPE 63 88 73 68 69

Figure S72.  Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'CBX4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00398 (Fisher's exact test), Q value = 0.1

Table S624.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CBX4 MUTATED 4 0 0 2 0
CBX4 WILD-TYPE 49 55 116 85 56

Figure S73.  Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'CBX4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.79

Table S625.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CBX4 MUTATED 2 1 2 0 1 0
CBX4 WILD-TYPE 38 63 89 84 47 41
'CBX4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.82

Table S626.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CBX4 MUTATED 2 1 1 2 0
CBX4 WILD-TYPE 41 94 56 124 47
'CBX4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0538 (Fisher's exact test), Q value = 0.51

Table S627.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CBX4 MUTATED 2 1 0 3
CBX4 WILD-TYPE 108 79 103 47
'CBX4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.32 (Fisher's exact test), Q value = 0.78

Table S628.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CBX4 MUTATED 2 0 3 1 0
CBX4 WILD-TYPE 71 83 97 32 54
'MTA1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S629.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
MTA1 MUTATED 1 3 2
MTA1 WILD-TYPE 91 146 123
'MTA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.66

Table S630.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
MTA1 MUTATED 3 3 0
MTA1 WILD-TYPE 89 158 120
'MTA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.04 (Fisher's exact test), Q value = 0.42

Table S631.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
MTA1 MUTATED 4 1 0 1 0
MTA1 WILD-TYPE 64 87 74 67 69

Figure S74.  Get High-res Image Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'MTA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.77

Table S632.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
MTA1 MUTATED 2 1 3 0 0
MTA1 WILD-TYPE 51 54 113 87 56
'MTA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.53

Table S633.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
MTA1 MUTATED 2 3 0 1 0 0
MTA1 WILD-TYPE 38 61 91 83 48 41
'MTA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0666 (Fisher's exact test), Q value = 0.55

Table S634.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
MTA1 MUTATED 2 2 2 0 0
MTA1 WILD-TYPE 41 93 55 126 47
'MTA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.82

Table S635.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
MTA1 MUTATED 4 1 1 0
MTA1 WILD-TYPE 106 79 102 50
'MTA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.68

Table S636.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
MTA1 MUTATED 2 3 0 1 0
MTA1 WILD-TYPE 71 80 100 32 54
'CRIP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00148 (Fisher's exact test), Q value = 0.049

Table S637.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
CRIP3 MUTATED 0 0 6
CRIP3 WILD-TYPE 92 149 119

Figure S75.  Get High-res Image Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CRIP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.68

Table S638.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
CRIP3 MUTATED 0 5 1
CRIP3 WILD-TYPE 92 156 119
'CRIP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.8

Table S639.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
CRIP3 MUTATED 2 2 0 0 2
CRIP3 WILD-TYPE 66 86 74 68 67
'CRIP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.771 (Fisher's exact test), Q value = 0.94

Table S640.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
CRIP3 MUTATED 0 1 2 1 2
CRIP3 WILD-TYPE 53 54 114 86 54
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.394 (Fisher's exact test), Q value = 0.8

Table S641.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
CRIP3 MUTATED 1 1 0 3 1 0
CRIP3 WILD-TYPE 39 63 91 81 47 41
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 0.8

Table S642.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
CRIP3 MUTATED 1 1 1 1 2
CRIP3 WILD-TYPE 42 94 56 125 45
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.76

Table S643.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
CRIP3 MUTATED 2 0 4 0
CRIP3 WILD-TYPE 108 80 99 50
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.66

Table S644.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
CRIP3 MUTATED 0 1 1 1 3
CRIP3 WILD-TYPE 73 82 99 32 51
'NR4A2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S645.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
NR4A2 MUTATED 1 3 2
NR4A2 WILD-TYPE 91 146 123
'NR4A2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S646.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
NR4A2 MUTATED 1 4 1
NR4A2 WILD-TYPE 91 157 119
'NR4A2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.77

Table S647.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
NR4A2 MUTATED 2 0 1 0 2
NR4A2 WILD-TYPE 66 88 73 68 67
'NR4A2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.66

Table S648.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
NR4A2 MUTATED 2 0 1 0 2
NR4A2 WILD-TYPE 51 55 115 87 54
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 0.92

Table S649.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
NR4A2 MUTATED 1 1 1 3 0 0
NR4A2 WILD-TYPE 39 63 90 81 48 41
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.114 (Fisher's exact test), Q value = 0.66

Table S650.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
NR4A2 MUTATED 1 0 2 1 2
NR4A2 WILD-TYPE 42 95 55 125 45
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.809 (Fisher's exact test), Q value = 0.95

Table S651.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
NR4A2 MUTATED 3 1 2 0
NR4A2 WILD-TYPE 107 79 101 50
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.68

Table S652.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
NR4A2 MUTATED 3 1 0 0 2
NR4A2 WILD-TYPE 70 82 100 33 52
'HNF1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0189 (Fisher's exact test), Q value = 0.29

Table S653.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
HNF1A MUTATED 5 3 0
HNF1A WILD-TYPE 87 146 125

Figure S76.  Get High-res Image Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HNF1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S654.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
HNF1A MUTATED 2 4 2
HNF1A WILD-TYPE 90 157 118
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 0.55

Table S655.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
HNF1A MUTATED 2 5 0 0 1
HNF1A WILD-TYPE 66 83 74 68 68
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.78

Table S656.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
HNF1A MUTATED 1 1 5 0 1
HNF1A WILD-TYPE 52 54 111 87 55
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0641 (Fisher's exact test), Q value = 0.55

Table S657.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
HNF1A MUTATED 1 4 0 1 2 0
HNF1A WILD-TYPE 39 60 91 83 46 41
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.72

Table S658.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
HNF1A MUTATED 1 5 0 2 0
HNF1A WILD-TYPE 42 90 57 124 47
'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.66

Table S659.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
HNF1A MUTATED 1 0 4 2
HNF1A WILD-TYPE 109 80 99 48
'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.77

Table S660.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
HNF1A MUTATED 1 4 1 1 0
HNF1A WILD-TYPE 72 79 99 32 54
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.77

Table S661.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
KRAS MUTATED 3 1 2
KRAS WILD-TYPE 89 148 123
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.673 (Fisher's exact test), Q value = 0.92

Table S662.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
KRAS MUTATED 1 2 3
KRAS WILD-TYPE 91 159 117
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 0.85

Table S663.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
KRAS MUTATED 1 0 2 1 2
KRAS WILD-TYPE 67 88 72 67 67
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.72

Table S664.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
KRAS MUTATED 1 0 1 4 0
KRAS WILD-TYPE 52 55 115 83 56
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.691 (Fisher's exact test), Q value = 0.92

Table S665.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
KRAS MUTATED 0 1 1 3 0 1
KRAS WILD-TYPE 40 63 90 81 48 40
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.122 (Fisher's exact test), Q value = 0.66

Table S666.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
KRAS MUTATED 0 0 3 3 0
KRAS WILD-TYPE 43 95 54 123 47
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.69

Table S667.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
KRAS MUTATED 3 0 0 1
KRAS WILD-TYPE 107 80 103 49
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.607 (Fisher's exact test), Q value = 0.9

Table S668.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
KRAS MUTATED 2 0 1 0 1
KRAS WILD-TYPE 71 83 99 33 53
'PGBD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 0.95

Table S669.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PGBD1 MUTATED 0 2 1
PGBD1 WILD-TYPE 92 147 124
'PGBD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 0.95

Table S670.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PGBD1 MUTATED 0 2 1
PGBD1 WILD-TYPE 92 159 119
'PGBD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S671.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PGBD1 MUTATED 0 1 1 0 1
PGBD1 WILD-TYPE 68 87 73 68 68
'PGBD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 0.81

Table S672.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PGBD1 MUTATED 0 1 0 1 1
PGBD1 WILD-TYPE 53 54 116 86 55
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 0.87

Table S673.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PGBD1 MUTATED 0 1 0 1 0 1
PGBD1 WILD-TYPE 40 63 91 83 48 40
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.827 (Fisher's exact test), Q value = 0.96

Table S674.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PGBD1 MUTATED 0 1 0 1 1
PGBD1 WILD-TYPE 43 94 57 125 46
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.82

Table S675.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PGBD1 MUTATED 0 1 2 0
PGBD1 WILD-TYPE 110 79 101 50
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.909 (Fisher's exact test), Q value = 0.98

Table S676.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PGBD1 MUTATED 0 1 1 0 1
PGBD1 WILD-TYPE 73 82 99 33 53
'LATS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.708 (Fisher's exact test), Q value = 0.92

Table S677.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
LATS1 MUTATED 1 4 2
LATS1 WILD-TYPE 91 145 123
'LATS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 0.9

Table S678.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
LATS1 MUTATED 2 4 1
LATS1 WILD-TYPE 90 157 119
'LATS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 0.88

Table S679.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
LATS1 MUTATED 2 1 0 1 2
LATS1 WILD-TYPE 66 87 74 67 67
'LATS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.68

Table S680.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
LATS1 MUTATED 1 2 0 1 2
LATS1 WILD-TYPE 52 53 116 86 54
'LATS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 0.96

Table S681.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
LATS1 MUTATED 1 0 2 2 1 1
LATS1 WILD-TYPE 39 64 89 82 47 40
'LATS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 0.92

Table S682.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
LATS1 MUTATED 1 3 1 1 1
LATS1 WILD-TYPE 42 92 56 125 46
'LATS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S683.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
LATS1 MUTATED 2 2 2 1
LATS1 WILD-TYPE 108 78 101 49
'LATS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S684.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
LATS1 MUTATED 2 1 1 1 2
LATS1 WILD-TYPE 71 82 99 32 52
'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.231 (Fisher's exact test), Q value = 0.73

Table S685.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
KEAP1 MUTATED 4 10 3
KEAP1 WILD-TYPE 88 139 122
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.68

Table S686.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
KEAP1 MUTATED 6 9 2
KEAP1 WILD-TYPE 86 152 118
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.77

Table S687.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
KEAP1 MUTATED 7 3 2 2 3
KEAP1 WILD-TYPE 61 85 72 66 66
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S688.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
KEAP1 MUTATED 3 3 5 3 3
KEAP1 WILD-TYPE 50 52 111 84 53
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.62

Table S689.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
KEAP1 MUTATED 4 5 3 2 0 3
KEAP1 WILD-TYPE 36 59 88 82 48 38
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.251 (Fisher's exact test), Q value = 0.76

Table S690.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
KEAP1 MUTATED 4 5 4 3 1
KEAP1 WILD-TYPE 39 90 53 123 46
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.92

Table S691.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
KEAP1 MUTATED 6 3 3 3
KEAP1 WILD-TYPE 104 77 100 47
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.73

Table S692.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
KEAP1 MUTATED 3 7 2 2 1
KEAP1 WILD-TYPE 70 76 98 31 53
'SENP6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.395 (Fisher's exact test), Q value = 0.8

Table S693.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
SENP6 MUTATED 2 3 6
SENP6 WILD-TYPE 90 146 119
'SENP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0744 (Fisher's exact test), Q value = 0.58

Table S694.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
SENP6 MUTATED 0 5 6
SENP6 WILD-TYPE 92 156 114
'SENP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 0.95

Table S695.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
SENP6 MUTATED 3 2 1 2 3
SENP6 WILD-TYPE 65 86 73 66 66
'SENP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.72

Table S696.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
SENP6 MUTATED 4 2 2 1 2
SENP6 WILD-TYPE 49 53 114 86 54
'SENP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.82

Table S697.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
SENP6 MUTATED 0 4 3 3 0 1
SENP6 WILD-TYPE 40 60 88 81 48 40
'SENP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.43 (Fisher's exact test), Q value = 0.82

Table S698.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
SENP6 MUTATED 0 4 1 3 3
SENP6 WILD-TYPE 43 91 56 123 44
'SENP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.104 (Fisher's exact test), Q value = 0.63

Table S699.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
SENP6 MUTATED 3 6 2 0
SENP6 WILD-TYPE 107 74 101 50
'SENP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.93 (Fisher's exact test), Q value = 0.99

Table S700.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
SENP6 MUTATED 2 3 4 0 2
SENP6 WILD-TYPE 71 80 96 33 52
'FKBP4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 0.82

Table S701.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
FKBP4 MUTATED 0 3 1
FKBP4 WILD-TYPE 92 146 124
'FKBP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 0.88

Table S702.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
FKBP4 MUTATED 0 3 1
FKBP4 WILD-TYPE 92 158 119
'FKBP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 0.96

Table S703.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
FKBP4 MUTATED 1 1 0 0 1
FKBP4 WILD-TYPE 67 87 74 68 68
'FKBP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.675 (Fisher's exact test), Q value = 0.92

Table S704.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
FKBP4 MUTATED 0 0 2 0 1
FKBP4 WILD-TYPE 53 55 114 87 55
'FKBP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 0.96

Table S705.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
FKBP4 MUTATED 0 2 1 1 0 0
FKBP4 WILD-TYPE 40 62 90 83 48 41
'FKBP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.641 (Fisher's exact test), Q value = 0.91

Table S706.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
FKBP4 MUTATED 0 2 0 1 1
FKBP4 WILD-TYPE 43 93 57 125 46
'FKBP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S707.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
FKBP4 MUTATED 1 1 1 0
FKBP4 WILD-TYPE 109 79 102 50
'FKBP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.312 (Fisher's exact test), Q value = 0.78

Table S708.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
FKBP4 MUTATED 0 2 0 0 1
FKBP4 WILD-TYPE 73 81 100 33 53
'FOXK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S709.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
FOXK2 MUTATED 1 3 2
FOXK2 WILD-TYPE 91 146 123
'FOXK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.68

Table S710.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
FOXK2 MUTATED 0 5 1
FOXK2 WILD-TYPE 92 156 119
'FOXK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00814 (Fisher's exact test), Q value = 0.18

Table S711.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
FOXK2 MUTATED 2 0 0 0 4
FOXK2 WILD-TYPE 66 88 74 68 65

Figure S77.  Get High-res Image Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

'FOXK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.742 (Fisher's exact test), Q value = 0.92

Table S712.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
FOXK2 MUTATED 1 0 2 1 2
FOXK2 WILD-TYPE 52 55 114 86 54
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 0.82

Table S713.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
FOXK2 MUTATED 1 2 0 2 1 0
FOXK2 WILD-TYPE 39 62 91 82 47 41
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 0.79

Table S714.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
FOXK2 MUTATED 1 2 0 1 2
FOXK2 WILD-TYPE 42 93 57 125 45
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.73

Table S715.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
FOXK2 MUTATED 1 0 4 1
FOXK2 WILD-TYPE 109 80 99 49
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.8

Table S716.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
FOXK2 MUTATED 0 2 1 1 2
FOXK2 WILD-TYPE 73 81 99 32 52
'DSPP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 0.8

Table S717.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
DSPP MUTATED 3 8 10
DSPP WILD-TYPE 89 141 115
'DSPP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.92 (Fisher's exact test), Q value = 0.99

Table S718.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
DSPP MUTATED 6 9 6
DSPP WILD-TYPE 86 152 114
'DSPP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.737 (Fisher's exact test), Q value = 0.92

Table S719.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
DSPP MUTATED 5 4 5 2 5
DSPP WILD-TYPE 63 84 69 66 64
'DSPP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.72

Table S720.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
DSPP MUTATED 2 6 3 6 4
DSPP WILD-TYPE 51 49 113 81 52
'DSPP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.913 (Fisher's exact test), Q value = 0.98

Table S721.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
DSPP MUTATED 3 2 5 6 3 2
DSPP WILD-TYPE 37 62 86 78 45 39
'DSPP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.442 (Fisher's exact test), Q value = 0.82

Table S722.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
DSPP MUTATED 4 3 4 6 4
DSPP WILD-TYPE 39 92 53 120 43
'DSPP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 0.94

Table S723.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
DSPP MUTATED 5 4 7 4
DSPP WILD-TYPE 105 76 96 46
'DSPP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.72

Table S724.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
DSPP MUTATED 6 1 7 2 4
DSPP WILD-TYPE 67 82 93 31 50
'C10ORF28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.684 (Fisher's exact test), Q value = 0.92

Table S725.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
C10ORF28 MUTATED 0 2 2
C10ORF28 WILD-TYPE 92 147 123
'C10ORF28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.82

Table S726.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
C10ORF28 MUTATED 2 1 1
C10ORF28 WILD-TYPE 90 160 119
'C10ORF28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S727.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
C10ORF28 MUTATED 1 1 1 0 1
C10ORF28 WILD-TYPE 67 87 73 68 68
'C10ORF28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.166 (Fisher's exact test), Q value = 0.69

Table S728.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
C10ORF28 MUTATED 0 2 0 1 1
C10ORF28 WILD-TYPE 53 53 116 86 55
'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0362 (Fisher's exact test), Q value = 0.4

Table S729.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
C10ORF28 MUTATED 1 0 0 0 2 1
C10ORF28 WILD-TYPE 39 64 91 84 46 40

Figure S78.  Get High-res Image Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.849 (Fisher's exact test), Q value = 0.96

Table S730.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
C10ORF28 MUTATED 1 1 0 2 0
C10ORF28 WILD-TYPE 42 94 57 124 47
'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0133 (Fisher's exact test), Q value = 0.23

Table S731.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
C10ORF28 MUTATED 1 0 0 3
C10ORF28 WILD-TYPE 109 80 103 47

Figure S79.  Get High-res Image Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.16 (Fisher's exact test), Q value = 0.68

Table S732.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
C10ORF28 MUTATED 0 0 3 1 0
C10ORF28 WILD-TYPE 73 83 97 32 54
'PRAMEF4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.682 (Fisher's exact test), Q value = 0.92

Table S733.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
PRAMEF4 MUTATED 0 2 2
PRAMEF4 WILD-TYPE 92 147 123
'PRAMEF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.8

Table S734.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
PRAMEF4 MUTATED 1 3 0
PRAMEF4 WILD-TYPE 91 158 120
'PRAMEF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.79

Table S735.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
PRAMEF4 MUTATED 2 0 1 0 1
PRAMEF4 WILD-TYPE 66 88 73 68 68
'PRAMEF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 0.87

Table S736.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
PRAMEF4 MUTATED 1 0 2 0 1
PRAMEF4 WILD-TYPE 52 55 114 87 55
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.72

Table S737.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
PRAMEF4 MUTATED 0 1 0 1 0 2
PRAMEF4 WILD-TYPE 40 63 91 83 48 39
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.68

Table S738.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
PRAMEF4 MUTATED 0 1 2 0 1
PRAMEF4 WILD-TYPE 43 94 55 126 46
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 0.92

Table S739.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
PRAMEF4 MUTATED 2 0 2 0
PRAMEF4 WILD-TYPE 108 80 101 50
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 0.76

Table S740.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
PRAMEF4 MUTATED 1 1 0 0 2
PRAMEF4 WILD-TYPE 72 82 100 33 52
'RPS6KA5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S741.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
RPS6KA5 MUTATED 1 2 2
RPS6KA5 WILD-TYPE 91 147 123
'RPS6KA5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 0.78

Table S742.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
RPS6KA5 MUTATED 0 4 1
RPS6KA5 WILD-TYPE 92 157 119
'RPS6KA5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 0.9

Table S743.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
RPS6KA5 MUTATED 1 0 1 1 2
RPS6KA5 WILD-TYPE 67 88 73 67 67
'RPS6KA5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 0.79

Table S744.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
RPS6KA5 MUTATED 0 1 2 0 2
RPS6KA5 WILD-TYPE 53 54 114 87 54
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.78

Table S745.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
RPS6KA5 MUTATED 0 1 0 2 2 0
RPS6KA5 WILD-TYPE 40 63 91 82 46 41
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 0.82

Table S746.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
RPS6KA5 MUTATED 0 1 0 2 2
RPS6KA5 WILD-TYPE 43 94 57 124 45
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.77

Table S747.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
RPS6KA5 MUTATED 1 0 2 2
RPS6KA5 WILD-TYPE 109 80 101 48
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S748.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
RPS6KA5 MUTATED 0 1 2 0 2
RPS6KA5 WILD-TYPE 73 82 98 33 52
'DDX42 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.72

Table S749.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
DDX42 MUTATED 0 2 4
DDX42 WILD-TYPE 92 147 121
'DDX42 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.72

Table S750.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
DDX42 MUTATED 2 4 0
DDX42 WILD-TYPE 90 157 120
'DDX42 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.68

Table S751.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
DDX42 MUTATED 3 1 0 0 2
DDX42 WILD-TYPE 65 87 74 68 67
'DDX42 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0278 (Fisher's exact test), Q value = 0.37

Table S752.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
DDX42 MUTATED 2 2 0 0 2
DDX42 WILD-TYPE 51 53 116 87 54

Figure S80.  Get High-res Image Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

'DDX42 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.76

Table S753.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
DDX42 MUTATED 1 2 0 3 0 0
DDX42 WILD-TYPE 39 62 91 81 48 41
'DDX42 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0626 (Fisher's exact test), Q value = 0.55

Table S754.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
DDX42 MUTATED 1 3 0 0 2
DDX42 WILD-TYPE 42 92 57 126 45
'DDX42 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.79

Table S755.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
DDX42 MUTATED 3 0 3 0
DDX42 WILD-TYPE 107 80 100 50
'DDX42 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.72

Table S756.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
DDX42 MUTATED 2 1 0 1 2
DDX42 WILD-TYPE 71 82 100 32 52
'RHCG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.129 (Fisher's exact test), Q value = 0.67

Table S757.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
RHCG MUTATED 1 0 3
RHCG WILD-TYPE 91 149 122
'RHCG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.8

Table S758.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
RHCG MUTATED 1 3 0
RHCG WILD-TYPE 91 158 120
'RHCG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.77

Table S759.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
RHCG MUTATED 1 0 0 1 2
RHCG WILD-TYPE 67 88 74 67 67
'RHCG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.77

Table S760.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
RHCG MUTATED 0 1 1 0 2
RHCG WILD-TYPE 53 54 115 87 54
'RHCG MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S761.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
RHCG MUTATED 1 0 1 2 0 0
RHCG WILD-TYPE 39 64 90 82 48 41
'RHCG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0837 (Fisher's exact test), Q value = 0.59

Table S762.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
RHCG MUTATED 2 0 0 1 1
RHCG WILD-TYPE 41 95 57 125 46
'RHCG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 0.98

Table S763.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
RHCG MUTATED 1 1 2 0
RHCG WILD-TYPE 109 79 101 50
'RHCG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.66

Table S764.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
RHCG MUTATED 0 0 1 1 2
RHCG WILD-TYPE 73 83 99 32 52
'SWAP70 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.854 (Fisher's exact test), Q value = 0.96

Table S765.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
SWAP70 MUTATED 1 3 1
SWAP70 WILD-TYPE 91 146 124
'SWAP70 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S766.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
SWAP70 MUTATED 1 2 2
SWAP70 WILD-TYPE 91 159 118
'SWAP70 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.77

Table S767.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
SWAP70 MUTATED 2 0 2 1 0
SWAP70 WILD-TYPE 66 88 72 67 69
'SWAP70 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.749 (Fisher's exact test), Q value = 0.93

Table S768.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
SWAP70 MUTATED 1 1 1 2 0
SWAP70 WILD-TYPE 52 54 115 85 56
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 0.9

Table S769.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
SWAP70 MUTATED 1 1 2 0 1 0
SWAP70 WILD-TYPE 39 63 89 84 47 41
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 0.92

Table S770.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
SWAP70 MUTATED 1 2 1 1 0
SWAP70 WILD-TYPE 42 93 56 125 47
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.66

Table S771.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
SWAP70 MUTATED 1 2 0 2
SWAP70 WILD-TYPE 109 78 103 48
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 0.8

Table S772.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
SWAP70 MUTATED 0 1 3 1 0
SWAP70 WILD-TYPE 73 82 97 32 54
'BIN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.78

Table S773.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
BIN1 MUTATED 0 1 3
BIN1 WILD-TYPE 92 148 122
'BIN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 0.92

Table S774.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
BIN1 MUTATED 0 2 2
BIN1 WILD-TYPE 92 159 118
'BIN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.591 (Fisher's exact test), Q value = 0.89

Table S775.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
BIN1 MUTATED 0 1 1 0 2
BIN1 WILD-TYPE 68 87 73 68 67
'BIN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.82

Table S776.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
BIN1 MUTATED 0 0 1 1 2
BIN1 WILD-TYPE 53 55 115 86 54
'BIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S777.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
BIN1 MUTATED 1 0 1 2 0 0
BIN1 WILD-TYPE 39 64 90 82 48 41
'BIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0997 (Fisher's exact test), Q value = 0.62

Table S778.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
BIN1 MUTATED 1 0 0 1 2
BIN1 WILD-TYPE 42 95 57 125 45
'BIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 0.98

Table S779.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
BIN1 MUTATED 1 1 2 0
BIN1 WILD-TYPE 109 79 101 50
'BIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.66

Table S780.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
BIN1 MUTATED 0 0 1 1 2
BIN1 WILD-TYPE 73 83 99 32 52
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.68

Table S781.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 149 125
SMARCA4 MUTATED 1 8 2
SMARCA4 WILD-TYPE 91 141 123
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.82

Table S782.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 92 161 120
SMARCA4 MUTATED 1 5 5
SMARCA4 WILD-TYPE 91 156 115
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.79

Table S783.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 68 88 74 68 69
SMARCA4 MUTATED 4 2 2 2 0
SMARCA4 WILD-TYPE 64 86 72 66 69
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 0.82

Table S784.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 53 55 116 87 56
SMARCA4 MUTATED 3 1 3 3 0
SMARCA4 WILD-TYPE 50 54 113 84 56
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.736 (Fisher's exact test), Q value = 0.92

Table S785.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 64 91 84 48 41
SMARCA4 MUTATED 0 1 3 4 1 2
SMARCA4 WILD-TYPE 40 63 88 80 47 39
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.72

Table S786.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 43 95 57 126 47
SMARCA4 MUTATED 0 4 4 3 0
SMARCA4 WILD-TYPE 43 91 53 123 47
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.68

Table S787.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 110 80 103 50
SMARCA4 MUTATED 6 3 1 0
SMARCA4 WILD-TYPE 104 77 102 50
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.8

Table S788.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 73 83 100 33 54
SMARCA4 MUTATED 5 2 2 0 1
SMARCA4 WILD-TYPE 68 81 98 33 53
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/LIHC-TP/22623050/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/22542932/LIHC-TP.transferedmergedcluster.txt

  • Number of patients = 373

  • Number of significantly mutated genes = 99

  • Number of Molecular subtypes = 8

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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