Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 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.

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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