Correlation between gene mutation status and molecular subtypes
Liver Hepatocellular Carcinoma (Primary solid tumor)
14 July 2016  |  awg_lihc__2016_07_14
Maintainer Information
Citation Information
doi:10.7908/C1BG2NHB
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2016): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1BG2NHB
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 10 molecular subtypes across 373 patients, 46 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',  'RPPA_CHIERARCHICAL',  '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 'MIRSEQ_CNMF'.

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

  • KCNN3 mutation correlated to 'RPPA_CNMF' and 'RPPA_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'.

  • CNGA3 mutation correlated to 'RPPA_CNMF'.

  • SPHK1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

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

  • CRIP3 mutation correlated to 'CN_CNMF'.

  • SENP6 mutation correlated to 'RPPA_CNMF'.

  • FOXK2 mutation correlated to 'MRNASEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 99 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 46 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
CTNNB1 97 (26%) 276 0.00017
(0.0099) 		1e-05
(0.000762) 		0.0887
(0.616) 		0.00167
(0.0638) 		1e-05
(0.000762) 		1e-05
(0.000762) 		1e-05
(0.000762) 		1e-05
(0.000762) 		1e-05
(0.000762) 		1e-05
(0.000762)
TP53 114 (31%) 259 1e-05
(0.000762) 		0.158
(0.726) 		0.045
(0.493) 		0.0221
(0.359) 		1e-05
(0.000762) 		6e-05
(0.00396) 		0.00012
(0.00742) 		0.00028
(0.0151) 		0.00387
(0.115) 		0.00029
(0.0151)
BAP1 21 (6%) 352 0.712
(0.976) 		1e-05
(0.000762) 		0.0262
(0.399) 		0.0529
(0.535) 		1e-05
(0.000762) 		1e-05
(0.000762) 		0.00114
(0.047) 		0.00174
(0.0638) 		0.00343
(0.106) 		0.00076
(0.0327)
AXIN1 24 (6%) 349 0.00329
(0.105) 		0.0302
(0.417) 		0.0499
(0.515) 		0.196
(0.765) 		2e-05
(0.00141) 		0.00952
(0.219) 		1e-05
(0.000762) 		0.0341
(0.433) 		0.00593
(0.154) 		0.844
(1.00)
KCNN3 12 (3%) 361 0.0785
(0.598) 		0.291
(0.824) 		0.00043
(0.0203) 		0.00522
(0.14) 		0.378
(0.858) 		0.603
(0.956) 		0.841
(1.00) 		0.41
(0.871) 		0.277
(0.824) 		0.0637
(0.572)
TSC2 12 (3%) 361 0.0556
(0.535) 		0.0351
(0.435) 		0.261
(0.824) 		0.316
(0.844) 		0.00032
(0.0158) 		0.00059
(0.0265) 		0.483
(0.886) 		0.829
(1.00) 		0.493
(0.888) 		0.578
(0.947)
GPR110 6 (2%) 367 0.769
(0.993) 		0.442
(0.885) 		0.339
(0.847) 		0.606
(0.956) 		0.0356
(0.435) 		0.054
(0.535) 		0.0652
(0.572) 		0.00655
(0.166) 		0.725
(0.976) 		0.00493
(0.136)
PBRM1 9 (2%) 364 0.432
(0.885) 		0.204
(0.765) 		0.43
(0.885) 		0.606
(0.956) 		0.00904
(0.213) 		0.00774
(0.192) 		0.278
(0.824) 		0.012
(0.25) 		0.519
(0.912) 		0.165
(0.73)
CBX4 6 (2%) 367 0.147
(0.708) 		0.336
(0.847) 		0.214
(0.768) 		0.193
(0.765) 		0.00205
(0.07) 		0.00394
(0.115) 		0.332
(0.847) 		0.488
(0.888) 		0.0553
(0.535) 		0.32
(0.844)
RB1 21 (6%) 352 0.0546
(0.535) 		0.0147
(0.27) 		0.0864
(0.615) 		0.0762
(0.598) 		0.0403
(0.459) 		0.537
(0.914) 		0.0113
(0.243) 		0.515
(0.911) 		0.406
(0.87) 		0.444
(0.885)
TCHH 17 (5%) 356 0.0105
(0.231) 		0.0795
(0.601) 		0.182
(0.759) 		0.0171
(0.298) 		0.697
(0.974) 		0.973
(1.00) 		0.767
(0.993) 		0.804
(1.00) 		0.332
(0.847) 		0.948
(1.00)
KRTAP5-7 4 (1%) 369 0.461
(0.885) 		0.472
(0.885) 		0.083
(0.608) 		0.395
(0.858) 		0.918
(1.00) 		0.0785
(0.598) 		0.171
(0.736) 		0.531
(0.914) 		0.00302
(0.0997) 		0.255
(0.817)
CNGA3 11 (3%) 362 0.143
(0.708) 		0.93
(1.00) 		0.00407
(0.115) 		0.558
(0.928) 		0.592
(0.954) 		0.212
(0.768) 		0.655
(0.974) 		0.329
(0.847) 		0.675
(0.974) 		0.438
(0.885)
SPHK1 6 (2%) 367 0.391
(0.858) 		0.77
(0.993) 		0.769
(0.993) 		0.831
(1.00) 		0.0364
(0.435) 		0.0103
(0.231) 		0.523
(0.914) 		0.0939
(0.629) 		0.116
(0.681) 		0.106
(0.658)
CRIP3 6 (2%) 367 0.00168
(0.0638) 		0.15
(0.708) 		1
(1.00) 		0.688
(0.974) 		0.38
(0.858) 		0.77
(0.993) 		0.389
(0.858) 		0.394
(0.858) 		0.253
(0.816) 		0.124
(0.686)
SENP6 11 (3%) 362 0.394
(0.858) 		0.0744
(0.598) 		0.00204
(0.07) 		0.29
(0.824) 		0.795
(1.00) 		0.221
(0.778) 		0.468
(0.885) 		0.428
(0.885) 		0.105
(0.658) 		0.931
(1.00)
FOXK2 6 (2%) 367 1
(1.00) 		0.15
(0.708) 		0.00833
(0.201) 		0.74
(0.977) 		0.458
(0.885) 		0.342
(0.847) 		0.229
(0.784) 		0.367
(0.858)
ARID1A 32 (9%) 341 0.366
(0.858) 		0.591
(0.954) 		0.205
(0.765) 		0.542
(0.914) 		0.286
(0.824) 		0.217
(0.773) 		0.638
(0.971) 		0.725
(0.976) 		0.284
(0.824) 		0.967
(1.00)
CDC27 15 (4%) 358 0.794
(1.00) 		0.23
(0.784) 		1
(1.00) 		0.0368
(0.435) 		0.314
(0.844) 		0.394
(0.858) 		0.47
(0.885) 		0.505
(0.901) 		0.156
(0.726) 		0.12
(0.683)
CDKN2A 11 (3%) 362 0.861
(1.00) 		0.184
(0.759) 		0.205
(0.765) 		0.665
(0.974) 		0.625
(0.956) 		0.578
(0.947) 		0.47
(0.885) 		0.202
(0.765)
KRT2 12 (3%) 361 0.527
(0.914) 		0.29
(0.824) 		0.785
(1.00) 		0.827
(1.00) 		0.0876
(0.615) 		0.225
(0.78) 		0.451
(0.885) 		0.418
(0.884) 		0.0649
(0.572) 		0.478
(0.885)
NFE2L2 13 (3%) 360 0.0307
(0.417) 		0.675
(0.974) 		0.436
(0.885) 		0.0293
(0.417) 		0.147
(0.708) 		0.0963
(0.629) 		0.16
(0.728) 		0.0759
(0.598) 		0.135
(0.706) 		0.0213
(0.352)
PTEN 11 (3%) 362 0.851
(1.00) 		0.0676
(0.572) 		0.0713
(0.588) 		0.624
(0.956) 		0.0682
(0.572) 		0.0395
(0.455) 		0.36
(0.858) 		0.0384
(0.448) 		0.475
(0.885) 		0.149
(0.708)
ARID2 22 (6%) 351 0.846
(1.00) 		0.477
(0.885) 		0.664
(0.974) 		0.764
(0.993) 		0.483
(0.886) 		0.751
(0.986) 		0.49
(0.888) 		0.493
(0.888) 		0.945
(1.00) 		0.314
(0.844)
RBM10 8 (2%) 365 0.709
(0.976) 		0.198
(0.765) 		0.886
(1.00) 		0.787
(1.00) 		0.44
(0.885) 		0.776
(0.995) 		0.818
(1.00) 		0.753
(0.987) 		0.726
(0.976) 		0.248
(0.813)
ZNF512B 8 (2%) 365 0.343
(0.847) 		0.812
(1.00) 		0.0438
(0.487) 		0.364
(0.858) 		0.143
(0.708) 		0.584
(0.947) 		0.196
(0.765) 		0.86
(1.00) 		0.453
(0.885) 		1
(1.00)
KRT10 9 (2%) 364 1
(1.00) 		0.125
(0.686) 		0.251
(0.813) 		0.614
(0.956) 		0.514
(0.911) 		0.435
(0.885) 		0.125
(0.686) 		0.452
(0.885)
APOB 39 (10%) 334 0.224
(0.78) 		0.546
(0.915) 		0.734
(0.976) 		0.963
(1.00) 		0.0139
(0.27) 		0.0121
(0.25) 		0.899
(1.00) 		0.213
(0.768) 		0.0225
(0.359) 		0.0155
(0.275)
MLL4 19 (5%) 354 0.256
(0.817) 		0.232
(0.785) 		0.112
(0.681) 		0.113
(0.681) 		0.642
(0.973) 		0.459
(0.885) 		0.737
(0.976) 		0.693
(0.974) 		0.677
(0.974) 		0.837
(1.00)
ALB 43 (12%) 330 0.0485
(0.511) 		0.0492
(0.513) 		0.431
(0.885) 		0.294
(0.824) 		0.538
(0.914) 		0.524
(0.914) 		0.274
(0.824) 		0.884
(1.00) 		0.413
(0.875) 		0.0334
(0.43)
IL6ST 12 (3%) 361 0.0242
(0.381) 		0.367
(0.858) 		0.855
(1.00) 		0.62
(0.956) 		0.687
(0.974) 		0.548
(0.915) 		0.0665
(0.572) 		0.0213
(0.352) 		0.765
(0.993) 		0.518
(0.912)
C19ORF55 6 (2%) 367 0.393
(0.858) 		0.675
(0.974) 		0.722
(0.976) 		0.961
(1.00) 		0.726
(0.976) 		0.158
(0.726) 		0.783
(1.00) 		0.871
(1.00) 		0.0767
(0.598) 		0.674
(0.974)
PIK3CA 13 (3%) 360 1
(1.00) 		1
(1.00) 		1
(1.00) 		0.235
(0.788) 		0.528
(0.914) 		0.631
(0.962) 		0.375
(0.858) 		0.203
(0.765) 		0.47
(0.885) 		0.594
(0.954)
CELA1 6 (2%) 367 0.768
(0.993) 		0.444
(0.885) 		0.52
(0.912) 		0.507
(0.903) 		0.884
(1.00) 		0.947
(1.00) 		0.217
(0.773) 		0.538
(0.914) 		1
(1.00) 		0.894
(1.00)
RPS6KA3 14 (4%) 359 0.293
(0.824) 		0.205
(0.765) 		0.2
(0.765) 		0.582
(0.947) 		0.32
(0.844) 		0.343
(0.847) 		0.541
(0.914) 		0.899
(1.00) 		0.298
(0.828) 		0.946
(1.00)
NRD1 13 (3%) 360 0.877
(1.00) 		0.822
(1.00) 		0.0729
(0.597) 		0.959
(1.00) 		0.291
(0.824) 		0.454
(0.885) 		0.718
(0.976) 		0.381
(0.858) 		0.184
(0.759) 		0.805
(1.00)
EEF1A1 9 (2%) 364 0.0282
(0.417) 		0.393
(0.858) 		0.939
(1.00) 		0.833
(1.00) 		0.402
(0.865) 		0.331
(0.847) 		0.685
(0.974) 		0.0599
(0.56) 		0.325
(0.847) 		0.728
(0.976)
COG2 4 (1%) 369 0.683
(0.974) 		0.366
(0.858) 		0.114
(0.681) 		0.166
(0.73) 		0.886
(1.00) 		0.373
(0.858) 		1
(1.00) 		0.362
(0.858)
ATXN1 10 (3%) 363 0.658
(0.974) 		0.66
(0.974) 		0.886
(1.00) 		0.533
(0.914) 		0.284
(0.824) 		0.838
(1.00) 		0.197
(0.765) 		0.712
(0.976) 		0.0307
(0.417) 		0.207
(0.765)
KCTD20 5 (1%) 368 1
(1.00) 		0.318
(0.844) 		0.772
(0.994) 		0.867
(1.00) 		0.0522
(0.533) 		0.0693
(0.576) 		0.478
(0.885) 		0.184
(0.759) 		0.832
(1.00) 		0.733
(0.976)
CEP164 9 (2%) 364 0.576
(0.947) 		1
(1.00) 		0.5
(0.895) 		0.694
(0.974) 		0.806
(1.00) 		0.679
(0.974) 		0.857
(1.00) 		0.983
(1.00) 		1
(1.00) 		0.777
(0.995)
TCEAL6 4 (1%) 369 0.681
(0.974) 		0.367
(0.858) 		0.119
(0.683) 		0.167
(0.732) 		0.887
(1.00) 		0.374
(0.858) 		1
(1.00) 		0.365
(0.858)
DNAJC28 4 (1%) 369 0.461
(0.885) 		0.822
(1.00) 		0.0664
(0.572) 		0.397
(0.858) 		0.208
(0.765) 		0.186
(0.759) 		0.887
(1.00) 		0.105
(0.658) 		0.374
(0.858) 		0.889
(1.00)
FOXI1 5 (1%) 368 0.377
(0.858) 		0.614
(0.956) 		0.431
(0.885) 		1
(1.00) 		0.142
(0.708) 		0.0915
(0.621) 		0.544
(0.914) 		0.243
(0.809) 		0.87
(1.00) 		0.705
(0.976)
JAK1 14 (4%) 359 0.696
(0.974) 		1
(1.00) 		0.969
(1.00) 		0.512
(0.909) 		0.293
(0.824) 		0.148
(0.708) 		0.964
(1.00) 		0.821
(1.00) 		0.203
(0.765) 		0.342
(0.847)
DENND4B 12 (3%) 361 0.295
(0.824) 		0.268
(0.824) 		0.0589
(0.555) 		0.361
(0.858) 		0.143
(0.708) 		0.617
(0.956) 		0.0463
(0.493) 		0.537
(0.914) 		1
(1.00) 		0.346
(0.849)
BRD7 10 (3%) 363 0.661
(0.974) 		0.511
(0.908) 		0.619
(0.956) 		0.68
(0.974) 		0.351
(0.858) 		0.603
(0.956) 		0.572
(0.945) 		0.175
(0.741) 		0.801
(1.00) 		0.131
(0.696)
IDH1 8 (2%) 365 0.482
(0.886) 		0.25
(0.813) 		0.939
(1.00) 		0.389
(0.858) 		0.142
(0.708) 		0.235
(0.788) 		0.213
(0.768) 		0.387
(0.858) 		0.393
(0.858) 		0.173
(0.74)
PLA2G3 6 (2%) 367 0.395
(0.858) 		0.0951
(0.629) 		0.295
(0.824) 		0.142
(0.708) 		0.163
(0.73) 		0.126
(0.686) 		0.372
(0.858) 		0.0137
(0.27) 		0.724
(0.976) 		0.0365
(0.435)
HLA-DPB1 5 (1%) 368 1
(1.00) 		0.319
(0.844) 		0.478
(0.885) 		0.282
(0.824) 		0.17
(0.736) 		0.777
(0.995) 		0.688
(0.974) 		0.407
(0.87)
ALMS1 24 (6%) 349 0.489
(0.888) 		0.179
(0.756) 		0.52
(0.912) 		0.816
(1.00) 		0.79
(1.00) 		0.981
(1.00) 		0.44
(0.885) 		0.699
(0.974) 		0.484
(0.886) 		0.699
(0.974)
NUCB2 3 (1%) 370 0.62
(0.956) 		0.475
(0.885) 		1
(1.00) 		1
(1.00) 		0.399
(0.86) 		0.446
(0.885) 		0.015
(0.27) 		0.843
(1.00)
BAZ2A 11 (3%) 362 0.468
(0.885) 		0.357
(0.858) 		0.89
(1.00) 		0.552
(0.919) 		0.974
(1.00) 		0.685
(0.974) 		0.424
(0.885) 		0.582
(0.947) 		0.0766
(0.598) 		0.598
(0.956)
TAF1B 6 (2%) 367 0.202
(0.765) 		0.0961
(0.629) 		0.548
(0.915) 		0.249
(0.813) 		0.0827
(0.608) 		0.657
(0.974) 		0.809
(1.00) 		0.806
(1.00) 		0.462
(0.885) 		0.269
(0.824)
C1ORF125 11 (3%) 362 0.335
(0.847) 		0.0676
(0.572) 		0.0463
(0.493) 		0.116
(0.681) 		0.677
(0.974) 		0.816
(1.00) 		0.184
(0.759) 		0.0146
(0.27) 		0.0778
(0.598) 		0.226
(0.78)
AR 10 (3%) 363 0.475
(0.885) 		1
(1.00) 		0.335
(0.847) 		0.601
(0.956) 		0.716
(0.976) 		0.726
(0.976) 		0.475
(0.885) 		0.171
(0.736) 		0.206
(0.765) 		0.66
(0.974)
CREB3L3 5 (1%) 368 0.09
(0.617) 		0.454
(0.885) 		0.134
(0.706) 		0.623
(0.956) 		0.37
(0.858) 		0.0816
(0.608) 		1
(1.00) 		0.163
(0.73)
LFNG 7 (2%) 366 0.498
(0.893) 		0.624
(0.956) 		0.882
(1.00) 		0.388
(0.858) 		0.699
(0.974) 		0.902
(1.00) 		0.441
(0.885) 		0.467
(0.885) 		0.76
(0.992) 		0.536
(0.914)
FZR1 6 (2%) 367 0.581
(0.947) 		1
(1.00) 		0.484
(0.886) 		1
(1.00) 		0.321
(0.844) 		0.465
(0.885) 		0.793
(1.00) 		0.0295
(0.417) 		0.198
(0.765) 		0.0869
(0.615)
TRIOBP 11 (3%) 362 1
(1.00) 		0.12
(0.683) 		0.94
(1.00) 		0.907
(1.00) 		0.342
(0.847) 		0.378
(0.858) 		0.378
(0.858) 		0.464
(0.885) 		0.0966
(0.629) 		0.403
(0.865)
GJB1 3 (1%) 370 1
(1.00) 		0.793
(1.00) 		0.261
(0.824) 		0.724
(0.976) 		0.229
(0.784) 		0.908
(1.00) 		0.149
(0.708) 		1
(1.00)
DYRK1A 7 (2%) 366 0.0328
(0.43) 		0.89
(1.00) 		1
(1.00) 		0.395
(0.858) 		0.839
(1.00) 		0.639
(0.971) 		0.263
(0.824) 		0.481
(0.886) 		0.768
(0.993) 		0.292
(0.824)
TNPO1 9 (2%) 364 0.435
(0.885) 		0.909
(1.00) 		0.498
(0.893) 		0.249
(0.813) 		0.344
(0.847) 		0.505
(0.901) 		0.612
(0.956) 		0.468
(0.885) 		0.186
(0.759) 		0.628
(0.959)
PDZD4 4 (1%) 369 0.302
(0.832) 		1
(1.00) 		0.731
(0.976) 		0.247
(0.813) 		0.495
(0.891) 		0.285
(0.824)
CCNA2 5 (1%) 368 0.455
(0.885) 		0.727
(0.976) 		1
(1.00) 		1
(1.00) 		0.0945
(0.629) 		0.791
(1.00) 		0.241
(0.806) 		0.21
(0.768) 		0.396
(0.858) 		0.254
(0.817)
AHCTF1 8 (2%) 365 0.54
(0.914) 		0.812
(1.00) 		0.6
(0.956) 		0.737
(0.976) 		0.542
(0.914) 		0.979
(1.00) 		0.908
(1.00) 		0.977
(1.00)
RXRB 8 (2%) 365 0.817
(1.00) 		0.662
(0.974) 		0.82
(1.00) 		0.679
(0.974) 		0.429
(0.885) 		0.76
(0.992) 		0.49
(0.888) 		0.812
(1.00) 		0.92
(1.00) 		0.878
(1.00)
PARP1 5 (1%) 368 0.536
(0.914) 		0.854
(1.00) 		0.272
(0.824) 		0.659
(0.974) 		0.341
(0.847) 		0.595
(0.955) 		0.618
(0.956) 		0.532
(0.914)
NBEA 21 (6%) 352 0.686
(0.974) 		0.408
(0.87) 		0.0313
(0.419) 		0.164
(0.73) 		0.86
(1.00) 		0.913
(1.00) 		0.274
(0.824) 		0.149
(0.708) 		0.729
(0.976) 		0.711
(0.976)
H6PD 5 (1%) 368 0.538
(0.914) 		0.615
(0.956) 		0.274
(0.824) 		0.153
(0.717) 		0.431
(0.885) 		0.117
(0.683) 		0.871
(1.00) 		0.314
(0.844)
VPS4B 5 (1%) 368 0.737
(0.976) 		0.0458
(0.493) 		0.0866
(0.615) 		0.288
(0.824) 		0.758
(0.992) 		0.302
(0.832) 		0.199
(0.765) 		0.0737
(0.598)
HNRNPL 8 (2%) 365 0.541
(0.914) 		0.309
(0.844) 		0.847
(1.00) 		0.206
(0.765) 		0.0279
(0.417) 		0.297
(0.828) 		0.282
(0.824) 		0.765
(0.993) 		0.698
(0.974) 		0.594
(0.954)
FILIP1 13 (3%) 360 0.821
(1.00) 		0.364
(0.858) 		0.711
(0.976) 		0.708
(0.976) 		0.299
(0.83) 		0.444
(0.885) 		0.723
(0.976) 		0.375
(0.858) 		0.49
(0.888) 		0.573
(0.945)
FAM22F 4 (1%) 369 0.131
(0.696) 		0.0904
(0.617) 		1
(1.00) 		0.69
(0.974) 		0.0253
(0.392) 		0.316
(0.844) 		0.739
(0.977) 		0.39
(0.858) 		0.0858
(0.615) 		0.276
(0.824)
GPSM2 4 (1%) 369 0.464
(0.885) 		0.686
(0.974) 		1
(1.00) 		0.685
(0.974) 		0.68
(0.974) 		0.872
(1.00) 		0.969
(1.00) 		0.645
(0.974) 		0.0851
(0.615) 		0.846
(1.00)
RCCD1 5 (1%) 368 0.308
(0.844) 		0.857
(1.00) 		0.781
(0.999) 		0.463
(0.885) 		0.711
(0.976) 		0.457
(0.885) 		0.348
(0.853) 		0.624
(0.956)
PTGR1 5 (1%) 368 0.22
(0.777) 		0.619
(0.956) 		1
(1.00) 		0.938
(1.00) 		0.839
(1.00) 		0.447
(0.885) 		0.927
(1.00) 		0.322
(0.844) 		0.81
(1.00) 		0.193
(0.765)
SAMM50 3 (1%) 370 0.615
(0.956) 		0.614
(0.956) 		0.116
(0.681) 		0.169
(0.736) 		0.533
(0.914) 		0.0992
(0.634) 		0.862
(1.00) 		0.141
(0.708)
SGK269 8 (2%) 365 1
(1.00) 		0.089
(0.616) 		0.291
(0.824) 		0.695
(0.974) 		0.274
(0.824) 		0.647
(0.974) 		0.582
(0.947) 		0.331
(0.847) 		0.222
(0.778) 		0.015
(0.27)
LEO1 5 (1%) 368 0.143
(0.708) 		0.38
(0.858) 		0.127
(0.687) 		1
(1.00) 		0.805
(1.00) 		0.175
(0.741) 		0.431
(0.885) 		0.333
(0.847) 		0.265
(0.824) 		0.707
(0.976)
CD97 5 (1%) 368 0.453
(0.885) 		0.854
(1.00) 		0.369
(0.858) 		0.144
(0.708) 		0.737
(0.976) 		0.186
(0.759) 		0.326
(0.847) 		0.519
(0.912)
SKA3 4 (1%) 369 0.683
(0.974) 		0.219
(0.777) 		0.419
(0.884) 		0.718
(0.976) 		0.281
(0.824) 		0.944
(1.00) 		0.373
(0.858) 		0.845
(1.00)
MTA1 6 (2%) 367 1
(1.00) 		0.121
(0.686) 		0.0409
(0.46) 		0.29
(0.824) 		0.0571
(0.544) 		0.0671
(0.572) 		0.463
(0.885) 		0.159
(0.726)
NR4A2 6 (2%) 367 1
(1.00) 		0.579
(0.947) 		0.849
(1.00) 		0.96
(1.00) 		0.272
(0.824) 		0.111
(0.681) 		0.677
(0.974) 		0.115
(0.681) 		0.81
(1.00) 		0.147
(0.708)
HNF1A 8 (2%) 365 0.0195
(0.333) 		1
(1.00) 		0.37
(0.858) 		0.394
(0.858) 		0.0672
(0.572) 		0.319
(0.844) 		0.0638
(0.572) 		0.207
(0.765) 		0.126
(0.686) 		0.284
(0.824)
KRAS 6 (2%) 367 0.291
(0.824) 		0.672
(0.974) 		0.544
(0.914) 		1
(1.00) 		0.54
(0.914) 		0.188
(0.762) 		0.694
(0.974) 		0.119
(0.683) 		0.173
(0.74) 		0.609
(0.956)
PGBD1 3 (1%) 370 0.788
(1.00) 		0.791
(1.00) 		0.747
(0.984) 		0.728
(0.976) 		1
(1.00) 		0.41
(0.871) 		0.559
(0.929) 		0.827
(1.00) 		0.464
(0.885) 		0.909
(1.00)
LATS1 7 (2%) 366 0.709
(0.976) 		0.623
(0.956) 		0.337
(0.847) 		0.394
(0.858) 		0.574
(0.945) 		0.145
(0.708) 		0.856
(1.00) 		0.666
(0.974) 		1
(1.00) 		0.613
(0.956)
KEAP1 17 (5%) 356 0.23
(0.784) 		0.14
(0.708) 		0.436
(0.885) 		0.931
(1.00) 		0.275
(0.824) 		0.939
(1.00) 		0.1
(0.636) 		0.257
(0.817) 		0.724
(0.976) 		0.232
(0.785)
FKBP4 4 (1%) 369 0.458
(0.885) 		0.573
(0.945) 		0.676
(0.974) 		0.0982
(0.631) 		0.838
(1.00) 		0.671
(0.974) 		0.839
(1.00) 		0.641
(0.973) 		1
(1.00) 		0.31
(0.844)
DSPP 21 (6%) 352 0.36
(0.858) 		0.92
(1.00) 		0.619
(0.956) 		0.334
(0.847) 		0.738
(0.976) 		0.213
(0.768) 		0.915
(1.00) 		0.442
(0.885) 		0.775
(0.995) 		0.222
(0.778)
C10ORF28 4 (1%) 369 0.683
(0.974) 		0.469
(0.885) 		1
(1.00) 		0.164
(0.73) 		0.0369
(0.435) 		0.85
(1.00) 		0.0136
(0.27) 		0.161
(0.728)
PRAMEF4 4 (1%) 369 0.684
(0.974) 		0.369
(0.858) 		0.584
(0.947) 		0.708
(0.976) 		0.337
(0.847) 		0.565
(0.937) 		0.189
(0.762) 		0.159
(0.726) 		0.69
(0.974) 		0.248
(0.813)
RPS6KA5 5 (1%) 368 1
(1.00) 		0.317
(0.844) 		1
(1.00) 		0.687
(0.974) 		0.621
(0.956) 		0.332
(0.847) 		0.312
(0.844) 		0.427
(0.885) 		0.286
(0.824) 		0.522
(0.914)
DDX42 6 (2%) 367 0.202
(0.765) 		0.209
(0.767) 		0.688
(0.974) 		0.458
(0.885) 		0.158
(0.726) 		0.0291
(0.417) 		0.252
(0.815) 		0.0628
(0.572) 		0.339
(0.847) 		0.226
(0.78)
RHCG 4 (1%) 369 0.13
(0.696) 		0.366
(0.858) 		0.745
(0.982) 		0.116
(0.681) 		0.277
(0.824) 		0.262
(0.824) 		0.687
(0.974) 		0.0825
(0.608) 		0.914
(1.00) 		0.124
(0.686)
SWAP70 5 (1%) 368 0.853
(1.00) 		1
(1.00) 		0.545
(0.914) 		0.464
(0.885) 		0.291
(0.824) 		0.749
(0.985) 		0.62
(0.956) 		0.693
(0.974) 		0.111
(0.681) 		0.388
(0.858)
BIN1 4 (1%) 369 0.303
(0.833) 		0.684
(0.974) 		0.0332
(0.43) 		0.249
(0.813) 		0.593
(0.954) 		0.486
(0.887) 		0.683
(0.974) 		0.0978
(0.631) 		0.913
(1.00) 		0.126
(0.686)
SMARCA4 11 (3%) 362 0.132
(0.701) 		0.427
(0.885) 		0.272
(0.824) 		0.0543
(0.535) 		0.339
(0.847) 		0.477
(0.885) 		0.736
(0.976) 		0.197
(0.765) 		0.144
(0.708) 		0.377
(0.858)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

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 = 0.158 (Fisher's exact test), Q value = 0.73

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 'RPPA_CNMF'

P value = 0.045 (Fisher's exact test), Q value = 0.49

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
TP53 MUTATED 17 17 4 9 12 0
TP53 WILD-TYPE 23 57 14 14 11 2

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

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0221 (Fisher's exact test), Q value = 0.36

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
TP53 MUTATED 12 9 19 9 10
TP53 WILD-TYPE 26 37 19 10 29

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: '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 S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.004

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: '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 S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0074

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

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

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00028 (Fisher's exact test), Q value = 0.015

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: '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 S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00387 (Fisher's exact test), Q value = 0.11

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: '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 S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00029 (Fisher's exact test), Q value = 0.015

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: '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 S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00017 (Fisher's exact test), Q value = 0.0099

Table S11.  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 S10.  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 = 0.00076

Table S12.  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 S11.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0887 (Fisher's exact test), Q value = 0.62

Table S13.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CTNNB1 MUTATED 8 25 1 3 5 0
CTNNB1 WILD-TYPE 32 49 17 20 18 2
'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00167 (Fisher's exact test), Q value = 0.064

Table S14.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CTNNB1 MUTATED 1 14 8 5 14
CTNNB1 WILD-TYPE 37 32 30 14 25

Figure S12.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S15.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: '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 S13.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S16.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: '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 S14.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S17.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: '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 S15.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S18.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: '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 S16.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S19.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: '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 S17.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S20.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: '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 S18.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00329 (Fisher's exact test), Q value = 0.11

Table S21.  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 S19.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'AXIN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0302 (Fisher's exact test), Q value = 0.42

Table S22.  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 S20.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'AXIN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0499 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
AXIN1 MUTATED 1 3 0 5 2 0
AXIN1 WILD-TYPE 39 71 18 18 21 2

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

'AXIN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.76

Table S24.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
AXIN1 MUTATED 4 2 1 3 1
AXIN1 WILD-TYPE 34 44 37 16 38
'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0014

Table S25.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: '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 S22.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00952 (Fisher's exact test), Q value = 0.22

Table S26.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: '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 S23.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S27.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: '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 S24.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0341 (Fisher's exact test), Q value = 0.43

Table S28.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: '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 S25.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00593 (Fisher's exact test), Q value = 0.15

Table S29.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #9: '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 S26.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.844 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0546 (Fisher's exact test), Q value = 0.53

Table S31.  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 = 0.0147 (Fisher's exact test), Q value = 0.27

Table S32.  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 S27.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0864 (Fisher's exact test), Q value = 0.61

Table S33.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
RB1 MUTATED 2 3 2 3 3 1
RB1 WILD-TYPE 38 71 16 20 20 1
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0762 (Fisher's exact test), Q value = 0.6

Table S34.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
RB1 MUTATED 2 2 2 5 3
RB1 WILD-TYPE 36 44 36 14 36
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0403 (Fisher's exact test), Q value = 0.46

Table S35.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: '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 S28.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 0.91

Table S36.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.0113 (Fisher's exact test), Q value = 0.24

Table S37.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: '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 S29.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.515 (Fisher's exact test), Q value = 0.91

Table S38.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.406 (Fisher's exact test), Q value = 0.87

Table S39.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.444 (Fisher's exact test), Q value = 0.89

Table S40.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.366 (Fisher's exact test), Q value = 0.86

Table S41.  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 = 0.591 (Fisher's exact test), Q value = 0.95

Table S42.  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 'RPPA_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.76

Table S43.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
ARID1A MUTATED 3 8 2 1 5 1
ARID1A WILD-TYPE 37 66 16 22 18 1
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.542 (Fisher's exact test), Q value = 0.91

Table S44.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
ARID1A MUTATED 2 4 5 3 6
ARID1A WILD-TYPE 36 42 33 16 33
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.82

Table S45.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.77

Table S46.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.97

Table S47.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.725 (Fisher's exact test), Q value = 0.98

Table S48.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.284 (Fisher's exact test), Q value = 0.82

Table S49.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.967 (Fisher's exact test), Q value = 1

Table S50.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.712 (Fisher's exact test), Q value = 0.98

Table S51.  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 = 0.00076

Table S52.  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 S30.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0262 (Fisher's exact test), Q value = 0.4

Table S53.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
BAP1 MUTATED 5 2 4 0 1 0
BAP1 WILD-TYPE 35 72 14 23 22 2

Figure S31.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0529 (Fisher's exact test), Q value = 0.53

Table S54.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
BAP1 MUTATED 7 2 2 0 1
BAP1 WILD-TYPE 31 44 36 19 38
'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S55.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: '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 S32.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00076

Table S56.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: '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 S33.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00114 (Fisher's exact test), Q value = 0.047

Table S57.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: '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 S34.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00174 (Fisher's exact test), Q value = 0.064

Table S58.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: '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 S35.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00343 (Fisher's exact test), Q value = 0.11

Table S59.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: '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 S36.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00076 (Fisher's exact test), Q value = 0.033

Table S60.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: '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 S37.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S61.  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 = 0.23 (Fisher's exact test), Q value = 0.78

Table S62.  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 'RPPA_CNMF'

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

Table S63.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CDC27 MUTATED 2 4 1 1 1 0
CDC27 WILD-TYPE 38 70 17 22 22 2
'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0368 (Fisher's exact test), Q value = 0.44

Table S64.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CDC27 MUTATED 0 1 1 2 5
CDC27 WILD-TYPE 38 45 37 17 34

Figure S38.  Get High-res Image Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 0.84

Table S65.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.394 (Fisher's exact test), Q value = 0.86

Table S66.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.47 (Fisher's exact test), Q value = 0.89

Table S67.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.505 (Fisher's exact test), Q value = 0.9

Table S68.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.156 (Fisher's exact test), Q value = 0.73

Table S69.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.12 (Fisher's exact test), Q value = 0.68

Table S70.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: '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 = 1

Table S71.  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 = 0.184 (Fisher's exact test), Q value = 0.76

Table S72.  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 = 0.205 (Fisher's exact test), Q value = 0.76

Table S73.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.665 (Fisher's exact test), Q value = 0.97

Table S74.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.625 (Fisher's exact test), Q value = 0.96

Table S75.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.578 (Fisher's exact test), Q value = 0.95

Table S76.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.47 (Fisher's exact test), Q value = 0.89

Table S77.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.202 (Fisher's exact test), Q value = 0.76

Table S78.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.527 (Fisher's exact test), Q value = 0.91

Table S79.  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 = 0.29 (Fisher's exact test), Q value = 0.82

Table S80.  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 'RPPA_CNMF'

P value = 0.785 (Fisher's exact test), Q value = 1

Table S81.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
KRT2 MUTATED 1 3 1 0 0 0
KRT2 WILD-TYPE 39 71 17 23 23 2
'KRT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S82.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
KRT2 MUTATED 1 2 0 0 2
KRT2 WILD-TYPE 37 44 38 19 37
'KRT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0876 (Fisher's exact test), Q value = 0.62

Table S83.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.225 (Fisher's exact test), Q value = 0.78

Table S84.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.451 (Fisher's exact test), Q value = 0.89

Table S85.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.418 (Fisher's exact test), Q value = 0.88

Table S86.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0649 (Fisher's exact test), Q value = 0.57

Table S87.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.478 (Fisher's exact test), Q value = 0.89

Table S88.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0307 (Fisher's exact test), Q value = 0.42

Table S89.  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 S39.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.675 (Fisher's exact test), Q value = 0.97

Table S90.  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 'RPPA_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.89

Table S91.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
NFE2L2 MUTATED 0 4 0 0 0 0
NFE2L2 WILD-TYPE 40 70 18 23 23 2
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0293 (Fisher's exact test), Q value = 0.42

Table S92.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
NFE2L2 MUTATED 0 4 0 0 0
NFE2L2 WILD-TYPE 38 42 38 19 39

Figure S40.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.71

Table S93.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0963 (Fisher's exact test), Q value = 0.63

Table S94.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.73

Table S95.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0759 (Fisher's exact test), Q value = 0.6

Table S96.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.135 (Fisher's exact test), Q value = 0.71

Table S97.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.0213 (Fisher's exact test), Q value = 0.35

Table S98.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: '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 S41.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.851 (Fisher's exact test), Q value = 1

Table S99.  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 = 0.57

Table S100.  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 'RPPA_CNMF'

P value = 0.0713 (Fisher's exact test), Q value = 0.59

Table S101.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
PTEN MUTATED 0 2 0 1 1 1
PTEN WILD-TYPE 40 72 18 22 22 1
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.624 (Fisher's exact test), Q value = 0.96

Table S102.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
PTEN MUTATED 0 1 2 0 2
PTEN WILD-TYPE 38 45 36 19 37
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0682 (Fisher's exact test), Q value = 0.57

Table S103.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0395 (Fisher's exact test), Q value = 0.45

Table S104.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: '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 S42.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 0.86

Table S105.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0384 (Fisher's exact test), Q value = 0.45

Table S106.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: '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 S43.  Get High-res Image Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.89

Table S107.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.149 (Fisher's exact test), Q value = 0.71

Table S108.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.846 (Fisher's exact test), Q value = 1

Table S109.  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 = 0.477 (Fisher's exact test), Q value = 0.89

Table S110.  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 'RPPA_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 0.97

Table S111.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
ARID2 MUTATED 2 5 0 0 0 0
ARID2 WILD-TYPE 38 69 18 23 23 2
'ARID2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.764 (Fisher's exact test), Q value = 0.99

Table S112.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
ARID2 MUTATED 1 2 1 0 3
ARID2 WILD-TYPE 37 44 37 19 36
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S113.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.751 (Fisher's exact test), Q value = 0.99

Table S114.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.49 (Fisher's exact test), Q value = 0.89

Table S115.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.493 (Fisher's exact test), Q value = 0.89

Table S116.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.945 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.314 (Fisher's exact test), Q value = 0.84

Table S118.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.709 (Fisher's exact test), Q value = 0.98

Table S119.  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 = 0.198 (Fisher's exact test), Q value = 0.76

Table S120.  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 'RPPA_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 1

Table S121.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
RBM10 MUTATED 1 1 0 1 0 0
RBM10 WILD-TYPE 39 73 18 22 23 2
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.787 (Fisher's exact test), Q value = 1

Table S122.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
RBM10 MUTATED 1 0 1 0 1
RBM10 WILD-TYPE 37 46 37 19 38
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.89

Table S123.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.776 (Fisher's exact test), Q value = 1

Table S124.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.818 (Fisher's exact test), Q value = 1

Table S125.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.753 (Fisher's exact test), Q value = 0.99

Table S126.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.726 (Fisher's exact test), Q value = 0.98

Table S127.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.248 (Fisher's exact test), Q value = 0.81

Table S128.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.343 (Fisher's exact test), Q value = 0.85

Table S129.  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 = 0.812 (Fisher's exact test), Q value = 1

Table S130.  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 'RPPA_CNMF'

P value = 0.0438 (Fisher's exact test), Q value = 0.49

Table S131.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
ZNF512B MUTATED 3 1 0 0 1 1
ZNF512B WILD-TYPE 37 73 18 23 22 1

Figure S44.  Get High-res Image Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ZNF512B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 0.86

Table S132.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
ZNF512B MUTATED 0 1 3 1 1
ZNF512B WILD-TYPE 38 45 35 18 38
'ZNF512B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.71

Table S133.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.584 (Fisher's exact test), Q value = 0.95

Table S134.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.196 (Fisher's exact test), Q value = 0.76

Table S135.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.86 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.453 (Fisher's exact test), Q value = 0.89

Table S137.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #9: '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 S138.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0785 (Fisher's exact test), Q value = 0.6

Table S139.  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 = 0.82

Table S140.  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 'RPPA_CNMF'

P value = 0.00043 (Fisher's exact test), Q value = 0.02

Table S141.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
KCNN3 MUTATED 0 0 0 5 0 0
KCNN3 WILD-TYPE 40 74 18 18 23 2

Figure S45.  Get High-res Image Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KCNN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00522 (Fisher's exact test), Q value = 0.14

Table S142.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
KCNN3 MUTATED 1 0 1 3 0
KCNN3 WILD-TYPE 37 46 37 16 39

Figure S46.  Get High-res Image Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.86

Table S143.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.603 (Fisher's exact test), Q value = 0.96

Table S144.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.841 (Fisher's exact test), Q value = 1

Table S145.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.41 (Fisher's exact test), Q value = 0.87

Table S146.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.277 (Fisher's exact test), Q value = 0.82

Table S147.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.0637 (Fisher's exact test), Q value = 0.57

Table S148.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #10: '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 S149.  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 = 0.69

Table S150.  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 = 0.81

Table S151.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.614 (Fisher's exact test), Q value = 0.96

Table S152.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.514 (Fisher's exact test), Q value = 0.91

Table S153.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.435 (Fisher's exact test), Q value = 0.89

Table S154.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.69

Table S155.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.452 (Fisher's exact test), Q value = 0.89

Table S156.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.224 (Fisher's exact test), Q value = 0.78

Table S157.  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 = 0.546 (Fisher's exact test), Q value = 0.91

Table S158.  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 'RPPA_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
APOB MUTATED 5 9 1 4 1 0
APOB WILD-TYPE 35 65 17 19 22 2
'APOB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
APOB MUTATED 3 5 5 2 5
APOB WILD-TYPE 35 41 33 17 34
'APOB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.27

Table S161.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #5: '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 S47.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'APOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.25

Table S162.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #6: '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 S48.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'APOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.899 (Fisher's exact test), Q value = 1

Table S163.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.213 (Fisher's exact test), Q value = 0.77

Table S164.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0225 (Fisher's exact test), Q value = 0.36

Table S165.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #9: '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 S49.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0155 (Fisher's exact test), Q value = 0.27

Table S166.  Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #10: '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 S50.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.82

Table S167.  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 = 0.232 (Fisher's exact test), Q value = 0.79

Table S168.  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 'RPPA_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.68

Table S169.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
MLL4 MUTATED 4 2 1 2 1 1
MLL4 WILD-TYPE 36 72 17 21 22 1
'MLL4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.113 (Fisher's exact test), Q value = 0.68

Table S170.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
MLL4 MUTATED 0 2 5 2 2
MLL4 WILD-TYPE 38 44 33 17 37
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 0.97

Table S171.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.459 (Fisher's exact test), Q value = 0.89

Table S172.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.98

Table S173.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.693 (Fisher's exact test), Q value = 0.97

Table S174.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.677 (Fisher's exact test), Q value = 0.97

Table S175.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.837 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0485 (Fisher's exact test), Q value = 0.51

Table S177.  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 S51.  Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'ALB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.51

Table S178.  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 S52.  Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'ALB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 0.89

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
ALB MUTATED 3 10 1 0 1 0
ALB WILD-TYPE 37 64 17 23 22 2
'ALB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.294 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
ALB MUTATED 2 5 1 1 6
ALB WILD-TYPE 36 41 37 18 33
'ALB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 0.91

Table S181.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.524 (Fisher's exact test), Q value = 0.91

Table S182.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.274 (Fisher's exact test), Q value = 0.82

Table S183.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.884 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.413 (Fisher's exact test), Q value = 0.88

Table S185.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.0334 (Fisher's exact test), Q value = 0.43

Table S186.  Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #10: '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 S53.  Get High-res Image Gene #19: 'ALB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'TSC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0556 (Fisher's exact test), Q value = 0.53

Table S187.  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 = 0.0351 (Fisher's exact test), Q value = 0.44

Table S188.  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 S54.  Get High-res Image Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TSC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.261 (Fisher's exact test), Q value = 0.82

Table S189.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
TSC2 MUTATED 4 2 0 0 2 0
TSC2 WILD-TYPE 36 72 18 23 21 2
'TSC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.84

Table S190.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
TSC2 MUTATED 3 2 3 0 0
TSC2 WILD-TYPE 35 44 35 19 39
'TSC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.016

Table S191.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #5: '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 S55.  Get High-res Image Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TSC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.027

Table S192.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #6: '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 S56.  Get High-res Image Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TSC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S193.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.829 (Fisher's exact test), Q value = 1

Table S194.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.493 (Fisher's exact test), Q value = 0.89

Table S195.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.578 (Fisher's exact test), Q value = 0.95

Table S196.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0242 (Fisher's exact test), Q value = 0.38

Table S197.  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 S57.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IL6ST MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.86

Table S198.  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 'RPPA_CNMF'

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

Table S199.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
IL6ST MUTATED 2 5 0 0 1 0
IL6ST WILD-TYPE 38 69 18 23 22 2
'IL6ST MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.62 (Fisher's exact test), Q value = 0.96

Table S200.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
IL6ST MUTATED 1 4 1 1 1
IL6ST WILD-TYPE 37 42 37 18 38
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 0.97

Table S201.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.548 (Fisher's exact test), Q value = 0.91

Table S202.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.0665 (Fisher's exact test), Q value = 0.57

Table S203.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0213 (Fisher's exact test), Q value = 0.35

Table S204.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: '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 S58.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.765 (Fisher's exact test), Q value = 0.99

Table S205.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.91

Table S206.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.86

Table S207.  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 = 0.675 (Fisher's exact test), Q value = 0.97

Table S208.  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 'RPPA_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 0.98

Table S209.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
C19ORF55 MUTATED 1 2 1 0 1 0
C19ORF55 WILD-TYPE 39 72 17 23 22 2
'C19ORF55 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.961 (Fisher's exact test), Q value = 1

Table S210.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
C19ORF55 MUTATED 1 1 1 1 1
C19ORF55 WILD-TYPE 37 45 37 18 38
'C19ORF55 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.726 (Fisher's exact test), Q value = 0.98

Table S211.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.158 (Fisher's exact test), Q value = 0.73

Table S212.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.783 (Fisher's exact test), Q value = 1

Table S213.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.871 (Fisher's exact test), Q value = 1

Table S214.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0767 (Fisher's exact test), Q value = 0.6

Table S215.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.97

Table S216.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #10: '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 S217.  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 S218.  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 'RPPA_CNMF'

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

Table S219.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
PIK3CA MUTATED 1 3 0 1 0 0
PIK3CA WILD-TYPE 39 71 18 22 23 2
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.79

Table S220.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
PIK3CA MUTATED 0 3 1 1 0
PIK3CA WILD-TYPE 38 43 37 18 39
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 0.91

Table S221.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.631 (Fisher's exact test), Q value = 0.96

Table S222.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.375 (Fisher's exact test), Q value = 0.86

Table S223.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.203 (Fisher's exact test), Q value = 0.76

Table S224.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.47 (Fisher's exact test), Q value = 0.89

Table S225.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.594 (Fisher's exact test), Q value = 0.95

Table S226.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.768 (Fisher's exact test), Q value = 0.99

Table S227.  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 = 0.444 (Fisher's exact test), Q value = 0.89

Table S228.  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 'RPPA_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 0.91

Table S229.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CELA1 MUTATED 1 1 1 0 1 0
CELA1 WILD-TYPE 39 73 17 23 22 2
'CELA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.507 (Fisher's exact test), Q value = 0.9

Table S230.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CELA1 MUTATED 2 0 1 0 1
CELA1 WILD-TYPE 36 46 37 19 38
'CELA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.884 (Fisher's exact test), Q value = 1

Table S231.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.947 (Fisher's exact test), Q value = 1

Table S232.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.217 (Fisher's exact test), Q value = 0.77

Table S233.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.538 (Fisher's exact test), Q value = 0.91

Table S234.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #8: '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 S235.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.894 (Fisher's exact test), Q value = 1

Table S236.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.293 (Fisher's exact test), Q value = 0.82

Table S237.  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 = 0.76

Table S238.  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 'RPPA_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.76

Table S239.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
RPS6KA3 MUTATED 0 3 0 1 3 0
RPS6KA3 WILD-TYPE 40 71 18 22 20 2
'RPS6KA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.582 (Fisher's exact test), Q value = 0.95

Table S240.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
RPS6KA3 MUTATED 2 1 1 2 1
RPS6KA3 WILD-TYPE 36 45 37 17 38
'RPS6KA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.84

Table S241.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.343 (Fisher's exact test), Q value = 0.85

Table S242.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.541 (Fisher's exact test), Q value = 0.91

Table S243.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #7: '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 = 1

Table S244.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.298 (Fisher's exact test), Q value = 0.83

Table S245.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.946 (Fisher's exact test), Q value = 1

Table S246.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.877 (Fisher's exact test), Q value = 1

Table S247.  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 = 0.822 (Fisher's exact test), Q value = 1

Table S248.  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 'RPPA_CNMF'

P value = 0.0729 (Fisher's exact test), Q value = 0.6

Table S249.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
NRD1 MUTATED 4 4 0 0 0 1
NRD1 WILD-TYPE 36 70 18 23 23 1
'NRD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.959 (Fisher's exact test), Q value = 1

Table S250.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
NRD1 MUTATED 2 3 2 0 2
NRD1 WILD-TYPE 36 43 36 19 37
'NRD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.82

Table S251.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.89

Table S252.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.718 (Fisher's exact test), Q value = 0.98

Table S253.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.381 (Fisher's exact test), Q value = 0.86

Table S254.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.184 (Fisher's exact test), Q value = 0.76

Table S255.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.805 (Fisher's exact test), Q value = 1

Table S256.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0282 (Fisher's exact test), Q value = 0.42

Table S257.  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 S59.  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 = 0.86

Table S258.  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 'RPPA_CNMF'

P value = 0.939 (Fisher's exact test), Q value = 1

Table S259.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
EEF1A1 MUTATED 1 2 0 1 0 0
EEF1A1 WILD-TYPE 39 72 18 22 23 2
'EEF1A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S260.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
EEF1A1 MUTATED 1 1 0 1 1
EEF1A1 WILD-TYPE 37 45 38 18 38
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 0.86

Table S261.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.331 (Fisher's exact test), Q value = 0.85

Table S262.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.685 (Fisher's exact test), Q value = 0.97

Table S263.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0599 (Fisher's exact test), Q value = 0.56

Table S264.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.85

Table S265.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.728 (Fisher's exact test), Q value = 0.98

Table S266.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0105 (Fisher's exact test), Q value = 0.23

Table S267.  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 S60.  Get High-res Image Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TCHH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0795 (Fisher's exact test), Q value = 0.6

Table S268.  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 'RPPA_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.76

Table S269.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
TCHH MUTATED 0 2 0 2 2 0
TCHH WILD-TYPE 40 72 18 21 21 2
'TCHH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0171 (Fisher's exact test), Q value = 0.3

Table S270.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
TCHH MUTATED 1 2 0 3 0
TCHH WILD-TYPE 37 44 38 16 39

Figure S61.  Get High-res Image Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TCHH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.697 (Fisher's exact test), Q value = 0.97

Table S271.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.973 (Fisher's exact test), Q value = 1

Table S272.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.767 (Fisher's exact test), Q value = 0.99

Table S273.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.804 (Fisher's exact test), Q value = 1

Table S274.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.85

Table S275.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.948 (Fisher's exact test), Q value = 1

Table S276.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.683 (Fisher's exact test), Q value = 0.97

Table S277.  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 = 0.86

Table S278.  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 = 0.114 (Fisher's exact test), Q value = 0.68

Table S279.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.166 (Fisher's exact test), Q value = 0.73

Table S280.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.886 (Fisher's exact test), Q value = 1

Table S281.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.373 (Fisher's exact test), Q value = 0.86

Table S282.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #8: '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 S283.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.362 (Fisher's exact test), Q value = 0.86

Table S284.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.658 (Fisher's exact test), Q value = 0.97

Table S285.  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 = 0.66 (Fisher's exact test), Q value = 0.97

Table S286.  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 'RPPA_CNMF'

P value = 0.886 (Fisher's exact test), Q value = 1

Table S287.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
ATXN1 MUTATED 1 1 0 0 1 0
ATXN1 WILD-TYPE 39 73 18 23 22 2
'ATXN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 0.91

Table S288.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
ATXN1 MUTATED 0 1 1 1 0
ATXN1 WILD-TYPE 38 45 37 18 39
'ATXN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.82

Table S289.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.838 (Fisher's exact test), Q value = 1

Table S290.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.197 (Fisher's exact test), Q value = 0.76

Table S291.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.712 (Fisher's exact test), Q value = 0.98

Table S292.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0307 (Fisher's exact test), Q value = 0.42

Table S293.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #9: '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 S62.  Get High-res Image Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ATXN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.76

Table S294.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #10: '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 S295.  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 = 0.318 (Fisher's exact test), Q value = 0.84

Table S296.  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 'RPPA_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 0.99

Table S297.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
KCTD20 MUTATED 1 2 1 0 0 0
KCTD20 WILD-TYPE 39 72 17 23 23 2
'KCTD20 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.867 (Fisher's exact test), Q value = 1

Table S298.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
KCTD20 MUTATED 1 2 1 0 0
KCTD20 WILD-TYPE 37 44 37 19 39
'KCTD20 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0522 (Fisher's exact test), Q value = 0.53

Table S299.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0693 (Fisher's exact test), Q value = 0.58

Table S300.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.478 (Fisher's exact test), Q value = 0.89

Table S301.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.184 (Fisher's exact test), Q value = 0.76

Table S302.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #8: '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 = 1

Table S303.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.733 (Fisher's exact test), Q value = 0.98

Table S304.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.769 (Fisher's exact test), Q value = 0.99

Table S305.  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 = 0.89

Table S306.  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 'RPPA_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.85

Table S307.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
GPR110 MUTATED 0 1 1 1 0 0
GPR110 WILD-TYPE 40 73 17 22 23 2
'GPR110 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S308.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
GPR110 MUTATED 0 1 0 1 1
GPR110 WILD-TYPE 38 45 38 18 38
'GPR110 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0356 (Fisher's exact test), Q value = 0.44

Table S309.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #5: '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 S63.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'GPR110 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.054 (Fisher's exact test), Q value = 0.53

Table S310.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.57

Table S311.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.00655 (Fisher's exact test), Q value = 0.17

Table S312.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #8: '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 S64.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'GPR110 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.725 (Fisher's exact test), Q value = 0.98

Table S313.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.00493 (Fisher's exact test), Q value = 0.14

Table S314.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #10: '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 S65.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CEP164 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 0.95

Table S315.  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 S316.  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 'RPPA_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.89

Table S317.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CEP164 MUTATED 3 2 0 0 0 0
CEP164 WILD-TYPE 37 72 18 23 23 2
'CEP164 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 0.97

Table S318.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CEP164 MUTATED 1 2 2 0 0
CEP164 WILD-TYPE 37 44 36 19 39
'CEP164 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.806 (Fisher's exact test), Q value = 1

Table S319.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.97

Table S320.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.857 (Fisher's exact test), Q value = 1

Table S321.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #7: '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 S322.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #8: '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 S323.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.777 (Fisher's exact test), Q value = 1

Table S324.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.681 (Fisher's exact test), Q value = 0.97

Table S325.  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 = 0.86

Table S326.  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 = 0.119 (Fisher's exact test), Q value = 0.68

Table S327.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.73

Table S328.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.887 (Fisher's exact test), Q value = 1

Table S329.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.86

Table S330.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #8: '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 S331.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.365 (Fisher's exact test), Q value = 0.86

Table S332.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.461 (Fisher's exact test), Q value = 0.89

Table S333.  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 = 0.822 (Fisher's exact test), Q value = 1

Table S334.  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 'RPPA_CNMF'

P value = 0.0664 (Fisher's exact test), Q value = 0.57

Table S335.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
DNAJC28 MUTATED 1 1 0 0 0 1
DNAJC28 WILD-TYPE 39 73 18 23 23 1
'DNAJC28 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.86

Table S336.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
DNAJC28 MUTATED 1 0 0 0 2
DNAJC28 WILD-TYPE 37 46 38 19 37
'DNAJC28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.76

Table S337.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.186 (Fisher's exact test), Q value = 0.76

Table S338.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.887 (Fisher's exact test), Q value = 1

Table S339.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.105 (Fisher's exact test), Q value = 0.66

Table S340.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.374 (Fisher's exact test), Q value = 0.86

Table S341.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.889 (Fisher's exact test), Q value = 1

Table S342.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.377 (Fisher's exact test), Q value = 0.86

Table S343.  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 = 0.614 (Fisher's exact test), Q value = 0.96

Table S344.  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 'RPPA_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 0.89

Table S345.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
FOXI1 MUTATED 0 2 1 0 0 0
FOXI1 WILD-TYPE 40 72 17 23 23 2
'FOXI1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S346.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
FOXI1 MUTATED 0 1 1 0 1
FOXI1 WILD-TYPE 38 45 37 19 38
'FOXI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.71

Table S347.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0915 (Fisher's exact test), Q value = 0.62

Table S348.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.544 (Fisher's exact test), Q value = 0.91

Table S349.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.81

Table S350.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.87 (Fisher's exact test), Q value = 1

Table S351.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.705 (Fisher's exact test), Q value = 0.98

Table S352.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.461 (Fisher's exact test), Q value = 0.89

Table S353.  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 = 0.472 (Fisher's exact test), Q value = 0.89

Table S354.  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 'RPPA_CNMF'

P value = 0.083 (Fisher's exact test), Q value = 0.61

Table S355.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
KRTAP5-7 MUTATED 0 0 1 1 1 0
KRTAP5-7 WILD-TYPE 40 74 17 22 22 2
'KRTAP5-7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.86

Table S356.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
KRTAP5-7 MUTATED 1 0 0 1 1
KRTAP5-7 WILD-TYPE 37 46 38 18 38
'KRTAP5-7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.918 (Fisher's exact test), Q value = 1

Table S357.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0785 (Fisher's exact test), Q value = 0.6

Table S358.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.171 (Fisher's exact test), Q value = 0.74

Table S359.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.531 (Fisher's exact test), Q value = 0.91

Table S360.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.00302 (Fisher's exact test), Q value = 0.1

Table S361.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #9: '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 S66.  Get High-res Image Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.82

Table S362.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.696 (Fisher's exact test), Q value = 0.97

Table S363.  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 S364.  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 'RPPA_CNMF'

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

Table S365.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
JAK1 MUTATED 2 3 0 1 0 0
JAK1 WILD-TYPE 38 71 18 22 23 2
'JAK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.512 (Fisher's exact test), Q value = 0.91

Table S366.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
JAK1 MUTATED 0 3 2 0 1
JAK1 WILD-TYPE 38 43 36 19 38
'JAK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.82

Table S367.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.148 (Fisher's exact test), Q value = 0.71

Table S368.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #6: '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 S369.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 1

Table S370.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.203 (Fisher's exact test), Q value = 0.76

Table S371.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.342 (Fisher's exact test), Q value = 0.85

Table S372.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.295 (Fisher's exact test), Q value = 0.82

Table S373.  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 = 0.82

Table S374.  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 'RPPA_CNMF'

P value = 0.0589 (Fisher's exact test), Q value = 0.56

Table S375.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
DENND4B MUTATED 2 3 0 0 3 1
DENND4B WILD-TYPE 38 71 18 23 20 1
'DENND4B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 0.86

Table S376.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
DENND4B MUTATED 0 2 2 2 3
DENND4B WILD-TYPE 38 44 36 17 36
'DENND4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.71

Table S377.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.617 (Fisher's exact test), Q value = 0.96

Table S378.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.0463 (Fisher's exact test), Q value = 0.49

Table S379.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #7: '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 S67.  Get High-res Image Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'DENND4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 0.91

Table S380.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #8: '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 S381.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.346 (Fisher's exact test), Q value = 0.85

Table S382.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.661 (Fisher's exact test), Q value = 0.97

Table S383.  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 = 0.91

Table S384.  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 'RPPA_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 0.96

Table S385.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
BRD7 MUTATED 0 2 0 1 1 0
BRD7 WILD-TYPE 40 72 18 22 22 2
'BRD7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 0.97

Table S386.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
BRD7 MUTATED 2 1 0 0 1
BRD7 WILD-TYPE 36 45 38 19 38
'BRD7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 0.86

Table S387.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.603 (Fisher's exact test), Q value = 0.96

Table S388.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.572 (Fisher's exact test), Q value = 0.94

Table S389.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.175 (Fisher's exact test), Q value = 0.74

Table S390.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #8: '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 = 1

Table S391.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.131 (Fisher's exact test), Q value = 0.7

Table S392.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.89

Table S393.  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 = 0.81

Table S394.  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 'RPPA_CNMF'

P value = 0.939 (Fisher's exact test), Q value = 1

Table S395.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
IDH1 MUTATED 1 2 0 0 1 0
IDH1 WILD-TYPE 39 72 18 23 22 2
'IDH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.389 (Fisher's exact test), Q value = 0.86

Table S396.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
IDH1 MUTATED 2 2 0 0 0
IDH1 WILD-TYPE 36 44 38 19 39
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.71

Table S397.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.79

Table S398.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.213 (Fisher's exact test), Q value = 0.77

Table S399.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.387 (Fisher's exact test), Q value = 0.86

Table S400.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.393 (Fisher's exact test), Q value = 0.86

Table S401.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.173 (Fisher's exact test), Q value = 0.74

Table S402.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.143 (Fisher's exact test), Q value = 0.71

Table S403.  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 = 0.93 (Fisher's exact test), Q value = 1

Table S404.  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 'RPPA_CNMF'

P value = 0.00407 (Fisher's exact test), Q value = 0.12

Table S405.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CNGA3 MUTATED 0 0 1 1 1 1
CNGA3 WILD-TYPE 40 74 17 22 22 1

Figure S68.  Get High-res Image Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CNGA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 0.93

Table S406.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CNGA3 MUTATED 1 0 1 1 1
CNGA3 WILD-TYPE 37 46 37 18 38
'CNGA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 0.95

Table S407.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.212 (Fisher's exact test), Q value = 0.77

Table S408.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.655 (Fisher's exact test), Q value = 0.97

Table S409.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.329 (Fisher's exact test), Q value = 0.85

Table S410.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.97

Table S411.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.438 (Fisher's exact test), Q value = 0.89

Table S412.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.395 (Fisher's exact test), Q value = 0.86

Table S413.  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 = 0.0951 (Fisher's exact test), Q value = 0.63

Table S414.  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 'RPPA_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.82

Table S415.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
PLA2G3 MUTATED 0 2 0 1 2 0
PLA2G3 WILD-TYPE 40 72 18 22 21 2
'PLA2G3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.71

Table S416.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
PLA2G3 MUTATED 1 2 0 2 0
PLA2G3 WILD-TYPE 37 44 38 17 39
'PLA2G3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.73

Table S417.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.69

Table S418.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.86

Table S419.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0137 (Fisher's exact test), Q value = 0.27

Table S420.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #8: '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 S69.  Get High-res Image Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 0.98

Table S421.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.0365 (Fisher's exact test), Q value = 0.44

Table S422.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #10: '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 S70.  Get High-res Image Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HLA-DPB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S423.  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 = 0.319 (Fisher's exact test), Q value = 0.84

Table S424.  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 = 0.478 (Fisher's exact test), Q value = 0.89

Table S425.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.282 (Fisher's exact test), Q value = 0.82

Table S426.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.17 (Fisher's exact test), Q value = 0.74

Table S427.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.777 (Fisher's exact test), Q value = 1

Table S428.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.688 (Fisher's exact test), Q value = 0.97

Table S429.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.407 (Fisher's exact test), Q value = 0.87

Table S430.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.489 (Fisher's exact test), Q value = 0.89

Table S431.  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 = 0.76

Table S432.  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 'RPPA_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 0.91

Table S433.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
ALMS1 MUTATED 2 4 1 0 3 0
ALMS1 WILD-TYPE 38 70 17 23 20 2
'ALMS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.816 (Fisher's exact test), Q value = 1

Table S434.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
ALMS1 MUTATED 2 2 3 0 3
ALMS1 WILD-TYPE 36 44 35 19 36
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S435.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #5: '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 S436.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.44 (Fisher's exact test), Q value = 0.89

Table S437.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.699 (Fisher's exact test), Q value = 0.97

Table S438.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.484 (Fisher's exact test), Q value = 0.89

Table S439.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.699 (Fisher's exact test), Q value = 0.97

Table S440.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.62 (Fisher's exact test), Q value = 0.96

Table S441.  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 = 0.475 (Fisher's exact test), Q value = 0.89

Table S442.  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 'RPPA_CNMF'

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

Table S443.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
NUCB2 MUTATED 1 2 0 0 0 0
NUCB2 WILD-TYPE 39 72 18 23 23 2
'NUCB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S444.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
NUCB2 MUTATED 1 1 0 0 1
NUCB2 WILD-TYPE 37 45 38 19 38
'NUCB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.399 (Fisher's exact test), Q value = 0.86

Table S445.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.446 (Fisher's exact test), Q value = 0.89

Table S446.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.015 (Fisher's exact test), Q value = 0.27

Table S447.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #9: '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 S71.  Get High-res Image Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NUCB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.843 (Fisher's exact test), Q value = 1

Table S448.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.468 (Fisher's exact test), Q value = 0.89

Table S449.  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 = 0.357 (Fisher's exact test), Q value = 0.86

Table S450.  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 'RPPA_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S451.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
BAZ2A MUTATED 2 4 0 0 1 0
BAZ2A WILD-TYPE 38 70 18 23 22 2
'BAZ2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 0.92

Table S452.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
BAZ2A MUTATED 0 3 2 0 2
BAZ2A WILD-TYPE 38 43 36 19 37
'BAZ2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S453.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.685 (Fisher's exact test), Q value = 0.97

Table S454.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.424 (Fisher's exact test), Q value = 0.89

Table S455.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.582 (Fisher's exact test), Q value = 0.95

Table S456.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.6

Table S457.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.598 (Fisher's exact test), Q value = 0.96

Table S458.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.202 (Fisher's exact test), Q value = 0.76

Table S459.  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 = 0.0961 (Fisher's exact test), Q value = 0.63

Table S460.  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 'RPPA_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.91

Table S461.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
TAF1B MUTATED 2 1 0 0 0 0
TAF1B WILD-TYPE 38 73 18 23 23 2
'TAF1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.81

Table S462.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
TAF1B MUTATED 0 0 2 0 1
TAF1B WILD-TYPE 38 46 36 19 38
'TAF1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0827 (Fisher's exact test), Q value = 0.61

Table S463.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.657 (Fisher's exact test), Q value = 0.97

Table S464.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.809 (Fisher's exact test), Q value = 1

Table S465.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.806 (Fisher's exact test), Q value = 1

Table S466.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.462 (Fisher's exact test), Q value = 0.89

Table S467.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.269 (Fisher's exact test), Q value = 0.82

Table S468.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.335 (Fisher's exact test), Q value = 0.85

Table S469.  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 = 0.0676 (Fisher's exact test), Q value = 0.57

Table S470.  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 'RPPA_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.49

Table S471.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
C1ORF125 MUTATED 0 4 0 0 0 1
C1ORF125 WILD-TYPE 40 70 18 23 23 1

Figure S72.  Get High-res Image Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'C1ORF125 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.68

Table S472.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
C1ORF125 MUTATED 0 4 0 0 1
C1ORF125 WILD-TYPE 38 42 38 19 38
'C1ORF125 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.677 (Fisher's exact test), Q value = 0.97

Table S473.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.816 (Fisher's exact test), Q value = 1

Table S474.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.184 (Fisher's exact test), Q value = 0.76

Table S475.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0146 (Fisher's exact test), Q value = 0.27

Table S476.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #8: '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 S73.  Get High-res Image Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0778 (Fisher's exact test), Q value = 0.6

Table S477.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.78

Table S478.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.475 (Fisher's exact test), Q value = 0.89

Table S479.  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 S480.  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 'RPPA_CNMF'

P value = 0.335 (Fisher's exact test), Q value = 0.85

Table S481.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
AR MUTATED 1 1 1 1 2 0
AR WILD-TYPE 39 73 17 22 21 2
'AR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 0.96

Table S482.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
AR MUTATED 2 1 0 1 2
AR WILD-TYPE 36 45 38 18 37
'AR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.716 (Fisher's exact test), Q value = 0.98

Table S483.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.98

Table S484.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.475 (Fisher's exact test), Q value = 0.89

Table S485.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.74

Table S486.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.206 (Fisher's exact test), Q value = 0.76

Table S487.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.66 (Fisher's exact test), Q value = 0.97

Table S488.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.391 (Fisher's exact test), Q value = 0.86

Table S489.  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 = 0.99

Table S490.  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 'RPPA_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 0.99

Table S491.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
SPHK1 MUTATED 1 2 1 0 0 0
SPHK1 WILD-TYPE 39 72 17 23 23 2
'SPHK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.831 (Fisher's exact test), Q value = 1

Table S492.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
SPHK1 MUTATED 1 1 0 0 2
SPHK1 WILD-TYPE 37 45 38 19 37
'SPHK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.44

Table S493.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #5: '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 S74.  Get High-res Image Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SPHK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0103 (Fisher's exact test), Q value = 0.23

Table S494.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #6: '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 S75.  Get High-res Image Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SPHK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 0.91

Table S495.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0939 (Fisher's exact test), Q value = 0.63

Table S496.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.68

Table S497.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.106 (Fisher's exact test), Q value = 0.66

Table S498.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.09 (Fisher's exact test), Q value = 0.62

Table S499.  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 = 0.454 (Fisher's exact test), Q value = 0.89

Table S500.  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 = 0.71

Table S501.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.623 (Fisher's exact test), Q value = 0.96

Table S502.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.37 (Fisher's exact test), Q value = 0.86

Table S503.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.61

Table S504.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #8: '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 S505.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.163 (Fisher's exact test), Q value = 0.73

Table S506.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.498 (Fisher's exact test), Q value = 0.89

Table S507.  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 = 0.624 (Fisher's exact test), Q value = 0.96

Table S508.  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 'RPPA_CNMF'

P value = 0.882 (Fisher's exact test), Q value = 1

Table S509.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
LFNG MUTATED 2 3 0 0 0 0
LFNG WILD-TYPE 38 71 18 23 23 2
'LFNG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.388 (Fisher's exact test), Q value = 0.86

Table S510.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
LFNG MUTATED 1 1 0 0 3
LFNG WILD-TYPE 37 45 38 19 36
'LFNG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 0.97

Table S511.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.902 (Fisher's exact test), Q value = 1

Table S512.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.89

Table S513.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.467 (Fisher's exact test), Q value = 0.89

Table S514.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.76 (Fisher's exact test), Q value = 0.99

Table S515.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.536 (Fisher's exact test), Q value = 0.91

Table S516.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.581 (Fisher's exact test), Q value = 0.95

Table S517.  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 S518.  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 'RPPA_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.89

Table S519.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
FZR1 MUTATED 1 1 1 0 0 0
FZR1 WILD-TYPE 39 73 17 23 23 2
'FZR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S520.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
FZR1 MUTATED 0 1 1 0 1
FZR1 WILD-TYPE 38 45 37 19 38
'FZR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.84

Table S521.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.465 (Fisher's exact test), Q value = 0.89

Table S522.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.793 (Fisher's exact test), Q value = 1

Table S523.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0295 (Fisher's exact test), Q value = 0.42

Table S524.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #8: '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 S76.  Get High-res Image Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FZR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.76

Table S525.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.0869 (Fisher's exact test), Q value = 0.61

Table S526.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #10: '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 S527.  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 = 0.12 (Fisher's exact test), Q value = 0.68

Table S528.  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 'RPPA_CNMF'

P value = 0.94 (Fisher's exact test), Q value = 1

Table S529.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
TRIOBP MUTATED 2 4 1 1 0 0
TRIOBP WILD-TYPE 38 70 17 22 23 2
'TRIOBP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S530.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
TRIOBP MUTATED 1 3 2 0 2
TRIOBP WILD-TYPE 37 43 36 19 37
'TRIOBP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.85

Table S531.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.378 (Fisher's exact test), Q value = 0.86

Table S532.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.378 (Fisher's exact test), Q value = 0.86

Table S533.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.464 (Fisher's exact test), Q value = 0.89

Table S534.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0966 (Fisher's exact test), Q value = 0.63

Table S535.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.403 (Fisher's exact test), Q value = 0.86

Table S536.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #10: '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 S537.  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 = 0.793 (Fisher's exact test), Q value = 1

Table S538.  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 = 0.261 (Fisher's exact test), Q value = 0.82

Table S539.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.724 (Fisher's exact test), Q value = 0.98

Table S540.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.229 (Fisher's exact test), Q value = 0.78

Table S541.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.908 (Fisher's exact test), Q value = 1

Table S542.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.149 (Fisher's exact test), Q value = 0.71

Table S543.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #9: '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 S544.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0328 (Fisher's exact test), Q value = 0.43

Table S545.  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 S77.  Get High-res Image Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DYRK1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.89 (Fisher's exact test), Q value = 1

Table S546.  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 'RPPA_CNMF'

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

Table S547.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
DYRK1A MUTATED 1 2 0 0 0 0
DYRK1A WILD-TYPE 39 72 18 23 23 2
'DYRK1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.86

Table S548.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
DYRK1A MUTATED 1 0 0 0 2
DYRK1A WILD-TYPE 37 46 38 19 37
'DYRK1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S549.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.639 (Fisher's exact test), Q value = 0.97

Table S550.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.263 (Fisher's exact test), Q value = 0.82

Table S551.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.481 (Fisher's exact test), Q value = 0.89

Table S552.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.99

Table S553.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.292 (Fisher's exact test), Q value = 0.82

Table S554.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.435 (Fisher's exact test), Q value = 0.89

Table S555.  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 = 0.909 (Fisher's exact test), Q value = 1

Table S556.  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 'RPPA_CNMF'

P value = 0.498 (Fisher's exact test), Q value = 0.89

Table S557.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
TNPO1 MUTATED 2 2 1 2 0 0
TNPO1 WILD-TYPE 38 72 17 21 23 2
'TNPO1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.81

Table S558.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
TNPO1 MUTATED 0 1 2 2 2
TNPO1 WILD-TYPE 38 45 36 17 37
'TNPO1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.85

Table S559.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.9

Table S560.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.612 (Fisher's exact test), Q value = 0.96

Table S561.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.468 (Fisher's exact test), Q value = 0.89

Table S562.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.76

Table S563.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.628 (Fisher's exact test), Q value = 0.96

Table S564.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.302 (Fisher's exact test), Q value = 0.83

Table S565.  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 S566.  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 = 0.731 (Fisher's exact test), Q value = 0.98

Table S567.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.247 (Fisher's exact test), Q value = 0.81

Table S568.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.495 (Fisher's exact test), Q value = 0.89

Table S569.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.285 (Fisher's exact test), Q value = 0.82

Table S570.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.455 (Fisher's exact test), Q value = 0.89

Table S571.  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 = 0.727 (Fisher's exact test), Q value = 0.98

Table S572.  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 'RPPA_CNMF'

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

Table S573.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CCNA2 MUTATED 1 2 0 0 0 0
CCNA2 WILD-TYPE 39 72 18 23 23 2
'CCNA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S574.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CCNA2 MUTATED 0 1 1 0 1
CCNA2 WILD-TYPE 38 45 37 19 38
'CCNA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0945 (Fisher's exact test), Q value = 0.63

Table S575.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.791 (Fisher's exact test), Q value = 1

Table S576.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.241 (Fisher's exact test), Q value = 0.81

Table S577.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.21 (Fisher's exact test), Q value = 0.77

Table S578.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.396 (Fisher's exact test), Q value = 0.86

Table S579.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.254 (Fisher's exact test), Q value = 0.82

Table S580.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.54 (Fisher's exact test), Q value = 0.91

Table S581.  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 = 1

Table S582.  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 = 0.96

Table S583.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.737 (Fisher's exact test), Q value = 0.98

Table S584.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.542 (Fisher's exact test), Q value = 0.91

Table S585.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.979 (Fisher's exact test), Q value = 1

Table S586.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.908 (Fisher's exact test), Q value = 1

Table S587.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.977 (Fisher's exact test), Q value = 1

Table S588.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.817 (Fisher's exact test), Q value = 1

Table S589.  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 = 0.662 (Fisher's exact test), Q value = 0.97

Table S590.  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 'RPPA_CNMF'

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

Table S591.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
RXRB MUTATED 2 2 0 0 0 0
RXRB WILD-TYPE 38 72 18 23 23 2
'RXRB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 0.97

Table S592.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
RXRB MUTATED 0 1 2 0 1
RXRB WILD-TYPE 38 45 36 19 38
'RXRB MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.89

Table S593.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.76 (Fisher's exact test), Q value = 0.99

Table S594.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.89

Table S595.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.812 (Fisher's exact test), Q value = 1

Table S596.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.92 (Fisher's exact test), Q value = 1

Table S597.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.878 (Fisher's exact test), Q value = 1

Table S598.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.536 (Fisher's exact test), Q value = 0.91

Table S599.  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 = 0.854 (Fisher's exact test), Q value = 1

Table S600.  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 = 0.82

Table S601.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.97

Table S602.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.85

Table S603.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.595 (Fisher's exact test), Q value = 0.96

Table S604.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.96

Table S605.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.532 (Fisher's exact test), Q value = 0.91

Table S606.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.686 (Fisher's exact test), Q value = 0.97

Table S607.  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 = 0.408 (Fisher's exact test), Q value = 0.87

Table S608.  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 'RPPA_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.42

Table S609.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
NBEA MUTATED 0 4 2 2 5 0
NBEA WILD-TYPE 40 70 16 21 18 2

Figure S78.  Get High-res Image Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NBEA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.73

Table S610.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
NBEA MUTATED 1 2 3 4 3
NBEA WILD-TYPE 37 44 35 15 36
'NBEA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S611.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.913 (Fisher's exact test), Q value = 1

Table S612.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.274 (Fisher's exact test), Q value = 0.82

Table S613.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.149 (Fisher's exact test), Q value = 0.71

Table S614.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.729 (Fisher's exact test), Q value = 0.98

Table S615.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.711 (Fisher's exact test), Q value = 0.98

Table S616.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.91

Table S617.  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 = 0.96

Table S618.  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 = 0.274 (Fisher's exact test), Q value = 0.82

Table S619.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.153 (Fisher's exact test), Q value = 0.72

Table S620.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.431 (Fisher's exact test), Q value = 0.89

Table S621.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.117 (Fisher's exact test), Q value = 0.68

Table S622.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #8: '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 = 1

Table S623.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.314 (Fisher's exact test), Q value = 0.84

Table S624.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.737 (Fisher's exact test), Q value = 0.98

Table S625.  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 = 0.0458 (Fisher's exact test), Q value = 0.49

Table S626.  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 S79.  Get High-res Image Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'VPS4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0866 (Fisher's exact test), Q value = 0.61

Table S627.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.288 (Fisher's exact test), Q value = 0.82

Table S628.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.758 (Fisher's exact test), Q value = 0.99

Table S629.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.83

Table S630.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.199 (Fisher's exact test), Q value = 0.76

Table S631.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.0737 (Fisher's exact test), Q value = 0.6

Table S632.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.541 (Fisher's exact test), Q value = 0.91

Table S633.  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 = 0.309 (Fisher's exact test), Q value = 0.84

Table S634.  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 'RPPA_CNMF'

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

Table S635.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
HNRNPL MUTATED 2 2 0 0 1 0
HNRNPL WILD-TYPE 38 72 18 23 22 2
'HNRNPL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.76

Table S636.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
HNRNPL MUTATED 0 0 2 1 2
HNRNPL WILD-TYPE 38 46 36 18 37
'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.42

Table S637.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #5: '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 S80.  Get High-res Image Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.83

Table S638.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.282 (Fisher's exact test), Q value = 0.82

Table S639.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.765 (Fisher's exact test), Q value = 0.99

Table S640.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.698 (Fisher's exact test), Q value = 0.97

Table S641.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.594 (Fisher's exact test), Q value = 0.95

Table S642.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.821 (Fisher's exact test), Q value = 1

Table S643.  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 = 0.364 (Fisher's exact test), Q value = 0.86

Table S644.  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 'RPPA_CNMF'

P value = 0.711 (Fisher's exact test), Q value = 0.98

Table S645.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
FILIP1 MUTATED 2 5 2 1 0 0
FILIP1 WILD-TYPE 38 69 16 22 23 2
'FILIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 0.98

Table S646.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
FILIP1 MUTATED 2 2 2 0 4
FILIP1 WILD-TYPE 36 44 36 19 35
'FILIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.299 (Fisher's exact test), Q value = 0.83

Table S647.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.444 (Fisher's exact test), Q value = 0.89

Table S648.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.723 (Fisher's exact test), Q value = 0.98

Table S649.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.375 (Fisher's exact test), Q value = 0.86

Table S650.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.49 (Fisher's exact test), Q value = 0.89

Table S651.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.573 (Fisher's exact test), Q value = 0.94

Table S652.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.7

Table S653.  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 = 0.0904 (Fisher's exact test), Q value = 0.62

Table S654.  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 'RPPA_CNMF'

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

Table S655.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
FAM22F MUTATED 1 2 0 0 0 0
FAM22F WILD-TYPE 39 72 18 23 23 2
'FAM22F MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.69 (Fisher's exact test), Q value = 0.97

Table S656.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
FAM22F MUTATED 1 2 0 0 0
FAM22F WILD-TYPE 37 44 38 19 39
'FAM22F MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.39

Table S657.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #5: '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 S81.  Get High-res Image Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FAM22F MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.84

Table S658.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.739 (Fisher's exact test), Q value = 0.98

Table S659.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.39 (Fisher's exact test), Q value = 0.86

Table S660.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0858 (Fisher's exact test), Q value = 0.61

Table S661.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.276 (Fisher's exact test), Q value = 0.82

Table S662.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.464 (Fisher's exact test), Q value = 0.89

Table S663.  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 = 0.686 (Fisher's exact test), Q value = 0.97

Table S664.  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 'RPPA_CNMF'

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

Table S665.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
GPSM2 MUTATED 1 2 0 0 0 0
GPSM2 WILD-TYPE 39 72 18 23 23 2
'GPSM2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.685 (Fisher's exact test), Q value = 0.97

Table S666.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
GPSM2 MUTATED 0 2 1 0 0
GPSM2 WILD-TYPE 38 44 37 19 39
'GPSM2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 0.97

Table S667.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 1

Table S668.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #6: '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 S669.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.645 (Fisher's exact test), Q value = 0.97

Table S670.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0851 (Fisher's exact test), Q value = 0.61

Table S671.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.846 (Fisher's exact test), Q value = 1

Table S672.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.308 (Fisher's exact test), Q value = 0.84

Table S673.  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 = 1

Table S674.  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 = 0.781 (Fisher's exact test), Q value = 1

Table S675.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.463 (Fisher's exact test), Q value = 0.89

Table S676.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.711 (Fisher's exact test), Q value = 0.98

Table S677.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.457 (Fisher's exact test), Q value = 0.89

Table S678.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.85

Table S679.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.624 (Fisher's exact test), Q value = 0.96

Table S680.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.78

Table S681.  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 = 0.619 (Fisher's exact test), Q value = 0.96

Table S682.  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 'RPPA_CNMF'

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

Table S683.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
PTGR1 MUTATED 1 3 0 0 0 0
PTGR1 WILD-TYPE 39 71 18 23 23 2
'PTGR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.938 (Fisher's exact test), Q value = 1

Table S684.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
PTGR1 MUTATED 0 2 1 0 1
PTGR1 WILD-TYPE 38 44 37 19 38
'PTGR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.839 (Fisher's exact test), Q value = 1

Table S685.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.447 (Fisher's exact test), Q value = 0.89

Table S686.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.927 (Fisher's exact test), Q value = 1

Table S687.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.322 (Fisher's exact test), Q value = 0.84

Table S688.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.81 (Fisher's exact test), Q value = 1

Table S689.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.193 (Fisher's exact test), Q value = 0.76

Table S690.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.615 (Fisher's exact test), Q value = 0.96

Table S691.  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 = 0.614 (Fisher's exact test), Q value = 0.96

Table S692.  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 = 0.116 (Fisher's exact test), Q value = 0.68

Table S693.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.74

Table S694.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.533 (Fisher's exact test), Q value = 0.91

Table S695.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0992 (Fisher's exact test), Q value = 0.63

Table S696.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.862 (Fisher's exact test), Q value = 1

Table S697.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.141 (Fisher's exact test), Q value = 0.71

Table S698.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.432 (Fisher's exact test), Q value = 0.89

Table S699.  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 = 0.204 (Fisher's exact test), Q value = 0.76

Table S700.  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 'RPPA_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.89

Table S701.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
PBRM1 MUTATED 0 2 1 0 0 0
PBRM1 WILD-TYPE 40 72 17 23 23 2
'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S702.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
PBRM1 MUTATED 0 1 0 0 2
PBRM1 WILD-TYPE 38 45 38 19 37
'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00904 (Fisher's exact test), Q value = 0.21

Table S703.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: '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 S82.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00774 (Fisher's exact test), Q value = 0.19

Table S704.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: '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 S83.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.82

Table S705.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.012 (Fisher's exact test), Q value = 0.25

Table S706.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: '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 S84.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 0.91

Table S707.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.165 (Fisher's exact test), Q value = 0.73

Table S708.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: '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 S709.  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 = 0.089 (Fisher's exact test), Q value = 0.62

Table S710.  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 'RPPA_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.82

Table S711.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
SGK269 MUTATED 0 2 0 1 2 0
SGK269 WILD-TYPE 40 72 18 22 21 2
'SGK269 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.695 (Fisher's exact test), Q value = 0.97

Table S712.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
SGK269 MUTATED 1 2 2 0 0
SGK269 WILD-TYPE 37 44 36 19 39
'SGK269 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.82

Table S713.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.647 (Fisher's exact test), Q value = 0.97

Table S714.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.582 (Fisher's exact test), Q value = 0.95

Table S715.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.331 (Fisher's exact test), Q value = 0.85

Table S716.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.222 (Fisher's exact test), Q value = 0.78

Table S717.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.015 (Fisher's exact test), Q value = 0.27

Table S718.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #10: '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 S85.  Get High-res Image Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'LEO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.143 (Fisher's exact test), Q value = 0.71

Table S719.  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 = 0.38 (Fisher's exact test), Q value = 0.86

Table S720.  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 'RPPA_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.69

Table S721.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
LEO1 MUTATED 0 1 2 0 0 0
LEO1 WILD-TYPE 40 73 16 23 23 2
'LEO1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S722.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
LEO1 MUTATED 0 1 1 0 1
LEO1 WILD-TYPE 38 45 37 19 38
'LEO1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.805 (Fisher's exact test), Q value = 1

Table S723.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.74

Table S724.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.89

Table S725.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.333 (Fisher's exact test), Q value = 0.85

Table S726.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.82

Table S727.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.707 (Fisher's exact test), Q value = 0.98

Table S728.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.453 (Fisher's exact test), Q value = 0.89

Table S729.  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 = 1

Table S730.  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 = 0.369 (Fisher's exact test), Q value = 0.86

Table S731.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.144 (Fisher's exact test), Q value = 0.71

Table S732.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.737 (Fisher's exact test), Q value = 0.98

Table S733.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.186 (Fisher's exact test), Q value = 0.76

Table S734.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.326 (Fisher's exact test), Q value = 0.85

Table S735.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.519 (Fisher's exact test), Q value = 0.91

Table S736.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.683 (Fisher's exact test), Q value = 0.97

Table S737.  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 = 0.78

Table S738.  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 = 0.419 (Fisher's exact test), Q value = 0.88

Table S739.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.718 (Fisher's exact test), Q value = 0.98

Table S740.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.82

Table S741.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.944 (Fisher's exact test), Q value = 1

Table S742.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.373 (Fisher's exact test), Q value = 0.86

Table S743.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.845 (Fisher's exact test), Q value = 1

Table S744.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.147 (Fisher's exact test), Q value = 0.71

Table S745.  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 = 0.85

Table S746.  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 'RPPA_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.77

Table S747.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CBX4 MUTATED 2 0 0 1 0 0
CBX4 WILD-TYPE 38 74 18 22 23 2
'CBX4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.76

Table S748.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CBX4 MUTATED 2 0 1 0 0
CBX4 WILD-TYPE 36 46 37 19 39
'CBX4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00205 (Fisher's exact test), Q value = 0.07

Table S749.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #5: '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 S86.  Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CBX4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00394 (Fisher's exact test), Q value = 0.11

Table S750.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #6: '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 S87.  Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CBX4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.85

Table S751.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.488 (Fisher's exact test), Q value = 0.89

Table S752.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0553 (Fisher's exact test), Q value = 0.53

Table S753.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.84

Table S754.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #10: '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 S755.  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 = 0.121 (Fisher's exact test), Q value = 0.69

Table S756.  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 = 0.0409 (Fisher's exact test), Q value = 0.46

Table S757.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #5: '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 S88.  Get High-res Image Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MTA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.82

Table S758.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.0571 (Fisher's exact test), Q value = 0.54

Table S759.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0671 (Fisher's exact test), Q value = 0.57

Table S760.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.89

Table S761.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.159 (Fisher's exact test), Q value = 0.73

Table S762.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.00168 (Fisher's exact test), Q value = 0.064

Table S763.  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 S89.  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 = 0.71

Table S764.  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 'RPPA_CNMF'

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

Table S765.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
CRIP3 MUTATED 1 2 0 0 0 0
CRIP3 WILD-TYPE 39 72 18 23 23 2
'CRIP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S766.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
CRIP3 MUTATED 1 2 0 0 0
CRIP3 WILD-TYPE 37 44 38 19 39
'CRIP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.86

Table S767.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.77 (Fisher's exact test), Q value = 0.99

Table S768.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.389 (Fisher's exact test), Q value = 0.86

Table S769.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.86

Table S770.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.253 (Fisher's exact test), Q value = 0.82

Table S771.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.124 (Fisher's exact test), Q value = 0.69

Table S772.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #10: '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 S773.  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 = 0.95

Table S774.  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 'RPPA_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S775.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
NR4A2 MUTATED 2 2 0 1 0 0
NR4A2 WILD-TYPE 38 72 18 22 23 2
'NR4A2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S776.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
NR4A2 MUTATED 1 1 1 1 1
NR4A2 WILD-TYPE 37 45 37 18 38
'NR4A2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.82

Table S777.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.68

Table S778.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.677 (Fisher's exact test), Q value = 0.97

Table S779.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.115 (Fisher's exact test), Q value = 0.68

Table S780.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.81 (Fisher's exact test), Q value = 1

Table S781.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.147 (Fisher's exact test), Q value = 0.71

Table S782.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.0195 (Fisher's exact test), Q value = 0.33

Table S783.  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 S90.  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 S784.  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 'RPPA_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 0.86

Table S785.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
HNF1A MUTATED 0 5 1 1 0 0
HNF1A WILD-TYPE 40 69 17 22 23 2
'HNF1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 0.86

Table S786.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
HNF1A MUTATED 1 3 0 0 3
HNF1A WILD-TYPE 37 43 38 19 36
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0672 (Fisher's exact test), Q value = 0.57

Table S787.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.319 (Fisher's exact test), Q value = 0.84

Table S788.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.0638 (Fisher's exact test), Q value = 0.57

Table S789.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.76

Table S790.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.126 (Fisher's exact test), Q value = 0.69

Table S791.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.284 (Fisher's exact test), Q value = 0.82

Table S792.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.291 (Fisher's exact test), Q value = 0.82

Table S793.  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 = 0.672 (Fisher's exact test), Q value = 0.97

Table S794.  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 'RPPA_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 0.91

Table S795.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
KRAS MUTATED 2 1 0 0 0 0
KRAS WILD-TYPE 38 73 18 23 23 2
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S796.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
KRAS MUTATED 0 1 1 0 1
KRAS WILD-TYPE 38 45 37 19 38
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.54 (Fisher's exact test), Q value = 0.91

Table S797.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.188 (Fisher's exact test), Q value = 0.76

Table S798.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.694 (Fisher's exact test), Q value = 0.97

Table S799.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.119 (Fisher's exact test), Q value = 0.68

Table S800.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.173 (Fisher's exact test), Q value = 0.74

Table S801.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.609 (Fisher's exact test), Q value = 0.96

Table S802.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.788 (Fisher's exact test), Q value = 1

Table S803.  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 = 0.791 (Fisher's exact test), Q value = 1

Table S804.  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 'RPPA_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 0.98

Table S805.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
PGBD1 MUTATED 0 3 0 0 0 0
PGBD1 WILD-TYPE 40 71 18 23 23 2
'PGBD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.728 (Fisher's exact test), Q value = 0.98

Table S806.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
PGBD1 MUTATED 0 2 0 0 1
PGBD1 WILD-TYPE 38 44 38 19 38
'PGBD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S807.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.41 (Fisher's exact test), Q value = 0.87

Table S808.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.559 (Fisher's exact test), Q value = 0.93

Table S809.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 1

Table S810.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.464 (Fisher's exact test), Q value = 0.89

Table S811.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 1

Table S812.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.709 (Fisher's exact test), Q value = 0.98

Table S813.  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 = 0.623 (Fisher's exact test), Q value = 0.96

Table S814.  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 'RPPA_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.85

Table S815.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
LATS1 MUTATED 0 1 1 0 1 0
LATS1 WILD-TYPE 40 73 17 23 22 2
'LATS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.394 (Fisher's exact test), Q value = 0.86

Table S816.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
LATS1 MUTATED 0 0 1 1 1
LATS1 WILD-TYPE 38 46 37 18 38
'LATS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.94

Table S817.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.71

Table S818.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.856 (Fisher's exact test), Q value = 1

Table S819.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.666 (Fisher's exact test), Q value = 0.97

Table S820.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #8: '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 S821.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.613 (Fisher's exact test), Q value = 0.96

Table S822.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.23 (Fisher's exact test), Q value = 0.78

Table S823.  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 = 0.71

Table S824.  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 'RPPA_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.89

Table S825.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
KEAP1 MUTATED 1 4 2 0 2 0
KEAP1 WILD-TYPE 39 70 16 23 21 2
'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S826.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
KEAP1 MUTATED 2 2 1 1 3
KEAP1 WILD-TYPE 36 44 37 18 36
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.82

Table S827.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.939 (Fisher's exact test), Q value = 1

Table S828.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.1 (Fisher's exact test), Q value = 0.64

Table S829.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.257 (Fisher's exact test), Q value = 0.82

Table S830.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.98

Table S831.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.232 (Fisher's exact test), Q value = 0.79

Table S832.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.394 (Fisher's exact test), Q value = 0.86

Table S833.  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 = 0.6

Table S834.  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 'RPPA_CNMF'

P value = 0.00204 (Fisher's exact test), Q value = 0.07

Table S835.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
SENP6 MUTATED 4 0 0 0 0 1
SENP6 WILD-TYPE 36 74 18 23 23 1

Figure S91.  Get High-res Image Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'SENP6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.82

Table S836.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
SENP6 MUTATED 1 0 3 0 1
SENP6 WILD-TYPE 37 46 35 19 38
'SENP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S837.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.221 (Fisher's exact test), Q value = 0.78

Table S838.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.468 (Fisher's exact test), Q value = 0.89

Table S839.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.428 (Fisher's exact test), Q value = 0.89

Table S840.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.105 (Fisher's exact test), Q value = 0.66

Table S841.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.931 (Fisher's exact test), Q value = 1

Table S842.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.458 (Fisher's exact test), Q value = 0.89

Table S843.  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 = 0.573 (Fisher's exact test), Q value = 0.94

Table S844.  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 'RPPA_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 0.97

Table S845.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
FKBP4 MUTATED 0 2 0 1 0 0
FKBP4 WILD-TYPE 40 72 18 22 23 2
'FKBP4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0982 (Fisher's exact test), Q value = 0.63

Table S846.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
FKBP4 MUTATED 0 0 0 1 2
FKBP4 WILD-TYPE 38 46 38 18 37
'FKBP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S847.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.671 (Fisher's exact test), Q value = 0.97

Table S848.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #6: '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 = 1

Table S849.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.97

Table S850.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #8: '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 S851.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.31 (Fisher's exact test), Q value = 0.84

Table S852.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #10: '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 S853.  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 = 0.15 (Fisher's exact test), Q value = 0.71

Table S854.  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 = 0.00833 (Fisher's exact test), Q value = 0.2

Table S855.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #5: '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 S92.  Get High-res Image Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FOXK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 0.98

Table S856.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.458 (Fisher's exact test), Q value = 0.89

Table S857.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.342 (Fisher's exact test), Q value = 0.85

Table S858.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.78

Table S859.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.86

Table S860.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.36 (Fisher's exact test), Q value = 0.86

Table S861.  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 = 1

Table S862.  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 'RPPA_CNMF'

P value = 0.619 (Fisher's exact test), Q value = 0.96

Table S863.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
DSPP MUTATED 3 3 1 0 2 0
DSPP WILD-TYPE 37 71 17 23 21 2
'DSPP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.85

Table S864.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
DSPP MUTATED 4 2 0 1 2
DSPP WILD-TYPE 34 44 38 18 37
'DSPP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 0.98

Table S865.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.213 (Fisher's exact test), Q value = 0.77

Table S866.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.915 (Fisher's exact test), Q value = 1

Table S867.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.89

Table S868.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.775 (Fisher's exact test), Q value = 1

Table S869.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.222 (Fisher's exact test), Q value = 0.78

Table S870.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.683 (Fisher's exact test), Q value = 0.97

Table S871.  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 = 0.469 (Fisher's exact test), Q value = 0.89

Table S872.  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 S873.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.164 (Fisher's exact test), Q value = 0.73

Table S874.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.0369 (Fisher's exact test), Q value = 0.44

Table S875.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #7: '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 S93.  Get High-res Image Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S876.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.0136 (Fisher's exact test), Q value = 0.27

Table S877.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #9: '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 S94.  Get High-res Image Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.73

Table S878.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.684 (Fisher's exact test), Q value = 0.97

Table S879.  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 = 0.369 (Fisher's exact test), Q value = 0.86

Table S880.  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 'RPPA_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 0.95

Table S881.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
PRAMEF4 MUTATED 2 1 0 1 0 0
PRAMEF4 WILD-TYPE 38 73 18 22 23 2
'PRAMEF4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 0.98

Table S882.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
PRAMEF4 MUTATED 1 1 1 1 0
PRAMEF4 WILD-TYPE 37 45 37 18 39
'PRAMEF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.85

Table S883.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.565 (Fisher's exact test), Q value = 0.94

Table S884.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.189 (Fisher's exact test), Q value = 0.76

Table S885.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.73

Table S886.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.69 (Fisher's exact test), Q value = 0.97

Table S887.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.248 (Fisher's exact test), Q value = 0.81

Table S888.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #10: '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 S889.  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 = 0.317 (Fisher's exact test), Q value = 0.84

Table S890.  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 'RPPA_CNMF'

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

Table S891.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
RPS6KA5 MUTATED 1 2 0 0 0 0
RPS6KA5 WILD-TYPE 39 72 18 23 23 2
'RPS6KA5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 0.97

Table S892.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
RPS6KA5 MUTATED 0 2 1 0 0
RPS6KA5 WILD-TYPE 38 44 37 19 39
'RPS6KA5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S893.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.332 (Fisher's exact test), Q value = 0.85

Table S894.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.312 (Fisher's exact test), Q value = 0.84

Table S895.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.427 (Fisher's exact test), Q value = 0.89

Table S896.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.286 (Fisher's exact test), Q value = 0.82

Table S897.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.522 (Fisher's exact test), Q value = 0.91

Table S898.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.76

Table S899.  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 = 0.209 (Fisher's exact test), Q value = 0.77

Table S900.  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 'RPPA_CNMF'

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

Table S901.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
DDX42 MUTATED 0 3 0 0 1 0
DDX42 WILD-TYPE 40 71 18 23 22 2
'DDX42 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.89

Table S902.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
DDX42 MUTATED 0 2 0 1 1
DDX42 WILD-TYPE 38 44 38 18 38
'DDX42 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.73

Table S903.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.0291 (Fisher's exact test), Q value = 0.42

Table S904.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #6: '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 S95.  Get High-res Image Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DDX42 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.81

Table S905.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0628 (Fisher's exact test), Q value = 0.57

Table S906.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.339 (Fisher's exact test), Q value = 0.85

Table S907.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.226 (Fisher's exact test), Q value = 0.78

Table S908.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.13 (Fisher's exact test), Q value = 0.7

Table S909.  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 = 0.366 (Fisher's exact test), Q value = 0.86

Table S910.  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 'RPPA_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 0.98

Table S911.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
RHCG MUTATED 0 3 0 0 0 0
RHCG WILD-TYPE 40 71 18 23 23 2
'RHCG MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.116 (Fisher's exact test), Q value = 0.68

Table S912.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
RHCG MUTATED 0 3 0 0 0
RHCG WILD-TYPE 38 43 38 19 39
'RHCG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.82

Table S913.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.262 (Fisher's exact test), Q value = 0.82

Table S914.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.687 (Fisher's exact test), Q value = 0.97

Table S915.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0825 (Fisher's exact test), Q value = 0.61

Table S916.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.914 (Fisher's exact test), Q value = 1

Table S917.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.124 (Fisher's exact test), Q value = 0.69

Table S918.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.853 (Fisher's exact test), Q value = 1

Table S919.  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 S920.  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 'RPPA_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 0.91

Table S921.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
SWAP70 MUTATED 2 1 0 0 0 0
SWAP70 WILD-TYPE 38 73 18 23 23 2
'SWAP70 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.464 (Fisher's exact test), Q value = 0.89

Table S922.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
SWAP70 MUTATED 0 1 2 0 0
SWAP70 WILD-TYPE 38 45 36 19 39
'SWAP70 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.82

Table S923.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.98

Table S924.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.96

Table S925.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.693 (Fisher's exact test), Q value = 0.97

Table S926.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.68

Table S927.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.86

Table S928.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.303 (Fisher's exact test), Q value = 0.83

Table S929.  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 = 0.684 (Fisher's exact test), Q value = 0.97

Table S930.  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 'RPPA_CNMF'

P value = 0.0332 (Fisher's exact test), Q value = 0.43

Table S931.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
BIN1 MUTATED 0 0 2 1 0 0
BIN1 WILD-TYPE 40 74 16 22 23 2

Figure S96.  Get High-res Image Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'BIN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.81

Table S932.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
BIN1 MUTATED 2 0 0 0 1
BIN1 WILD-TYPE 36 46 38 19 38
'BIN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.593 (Fisher's exact test), Q value = 0.95

Table S933.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.486 (Fisher's exact test), Q value = 0.89

Table S934.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.683 (Fisher's exact test), Q value = 0.97

Table S935.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.0978 (Fisher's exact test), Q value = 0.63

Table S936.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.913 (Fisher's exact test), Q value = 1

Table S937.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.126 (Fisher's exact test), Q value = 0.69

Table S938.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #10: '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 = 0.132 (Fisher's exact test), Q value = 0.7

Table S939.  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 = 0.89

Table S940.  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 'RPPA_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.82

Table S941.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 74 18 23 23 2
SMARCA4 MUTATED 0 2 1 1 2 0
SMARCA4 WILD-TYPE 40 72 17 22 21 2
'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0543 (Fisher's exact test), Q value = 0.53

Table S942.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 38 46 38 19 39
SMARCA4 MUTATED 1 1 0 3 1
SMARCA4 WILD-TYPE 37 45 38 16 38
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.85

Table S943.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: '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 = 0.477 (Fisher's exact test), Q value = 0.89

Table S944.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: '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 = 0.98

Table S945.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: '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 = 0.76

Table S946.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: '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 = 0.144 (Fisher's exact test), Q value = 0.71

Table S947.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: '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 = 0.377 (Fisher's exact test), Q value = 0.86

Table S948.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: '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/26875919/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/26874095/LIHC-TP.transferedmergedcluster.txt

  • Number of patients = 373

  • Number of significantly mutated genes = 99

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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