Correlation between gene mutation status and molecular subtypes
Liver Hepatocellular Carcinoma
14 July 2016  |  awg_lihc__2016_07_14
Maintainer Information
Citation Information
doi:10.7908/C1CJ8D1F
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/C1CJ8D1F
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, 36 significant findings detected with P value < 0.05 and Q value < 0.25.

  • TP53 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', 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',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • 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 'METHLYATION_CNMF'.

  • TCHH mutation correlated to 'CN_CNMF'.

  • CNGA3 mutation correlated to 'RPPA_CNMF'.

  • KEAP1 mutation correlated to 'MIRSEQ_CNMF'.

  • SENP6 mutation correlated to 'RPPA_CNMF'.

  • FKBP4 mutation correlated to 'MIRSEQ_CNMF'.

  • SMARCA4 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

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, 36 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 4e-05
(0.0033) 		1e-05
(0.0011) 		0.0888
(0.671) 		0.00189
(0.0859) 		1e-05
(0.0011) 		1e-05
(0.0011) 		1e-05
(0.0011) 		1e-05
(0.0011) 		1e-05
(0.0011) 		1e-05
(0.0011)
BAP1 21 (6%) 352 0.605
(0.997) 		3e-05
(0.00297) 		0.0269
(0.512) 		0.0513
(0.591) 		0.00028
(0.0154) 		1e-05
(0.0011) 		0.00013
(0.00858) 		0.00417
(0.136) 		0.00505
(0.149) 		0.00191
(0.0859)
TP53 114 (31%) 259 1e-05
(0.0011) 		9e-05
(0.00636) 		0.0467
(0.562) 		0.0213
(0.439) 		4e-05
(0.0033) 		0.0268
(0.512) 		0.00245
(0.101) 		6e-05
(0.00457) 		0.0229
(0.462) 		0.00024
(0.014)
AXIN1 24 (6%) 349 0.00015
(0.00928) 		0.00801
(0.22) 		0.0509
(0.591) 		0.198
(0.852) 		0.00483
(0.149) 		0.23
(0.862) 		0.00312
(0.124) 		0.00425
(0.136) 		0.0235
(0.466) 		0.683
(1.00)
KCNN3 12 (3%) 361 0.0346
(0.537) 		0.758
(1.00) 		0.0003
(0.0156) 		0.00511
(0.149) 		0.275
(0.876) 		0.569
(0.997) 		0.948
(1.00) 		0.754
(1.00) 		0.951
(1.00) 		0.248
(0.862)
TSC2 12 (3%) 361 0.0412
(0.562) 		0.00379
(0.134) 		0.261
(0.868) 		0.318
(0.922) 		0.0967
(0.684) 		0.453
(0.96) 		0.995
(1.00) 		0.964
(1.00) 		0.0605
(0.596) 		0.991
(1.00)
TCHH 17 (5%) 356 0.00328
(0.125) 		0.153
(0.846) 		0.182
(0.852) 		0.0176
(0.405) 		0.629
(1.00) 		0.89
(1.00) 		0.853
(1.00) 		0.947
(1.00) 		0.444
(0.96) 		0.973
(1.00)
CNGA3 11 (3%) 362 0.403
(0.953) 		0.816
(1.00) 		0.00372
(0.134) 		0.56
(0.997) 		0.424
(0.96) 		0.288
(0.877) 		0.849
(1.00) 		0.542
(0.997) 		0.202
(0.852) 		0.154
(0.846)
KEAP1 17 (5%) 356 0.293
(0.877) 		0.113
(0.739) 		0.438
(0.96) 		0.934
(1.00) 		0.138
(0.808) 		1
(1.00) 		0.00414
(0.136) 		0.458
(0.96) 		0.699
(1.00) 		0.0759
(0.616)
SENP6 11 (3%) 362 0.22
(0.854) 		0.793
(1.00) 		0.00239
(0.101) 		0.29
(0.877) 		0.861
(1.00) 		0.727
(1.00) 		0.24
(0.862) 		0.799
(1.00) 		0.442
(0.96) 		0.645
(1.00)
FKBP4 4 (1%) 369 0.385
(0.952) 		0.363
(0.948) 		0.678
(1.00) 		0.0995
(0.694) 		0.346
(0.938) 		0.339
(0.936) 		0.00792
(0.22) 		0.218
(0.854) 		0.174
(0.852) 		0.435
(0.96)
SMARCA4 11 (3%) 362 0.0456
(0.562) 		0.914
(1.00) 		0.271
(0.876) 		0.0547
(0.596) 		0.779
(1.00) 		0.335
(0.936) 		0.401
(0.953) 		0.00111
(0.0549) 		0.582
(0.997) 		0.249
(0.862)
RB1 21 (6%) 352 0.0364
(0.537) 		0.189
(0.852) 		0.0869
(0.664) 		0.0773
(0.622) 		0.0107
(0.287) 		0.242
(0.862) 		0.0595
(0.596) 		0.531
(0.997) 		0.661
(1.00) 		0.731
(1.00)
ARID1A 32 (9%) 341 0.259
(0.868) 		0.727
(1.00) 		0.203
(0.852) 		0.545
(0.997) 		0.332
(0.936) 		0.769
(1.00) 		0.565
(0.997) 		0.835
(1.00) 		0.316
(0.922) 		0.777
(1.00)
CDC27 15 (4%) 358 0.716
(1.00) 		0.406
(0.953) 		1
(1.00) 		0.0367
(0.537) 		0.773
(1.00) 		0.407
(0.953) 		0.293
(0.877) 		0.591
(0.997) 		0.489
(0.975) 		0.0403
(0.562)
CDKN2A 11 (3%) 362 0.746
(1.00) 		0.0662
(0.601) 		0.13
(0.787) 		0.0577
(0.596) 		0.342
(0.936) 		0.2
(0.852) 		0.185
(0.852) 		0.679
(1.00)
KRT2 12 (3%) 361 0.0553
(0.596) 		0.521
(0.997) 		0.782
(1.00) 		0.831
(1.00) 		0.843
(1.00) 		0.567
(0.997) 		0.46
(0.96) 		0.541
(0.997) 		0.0121
(0.312) 		0.573
(0.997)
NFE2L2 13 (3%) 360 0.0829
(0.648) 		0.952
(1.00) 		0.436
(0.96) 		0.0294
(0.535) 		0.0608
(0.596) 		0.0896
(0.672) 		0.0743
(0.616) 		0.0965
(0.684) 		0.239
(0.862) 		0.0369
(0.537)
PTEN 11 (3%) 362 0.719
(1.00) 		0.172
(0.852) 		0.072
(0.613) 		0.623
(1.00) 		0.0659
(0.601) 		0.0702
(0.61) 		0.656
(1.00) 		0.0697
(0.61) 		0.632
(1.00) 		0.144
(0.813)
ARID2 22 (6%) 351 0.58
(0.997) 		0.71
(1.00) 		0.664
(1.00) 		0.763
(1.00) 		0.274
(0.876) 		0.683
(1.00) 		0.375
(0.952) 		0.267
(0.876) 		0.506
(0.989) 		0.216
(0.854)
RBM10 8 (2%) 365 0.563
(0.997) 		0.951
(1.00) 		0.887
(1.00) 		0.786
(1.00) 		0.19
(0.852) 		0.638
(1.00) 		0.461
(0.96) 		0.638
(1.00) 		0.78
(1.00) 		0.459
(0.96)
ZNF512B 8 (2%) 365 0.302
(0.894) 		0.563
(0.997) 		0.0447
(0.562) 		0.367
(0.949) 		0.677
(1.00) 		0.261
(0.868) 		0.819
(1.00) 		0.425
(0.96) 		0.0555
(0.596) 		0.848
(1.00)
KRT10 9 (2%) 364 0.918
(1.00) 		0.0725
(0.613) 		0.224
(0.857) 		0.468
(0.964) 		0.101
(0.698) 		0.483
(0.973) 		0.456
(0.96) 		0.119
(0.76)
APOB 39 (10%) 334 0.184
(0.852) 		0.138
(0.808) 		0.734
(1.00) 		0.964
(1.00) 		0.0476
(0.562) 		0.0185
(0.408) 		0.84
(1.00) 		0.212
(0.852) 		0.496
(0.98) 		0.246
(0.862)
MLL4 19 (5%) 354 0.178
(0.852) 		0.232
(0.862) 		0.11
(0.736) 		0.113
(0.739) 		0.924
(1.00) 		0.666
(1.00) 		0.688
(1.00) 		0.856
(1.00) 		0.696
(1.00) 		0.885
(1.00)
ALB 43 (12%) 330 0.407
(0.953) 		0.175
(0.852) 		0.43
(0.96) 		0.29
(0.877) 		0.182
(0.852) 		0.241
(0.862) 		0.0645
(0.601) 		0.397
(0.952) 		0.0941
(0.684) 		0.176
(0.852)
IL6ST 12 (3%) 361 0.0333
(0.537) 		0.0297
(0.535) 		0.854
(1.00) 		0.619
(1) 		0.06
(0.596) 		0.6
(0.997) 		0.0175
(0.405) 		0.0123
(0.312) 		0.545
(0.997) 		0.0872
(0.664)
C19ORF55 6 (2%) 367 0.291
(0.877) 		0.688
(1.00) 		0.722
(1.00) 		0.96
(1.00) 		0.746
(1.00) 		0.455
(0.96) 		0.968
(1.00) 		0.834
(1.00) 		0.0791
(0.627) 		0.725
(1.00)
PIK3CA 13 (3%) 360 1
(1.00) 		0.41
(0.954) 		1
(1.00) 		0.235
(0.862) 		0.64
(1.00) 		0.541
(0.997) 		0.556
(0.997) 		0.73
(1.00) 		0.472
(0.967) 		0.476
(0.973)
CELA1 6 (2%) 367 0.4
(0.953) 		0.573
(0.997) 		0.523
(0.997) 		0.51
(0.99) 		0.934
(1.00) 		1
(1.00) 		0.564
(0.997) 		0.606
(0.997) 		0.791
(1.00) 		0.739
(1.00)
RPS6KA3 14 (4%) 359 0.228
(0.859) 		0.361
(0.948) 		0.199
(0.852) 		0.583
(0.997) 		0.776
(1.00) 		0.716
(1.00) 		0.616
(0.999) 		0.695
(1.00) 		0.484
(0.973) 		0.854
(1.00)
NRD1 13 (3%) 360 1
(1.00) 		0.782
(1.00) 		0.0711
(0.612) 		0.958
(1.00) 		0.764
(1.00) 		0.503
(0.987) 		0.722
(1.00) 		0.628
(1.00) 		0.589
(0.997) 		0.536
(0.997)
EEF1A1 9 (2%) 364 0.0422
(0.562) 		0.389
(0.952) 		0.938
(1.00) 		0.831
(1.00) 		0.0698
(0.61) 		0.22
(0.854) 		0.539
(0.997) 		0.0831
(0.648) 		0.163
(0.852) 		0.21
(0.852)
COG2 4 (1%) 369 0.563
(0.997) 		0.21
(0.852) 		0.61
(0.997) 		0.597
(0.997) 		0.036
(0.537) 		0.342
(0.936) 		0.567
(0.997) 		0.481
(0.973)
ATXN1 10 (3%) 363 0.661
(1.00) 		0.459
(0.96) 		0.888
(1.00) 		0.531
(0.997) 		0.75
(1.00) 		0.423
(0.96) 		0.135
(0.808) 		0.735
(1.00) 		0.197
(0.852) 		0.284
(0.877)
KCTD20 5 (1%) 368 0.64
(1.00) 		0.608
(0.997) 		0.771
(1.00) 		0.867
(1.00) 		0.435
(0.96) 		0.183
(0.852) 		0.348
(0.94) 		0.362
(0.948) 		0.789
(1.00) 		0.509
(0.99)
GPR110 6 (2%) 367 0.883
(1.00) 		0.729
(1.00) 		0.34
(0.936) 		0.605
(0.997) 		0.0661
(0.601) 		0.0279
(0.521) 		0.29
(0.877) 		0.0467
(0.562) 		0.469
(0.964) 		0.0357
(0.537)
CEP164 9 (2%) 364 0.447
(0.96) 		0.887
(1.00) 		0.5
(0.987) 		0.696
(1.00) 		0.846
(1.00) 		0.66
(1.00) 		0.484
(0.973) 		0.73
(1.00) 		0.641
(1.00) 		1
(1.00)
TCEAL6 4 (1%) 369 0.566
(0.997) 		0.21
(0.852) 		0.609
(0.997) 		0.593
(0.997) 		0.0367
(0.537) 		0.342
(0.936) 		0.57
(0.997) 		0.48
(0.973)
DNAJC28 4 (1%) 369 0.383
(0.952) 		0.638
(1.00) 		0.0661
(0.601) 		0.397
(0.952) 		0.78
(1.00) 		1
(1.00) 		0.951
(1.00) 		0.596
(0.997) 		1
(1.00) 		0.658
(1.00)
FOXI1 5 (1%) 368 0.447
(0.96) 		0.79
(1.00) 		0.428
(0.96) 		1
(1.00) 		0.496
(0.98) 		0.17
(0.852) 		0.295
(0.88) 		0.587
(0.997) 		0.396
(0.952) 		0.563
(0.997)
KRTAP5-7 4 (1%) 369 0.384
(0.952) 		0.323
(0.932) 		0.0843
(0.652) 		0.395
(0.952) 		0.825
(1.00) 		1
(1.00) 		0.0467
(0.562) 		0.487
(0.974) 		0.327
(0.936) 		0.17
(0.852)
JAK1 14 (4%) 359 0.329
(0.936) 		0.0303
(0.536) 		0.968
(1.00) 		0.512
(0.991) 		0.228
(0.859) 		0.628
(1.00) 		0.774
(1.00) 		0.946
(1.00) 		0.829
(1.00) 		0.59
(0.997)
DENND4B 12 (3%) 361 0.125
(0.774) 		0.356
(0.948) 		0.0591
(0.596) 		0.364
(0.948) 		0.363
(0.948) 		0.354
(0.947) 		0.358
(0.948) 		0.926
(1.00) 		0.562
(0.997) 		0.234
(0.862)
BRD7 10 (3%) 363 0.364
(0.948) 		0.282
(0.877) 		0.617
(0.999) 		0.679
(1.00) 		0.369
(0.949) 		0.377
(0.952) 		0.587
(0.997) 		0.414
(0.96) 		0.963
(1.00) 		0.234
(0.862)
IDH1 8 (2%) 365 0.36
(0.948) 		0.0955
(0.684) 		0.939
(1.00) 		0.39
(0.952) 		0.405
(0.953) 		1
(1.00) 		0.221
(0.856) 		0.0653
(0.601) 		0.687
(1.00) 		0.144
(0.813)
PLA2G3 6 (2%) 367 0.293
(0.877) 		0.239
(0.862) 		0.293
(0.877) 		0.143
(0.813) 		0.376
(0.952) 		0.2
(0.852) 		0.598
(0.997) 		0.0759
(0.616) 		0.746
(1.00) 		0.0148
(0.359)
HLA-DPB1 5 (1%) 368 0.838
(1.00) 		0.789
(1.00) 		0.954
(1.00) 		1
(1.00) 		0.628
(1.00) 		0.261
(0.868) 		0.758
(1.00) 		0.763
(1.00)
ALMS1 24 (6%) 349 0.671
(1.00) 		0.723
(1.00) 		0.518
(0.997) 		0.818
(1.00) 		0.932
(1.00) 		0.274
(0.876) 		0.182
(0.852) 		0.127
(0.778) 		0.808
(1.00) 		0.424
(0.96)
NUCB2 3 (1%) 370 0.783
(1.00) 		0.722
(1.00) 		1
(1.00) 		1
(1.00) 		0.456
(0.96) 		1
(1.00) 		0.0427
(0.562) 		1
(1.00)
BAZ2A 11 (3%) 362 0.346
(0.938) 		1
(1.00) 		0.889
(1.00) 		0.552
(0.997) 		0.978
(1.00) 		0.937
(1.00) 		0.101
(0.698) 		0.756
(1.00) 		0.746
(1.00) 		0.875
(1.00)
TAF1B 6 (2%) 367 0.246
(0.862) 		0.207
(0.852) 		0.547
(0.997) 		0.25
(0.862) 		0.521
(0.997) 		1
(1.00) 		0.0558
(0.596) 		0.29
(0.877) 		0.44
(0.96) 		0.691
(1.00)
C1ORF125 11 (3%) 362 0.347
(0.938) 		0.172
(0.852) 		0.0477
(0.562) 		0.117
(0.755) 		0.396
(0.952) 		0.938
(1.00) 		0.0406
(0.562) 		0.395
(0.952) 		0.889
(1.00) 		0.0471
(0.562)
AR 10 (3%) 363 0.444
(0.96) 		0.774
(1.00) 		0.337
(0.936) 		0.6
(0.997) 		0.842
(1.00) 		0.933
(1.00) 		0.343
(0.936) 		0.426
(0.96) 		0.343
(0.936) 		0.493
(0.98)
SPHK1 6 (2%) 367 0.292
(0.877) 		0.61
(0.997) 		0.773
(1.00) 		0.831
(1.00) 		0.127
(0.778) 		0.0452
(0.562) 		0.208
(0.852) 		0.0782
(0.624) 		0.155
(0.849) 		0.142
(0.813)
CREB3L3 5 (1%) 368 0.271
(0.876) 		0.56
(0.997) 		0.185
(0.852) 		0.184
(0.852) 		0.68
(1.00) 		0.253
(0.863) 		0.0132
(0.326) 		0.707
(1.00)
LFNG 7 (2%) 366 0.634
(1.00) 		0.897
(1.00) 		0.88
(1.00) 		0.39
(0.952) 		0.332
(0.936) 		0.596
(0.997) 		0.365
(0.948) 		0.242
(0.862) 		0.685
(1.00) 		0.136
(0.808)
FZR1 6 (2%) 367 0.774
(1.00) 		0.777
(1.00) 		0.485
(0.973) 		1
(1.00) 		0.181
(0.852) 		0.318
(0.922) 		0.597
(0.997) 		0.395
(0.952) 		0.252
(0.863) 		0.421
(0.96)
TRIOBP 11 (3%) 362 0.926
(1.00) 		0.463
(0.96) 		0.939
(1.00) 		0.907
(1.00) 		0.182
(0.852) 		0.383
(0.952) 		0.219
(0.854) 		0.332
(0.936) 		0.102
(0.698) 		0.0682
(0.61)
GJB1 3 (1%) 370 1
(1.00) 		1
(1.00) 		0.899
(1.00) 		1
(1.00) 		0.739
(1.00) 		0.846
(1.00) 		0.799
(1.00) 		0.906
(1.00)
DYRK1A 7 (2%) 366 0.0757
(0.616) 		0.944
(1.00) 		1
(1.00) 		0.399
(0.953) 		0.779
(1.00) 		0.809
(1.00) 		0.424
(0.96) 		0.545
(0.997) 		0.891
(1.00) 		0.22
(0.854)
TNPO1 9 (2%) 364 0.267
(0.876) 		0.8
(1.00) 		0.503
(0.987) 		0.249
(0.862) 		0.621
(1) 		0.506
(0.989) 		0.808
(1.00) 		0.718
(1.00) 		0.456
(0.96) 		0.378
(0.952)
PDZD4 4 (1%) 369 0.458
(0.96) 		0.408
(0.953) 		0.269
(0.876) 		0.239
(0.862) 		0.236
(0.862) 		0.182
(0.852)
CCNA2 5 (1%) 368 0.38
(0.952) 		0.0961
(0.684) 		1
(1.00) 		1
(1.00) 		0.317
(0.922) 		1
(1.00) 		0.125
(0.774) 		0.334
(0.936) 		0.249
(0.862) 		0.213
(0.853)
AHCTF1 8 (2%) 365 0.824
(1.00) 		1
(1.00) 		0.848
(1.00) 		0.752
(1.00) 		0.424
(0.96) 		0.742
(1.00) 		0.761
(1.00) 		0.9
(1.00)
RXRB 8 (2%) 365 0.542
(0.997) 		0.173
(0.852) 		0.82
(1.00) 		0.677
(1.00) 		0.664
(1.00) 		0.73
(1.00) 		0.847
(1.00) 		0.843
(1.00) 		0.0952
(0.684) 		0.847
(1.00)
PARP1 5 (1%) 368 0.639
(1.00) 		0.44
(0.96) 		0.836
(1.00) 		0.541
(0.997) 		0.354
(0.947) 		0.774
(1.00) 		0.22
(0.854) 		0.172
(0.852)
NBEA 21 (6%) 352 0.783
(1.00) 		0.479
(0.973) 		0.0318
(0.537) 		0.165
(0.852) 		0.556
(0.997) 		1
(1.00) 		0.535
(0.997) 		0.904
(1.00) 		0.42
(0.96) 		0.546
(0.997)
H6PD 5 (1%) 368 0.642
(1.00) 		0.79
(1.00) 		0.541
(0.997) 		0.186
(0.852) 		0.629
(1.00) 		0.586
(0.997) 		0.821
(1.00) 		0.56
(0.997)
VPS4B 5 (1%) 368 0.745
(1.00) 		0.151
(0.843) 		0.224
(0.857) 		0.143
(0.813) 		0.546
(0.997) 		0.123
(0.774) 		0.218
(0.854) 		0.387
(0.952)
HNRNPL 8 (2%) 365 0.824
(1.00) 		0.839
(1.00) 		0.847
(1.00) 		0.206
(0.852) 		0.886
(1.00) 		0.891
(1.00) 		0.223
(0.857) 		0.781
(1.00) 		0.853
(1.00) 		0.826
(1.00)
FILIP1 13 (3%) 360 0.774
(1.00) 		0.298
(0.885) 		0.706
(1.00) 		0.708
(1.00) 		0.783
(1.00) 		0.0984
(0.691) 		0.656
(1.00) 		0.138
(0.808) 		0.0905
(0.673) 		0.34
(0.936)
FAM22F 4 (1%) 369 0.201
(0.852) 		0.106
(0.716) 		1
(1.00) 		0.689
(1.00) 		0.252
(0.863) 		0.288
(0.877) 		0.444
(0.96) 		0.567
(0.997) 		0.408
(0.953) 		0.947
(1.00)
GPSM2 4 (1%) 369 0.564
(0.997) 		0.806
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.616
(0.999) 		1
(1.00) 		0.974
(1.00) 		1
(1.00) 		0.742
(1.00) 		0.726
(1.00)
RCCD1 5 (1%) 368 0.162
(0.852) 		1
(1.00) 		0.617
(0.999) 		0.45
(0.96) 		0.823
(1.00) 		0.428
(0.96) 		0.494
(0.98) 		0.393
(0.952)
PTGR1 5 (1%) 368 0.197
(0.852) 		0.925
(1.00) 		1
(1.00) 		0.938
(1.00) 		0.655
(1.00) 		0.835
(1.00) 		0.856
(1.00) 		0.571
(0.997) 		0.211
(0.852) 		0.478
(0.973)
SAMM50 3 (1%) 370 0.783
(1.00) 		0.162
(0.852) 		0.611
(0.997) 		0.595
(0.997) 		0.0473
(0.562) 		0.164
(0.852) 		1
(1.00) 		0.35
(0.943)
PBRM1 9 (2%) 364 0.269
(0.876) 		0.658
(1.00) 		0.432
(0.96) 		0.604
(0.997) 		0.0395
(0.562) 		0.0212
(0.439) 		0.417
(0.96) 		0.0699
(0.61) 		0.392
(0.952) 		0.133
(0.803)
SGK269 8 (2%) 365 1
(1.00) 		0.112
(0.739) 		0.292
(0.877) 		0.695
(1.00) 		0.893
(1.00) 		0.589
(0.997) 		0.201
(0.852) 		0.343
(0.936) 		0.0562
(0.596) 		0.057
(0.596)
LEO1 5 (1%) 368 0.227
(0.859) 		0.48
(0.973) 		0.124
(0.774) 		1
(1.00) 		0.718
(1.00) 		0.391
(0.952) 		0.629
(1.00) 		0.51
(0.99) 		0.698
(1.00) 		0.439
(0.96)
CD97 5 (1%) 368 0.448
(0.96) 		1
(1.00) 		0.494
(0.98) 		0.168
(0.852) 		0.389
(0.952) 		0.672
(1.00) 		0.463
(0.96) 		0.289
(0.877)
SKA3 4 (1%) 369 0.565
(0.997) 		0.284
(0.877) 		0.658
(1.00) 		0.834
(1.00) 		0.58
(0.997) 		0.569
(0.997) 		0.601
(0.997) 		0.946
(1.00)
CBX4 6 (2%) 367 0.21
(0.852) 		0.019
(0.409) 		0.211
(0.852) 		0.191
(0.852) 		0.162
(0.852) 		0.0367
(0.537) 		0.245
(0.862) 		0.284
(0.877) 		0.0583
(0.596) 		0.369
(0.949)
MTA1 6 (2%) 367 0.881
(1.00) 		0.065
(0.601) 		0.615
(0.999) 		0.541
(0.997) 		0.174
(0.852) 		0.197
(0.852) 		0.956
(1.00) 		0.204
(0.852)
CRIP3 6 (2%) 367 0.052
(0.592) 		0.157
(0.852) 		1
(1.00) 		0.685
(1.00) 		0.462
(0.96) 		0.316
(0.922) 		0.771
(1.00) 		0.257
(0.867) 		0.557
(0.997) 		0.0648
(0.601)
NR4A2 6 (2%) 367 0.773
(1.00) 		0.612
(0.998) 		0.848
(1.00) 		0.962
(1.00) 		0.435
(0.96) 		0.186
(0.852) 		0.649
(1.00) 		0.163
(0.852) 		0.68
(1.00) 		0.279
(0.877)
HNF1A 8 (2%) 365 0.0185
(0.408) 		0.586
(0.997) 		0.368
(0.949) 		0.395
(0.952) 		0.093
(0.684) 		0.211
(0.852) 		0.058
(0.596) 		0.21
(0.852) 		0.152
(0.843) 		0.761
(1.00)
KRAS 6 (2%) 367 0.511
(0.991) 		0.0334
(0.537) 		0.547
(0.997) 		1
(1.00) 		0.532
(0.997) 		0.272
(0.876) 		0.94
(1.00) 		0.158
(0.852) 		0.486
(0.973) 		0.946
(1.00)
PGBD1 3 (1%) 370 0.632
(1.00) 		1
(1.00) 		0.744
(1.00) 		0.731
(1.00) 		1
(1.00) 		0.592
(0.997) 		1
(1.00) 		0.92
(1.00) 		0.871
(1.00) 		0.318
(0.922)
LATS1 7 (2%) 366 0.566
(0.997) 		0.584
(0.997) 		0.338
(0.936) 		0.395
(0.952) 		0.418
(0.96) 		0.609
(0.997) 		1
(1.00) 		0.674
(1.00) 		0.797
(1.00) 		0.647
(1.00)
FOXK2 6 (2%) 367 0.773
(1.00) 		0.444
(0.96) 		0.373
(0.952) 		0.61
(0.997) 		0.769
(1.00) 		0.503
(0.987) 		0.421
(0.96) 		0.104
(0.708)
DSPP 21 (6%) 352 0.96
(1.00) 		0.316
(0.922) 		0.621
(1) 		0.334
(0.936) 		0.459
(0.96) 		0.971
(1.00) 		0.985
(1.00) 		0.681
(1.00) 		0.266
(0.876) 		0.286
(0.877)
C10ORF28 4 (1%) 369 0.458
(0.96) 		0.319
(0.922) 		0.931
(1.00) 		0.694
(1.00) 		0.119
(0.76) 		0.402
(0.953) 		0.273
(0.876) 		0.429
(0.96)
PRAMEF4 4 (1%) 369 0.566
(0.997) 		0.513
(0.991) 		0.583
(0.997) 		0.707
(1.00) 		0.93
(1.00) 		0.834
(1.00) 		0.76
(1.00) 		0.228
(0.859) 		0.839
(1.00) 		0.249
(0.862)
RPS6KA5 5 (1%) 368 0.638
(1.00) 		0.789
(1.00) 		1
(1.00) 		0.688
(1.00) 		0.721
(1.00) 		0.163
(0.852) 		0.468
(0.964) 		0.674
(1.00) 		0.0754
(0.616) 		0.145
(0.813)
DDX42 6 (2%) 367 0.247
(0.862) 		0.208
(0.852) 		0.686
(1.00) 		0.46
(0.96) 		0.902
(1.00) 		0.609
(0.997) 		0.647
(1.00) 		0.584
(0.997) 		0.877
(1.00) 		0.385
(0.952)
RHCG 4 (1%) 369 0.202
(0.852) 		0.36
(0.948) 		0.743
(1.00) 		0.116
(0.755) 		0.269
(0.876) 		0.141
(0.813) 		0.642
(1.00) 		0.257
(0.867) 		0.805
(1.00) 		0.125
(0.774)
SWAP70 5 (1%) 368 1
(1.00) 		0.668
(1.00) 		0.548
(0.997) 		0.465
(0.961) 		0.745
(1.00) 		0.862
(1.00) 		0.523
(0.997) 		0.827
(1.00) 		0.759
(1.00) 		0.524
(0.997)
BIN1 4 (1%) 369 0.457
(0.96) 		0.806
(1.00) 		0.0336
(0.537) 		0.248
(0.862) 		0.695
(1.00) 		0.343
(0.936) 		0.259
(0.868) 		0.256
(0.867) 		0.902
(1.00) 		0.192
(0.852)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
TP53 MUTATED 12 74 27
TP53 WILD-TYPE 87 57 109

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 = 9e-05 (Fisher's exact test), Q value = 0.0064

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
TP53 MUTATED 32 47 30 5
TP53 WILD-TYPE 28 116 73 42

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.56

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 S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0213 (Fisher's exact test), Q value = 0.44

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 S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0033

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 127 90 49 72 29
TP53 MUTATED 48 37 12 13 1
TP53 WILD-TYPE 79 53 37 59 28

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.51

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
TP53 MUTATED 50 50 11 0
TP53 WILD-TYPE 103 96 50 7

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00245 (Fisher's exact test), Q value = 0.1

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 CLUS_7
ALL 44 60 103 45 63 40 13
TP53 MUTATED 25 20 26 8 16 15 3
TP53 WILD-TYPE 19 40 77 37 47 25 10

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0046

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
TP53 MUTATED 21 33 21 30 8 0
TP53 WILD-TYPE 19 54 33 93 48 8

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.46

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
TP53 MUTATED 14 27 20 3 12 23 11
TP53 WILD-TYPE 30 27 51 14 40 59 12

Figure S9.  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 = 0.00024 (Fisher's exact test), Q value = 0.014

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 CLUS_6
ALL 131 49 73 39 47 4
TP53 MUTATED 49 18 18 20 5 0
TP53 WILD-TYPE 82 31 55 19 42 4

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

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 4e-05 (Fisher's exact test), Q value = 0.0033

Table S11.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CTNNB1 MUTATED 36 17 44
CTNNB1 WILD-TYPE 63 114 92

Figure S11.  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 = 0.0011

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CTNNB1 MUTATED 9 69 9 10
CTNNB1 WILD-TYPE 51 94 94 37

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

'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0888 (Fisher's exact test), Q value = 0.67

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 = 0.00189 (Fisher's exact test), Q value = 0.086

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 S13.  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 = 0.0011

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 127 90 49 72 29
CTNNB1 MUTATED 13 8 6 63 6
CTNNB1 WILD-TYPE 114 82 43 9 23

Figure S14.  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 = 0.0011

Table S16.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CTNNB1 MUTATED 19 23 54 0
CTNNB1 WILD-TYPE 134 123 7 7

Figure S15.  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 = 0.0011

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 CLUS_7
ALL 44 60 103 45 63 40 13
CTNNB1 MUTATED 12 10 54 3 7 8 2
CTNNB1 WILD-TYPE 32 50 49 42 56 32 11

Figure S16.  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 = 0.0011

Table S18.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CTNNB1 MUTATED 11 15 6 16 47 1
CTNNB1 WILD-TYPE 29 72 48 107 9 7

Figure S17.  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 = 0.0011

Table S19.  Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CTNNB1 MUTATED 11 8 6 1 4 48 6
CTNNB1 WILD-TYPE 33 46 65 16 48 34 17

Figure S18.  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 = 0.0011

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 CLUS_6
ALL 131 49 73 39 47 4
CTNNB1 MUTATED 20 9 5 12 37 1
CTNNB1 WILD-TYPE 111 40 68 27 10 3

Figure S19.  Get High-res Image Gene #2: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0093

Table S21.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
AXIN1 MUTATED 1 4 18
AXIN1 WILD-TYPE 98 127 118

Figure S20.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'AXIN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00801 (Fisher's exact test), Q value = 0.22

Table S22.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
AXIN1 MUTATED 0 9 13 2
AXIN1 WILD-TYPE 60 154 90 45

Figure S21.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'AXIN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0509 (Fisher's exact test), Q value = 0.59

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
'AXIN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 0.85

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 = 0.00483 (Fisher's exact test), Q value = 0.15

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 127 90 49 72 29
AXIN1 MUTATED 17 3 0 3 1
AXIN1 WILD-TYPE 110 87 49 69 28

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 = 0.23 (Fisher's exact test), Q value = 0.86

Table S26.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
AXIN1 MUTATED 14 9 1 0
AXIN1 WILD-TYPE 139 137 60 7
'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00312 (Fisher's exact test), Q value = 0.12

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 CLUS_7
ALL 44 60 103 45 63 40 13
AXIN1 MUTATED 2 0 8 0 4 7 2
AXIN1 WILD-TYPE 42 60 95 45 59 33 11

Figure S23.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00425 (Fisher's exact test), Q value = 0.14

Table S28.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
AXIN1 MUTATED 2 0 8 11 2 0
AXIN1 WILD-TYPE 38 87 46 112 54 8

Figure S24.  Get High-res Image Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'AXIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.47

Table S29.  Gene #3: 'AXIN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
AXIN1 MUTATED 1 1 9 0 0 7 2
AXIN1 WILD-TYPE 43 53 62 17 52 75 21

Figure S25.  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 = 0.683 (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 CLUS_6
ALL 131 49 73 39 47 4
AXIN1 MUTATED 7 1 6 2 4 0
AXIN1 WILD-TYPE 124 48 67 37 43 4
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0364 (Fisher's exact test), Q value = 0.54

Table S31.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
RB1 MUTATED 1 11 8
RB1 WILD-TYPE 98 120 128

Figure S26.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.85

Table S32.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
RB1 MUTATED 2 6 10 3
RB1 WILD-TYPE 58 157 93 44
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0869 (Fisher's exact test), Q value = 0.66

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 = 0.0773 (Fisher's exact test), Q value = 0.62

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 = 0.0107 (Fisher's exact test), Q value = 0.29

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 127 90 49 72 29
RB1 MUTATED 13 7 0 1 0
RB1 WILD-TYPE 114 83 49 71 29

Figure S27.  Get High-res Image Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.86

Table S36.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
RB1 MUTATED 13 7 1 0
RB1 WILD-TYPE 140 139 60 7
'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0595 (Fisher's exact test), Q value = 0.6

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 CLUS_7
ALL 44 60 103 45 63 40 13
RB1 MUTATED 2 3 2 3 9 1 0
RB1 WILD-TYPE 42 57 101 42 54 39 13
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.531 (Fisher's exact test), Q value = 1

Table S38.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
RB1 MUTATED 1 4 4 10 1 0
RB1 WILD-TYPE 39 83 50 113 55 8
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S39.  Gene #4: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
RB1 MUTATED 2 2 7 0 3 4 0
RB1 WILD-TYPE 42 52 64 17 49 78 23
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.731 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
RB1 MUTATED 10 2 4 1 1 0
RB1 WILD-TYPE 121 47 69 38 46 4
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.87

Table S41.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
ARID1A MUTATED 10 7 14
ARID1A WILD-TYPE 89 124 122
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S42.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
ARID1A MUTATED 6 12 11 3
ARID1A WILD-TYPE 54 151 92 44
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 0.85

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 = 0.545 (Fisher's exact test), Q value = 1

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 = 0.332 (Fisher's exact test), Q value = 0.94

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 127 90 49 72 29
ARID1A MUTATED 14 4 5 8 1
ARID1A WILD-TYPE 113 86 44 64 28
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.769 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
ARID1A MUTATED 14 11 7 0
ARID1A WILD-TYPE 139 135 54 7
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
ARID1A MUTATED 4 4 7 5 4 6 2
ARID1A WILD-TYPE 40 56 96 40 59 34 11
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S48.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
ARID1A MUTATED 4 5 6 12 5 0
ARID1A WILD-TYPE 36 82 48 111 51 8
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.92

Table S49.  Gene #5: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
ARID1A MUTATED 2 3 10 1 5 5 4
ARID1A WILD-TYPE 42 51 61 16 47 77 19
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.777 (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 CLUS_6
ALL 131 49 73 39 47 4
ARID1A MUTATED 12 3 7 3 4 1
ARID1A WILD-TYPE 119 46 66 36 43 3
'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 1

Table S51.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
BAP1 MUTATED 5 6 10
BAP1 WILD-TYPE 94 125 126
'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.003

Table S52.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
BAP1 MUTATED 4 1 14 2
BAP1 WILD-TYPE 56 162 89 45

Figure S28.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.51

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 S29.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'BAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0513 (Fisher's exact test), Q value = 0.59

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

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 127 90 49 72 29
BAP1 MUTATED 16 0 3 1 1
BAP1 WILD-TYPE 111 90 46 71 28

Figure S30.  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 = 0.0011

Table S56.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
BAP1 MUTATED 20 0 1 0
BAP1 WILD-TYPE 133 146 60 7

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0086

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 CLUS_7
ALL 44 60 103 45 63 40 13
BAP1 MUTATED 0 2 3 3 13 0 0
BAP1 WILD-TYPE 44 58 100 42 50 40 13

Figure S32.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00417 (Fisher's exact test), Q value = 0.14

Table S58.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
BAP1 MUTATED 0 1 4 15 1 0
BAP1 WILD-TYPE 40 86 50 108 55 8

Figure S33.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00505 (Fisher's exact test), Q value = 0.15

Table S59.  Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
BAP1 MUTATED 3 0 7 1 8 1 1
BAP1 WILD-TYPE 41 54 64 16 44 81 22

Figure S34.  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 = 0.00191 (Fisher's exact test), Q value = 0.086

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 CLUS_6
ALL 131 49 73 39 47 4
BAP1 MUTATED 8 0 12 0 1 0
BAP1 WILD-TYPE 123 49 61 39 46 4

Figure S35.  Get High-res Image Gene #6: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.716 (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 99 131 136
CDC27 MUTATED 4 4 7
CDC27 WILD-TYPE 95 127 129
'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.406 (Fisher's exact test), Q value = 0.95

Table S62.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CDC27 MUTATED 2 10 2 1
CDC27 WILD-TYPE 58 153 101 46
'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 = 0.0367 (Fisher's exact test), Q value = 0.54

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 S36.  Get High-res Image Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
CDC27 MUTATED 5 3 1 5 1
CDC27 WILD-TYPE 122 87 48 67 28
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.407 (Fisher's exact test), Q value = 0.95

Table S66.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CDC27 MUTATED 5 5 5 0
CDC27 WILD-TYPE 148 141 56 7
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.88

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 CLUS_7
ALL 44 60 103 45 63 40 13
CDC27 MUTATED 2 4 3 1 1 2 2
CDC27 WILD-TYPE 42 56 100 44 62 38 11
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.591 (Fisher's exact test), Q value = 1

Table S68.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CDC27 MUTATED 1 3 1 5 5 0
CDC27 WILD-TYPE 39 84 53 118 51 8
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 0.98

Table S69.  Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CDC27 MUTATED 1 3 2 0 1 7 0
CDC27 WILD-TYPE 43 51 69 17 51 75 23
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.56

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 CLUS_6
ALL 131 49 73 39 47 4
CDC27 MUTATED 1 3 3 2 5 0
CDC27 WILD-TYPE 130 46 70 37 42 4

Figure S37.  Get High-res Image Gene #7: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.746 (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 99 131 136
CDKN2A MUTATED 3 5 3
CDKN2A WILD-TYPE 96 126 133
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0662 (Fisher's exact test), Q value = 0.6

Table S72.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CDKN2A MUTATED 1 8 0 2
CDKN2A WILD-TYPE 59 155 103 45
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.79

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 127 90 49 72 29
CDKN2A MUTATED 1 5 1 4 0
CDKN2A WILD-TYPE 126 85 48 68 29
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0577 (Fisher's exact test), Q value = 0.6

Table S74.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CDKN2A MUTATED 1 6 4 0
CDKN2A WILD-TYPE 152 140 57 7
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.342 (Fisher's exact test), Q value = 0.94

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 CLUS_7
ALL 44 60 103 45 63 40 13
CDKN2A MUTATED 1 3 6 1 0 0 0
CDKN2A WILD-TYPE 43 57 97 44 63 40 13
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.85

Table S76.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CDKN2A MUTATED 1 6 1 1 2 0
CDKN2A WILD-TYPE 39 81 53 122 54 8
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.85

Table S77.  Gene #8: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CDKN2A MUTATED 0 2 1 0 1 7 0
CDKN2A WILD-TYPE 44 52 70 17 51 75 23
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.679 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
CDKN2A MUTATED 4 3 1 1 2 0
CDKN2A WILD-TYPE 127 46 72 38 45 4
'KRT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0553 (Fisher's exact test), Q value = 0.6

Table S79.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
KRT2 MUTATED 3 1 8
KRT2 WILD-TYPE 96 130 128
'KRT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.521 (Fisher's exact test), Q value = 1

Table S80.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
KRT2 MUTATED 1 6 5 0
KRT2 WILD-TYPE 59 157 98 47
'KRT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.782 (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 = 0.831 (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 = 0.843 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
KRT2 MUTATED 5 2 2 3 0
KRT2 WILD-TYPE 122 88 47 69 29
'KRT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S84.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
KRT2 MUTATED 6 3 3 0
KRT2 WILD-TYPE 147 143 58 7
'KRT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.46 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
KRT2 MUTATED 1 0 3 2 2 3 0
KRT2 WILD-TYPE 43 60 100 43 61 37 13
'KRT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
KRT2 MUTATED 1 1 1 7 1 0
KRT2 WILD-TYPE 39 86 53 116 55 8
'KRT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0121 (Fisher's exact test), Q value = 0.31

Table S87.  Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
KRT2 MUTATED 0 0 4 0 1 2 4
KRT2 WILD-TYPE 44 54 67 17 51 80 19

Figure S38.  Get High-res Image Gene #9: 'KRT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.573 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
KRT2 MUTATED 3 1 5 1 1 0
KRT2 WILD-TYPE 128 48 68 38 46 4
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0829 (Fisher's exact test), Q value = 0.65

Table S89.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
NFE2L2 MUTATED 2 2 9
NFE2L2 WILD-TYPE 97 129 127
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.952 (Fisher's exact test), Q value = 1

Table S90.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
NFE2L2 MUTATED 2 7 3 1
NFE2L2 WILD-TYPE 58 156 100 46
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.96

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 = 0.0294 (Fisher's exact test), Q value = 0.53

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 S39.  Get High-res Image Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0608 (Fisher's exact test), Q value = 0.6

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 127 90 49 72 29
NFE2L2 MUTATED 3 2 0 5 3
NFE2L2 WILD-TYPE 124 88 49 67 26
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0896 (Fisher's exact test), Q value = 0.67

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
NFE2L2 MUTATED 2 6 5 0
NFE2L2 WILD-TYPE 151 140 56 7
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0743 (Fisher's exact test), Q value = 0.62

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 CLUS_7
ALL 44 60 103 45 63 40 13
NFE2L2 MUTATED 2 0 8 1 0 2 0
NFE2L2 WILD-TYPE 42 60 95 44 63 38 13
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0965 (Fisher's exact test), Q value = 0.68

Table S96.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
NFE2L2 MUTATED 1 2 0 4 6 0
NFE2L2 WILD-TYPE 39 85 54 119 50 8
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.86

Table S97.  Gene #10: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
NFE2L2 MUTATED 4 2 1 0 0 4 1
NFE2L2 WILD-TYPE 40 52 70 17 52 78 22
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0369 (Fisher's exact test), Q value = 0.54

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 CLUS_6
ALL 131 49 73 39 47 4
NFE2L2 MUTATED 3 0 2 1 6 0
NFE2L2 WILD-TYPE 128 49 71 38 41 4

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

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.719 (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 99 131 136
PTEN MUTATED 2 5 3
PTEN WILD-TYPE 97 126 133
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.85

Table S100.  Gene #11: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PTEN MUTATED 0 8 3 0
PTEN WILD-TYPE 60 155 100 47
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.072 (Fisher's exact test), Q value = 0.61

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 = 0.623 (Fisher's exact test), Q value = 1

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 = 0.0659 (Fisher's exact test), Q value = 0.6

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 127 90 49 72 29
PTEN MUTATED 1 5 0 4 0
PTEN WILD-TYPE 126 85 49 68 29
'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0702 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PTEN MUTATED 1 5 4 0
PTEN WILD-TYPE 152 141 57 7
'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
PTEN MUTATED 1 3 5 0 2 0 0
PTEN WILD-TYPE 43 57 98 45 61 40 13
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0697 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PTEN MUTATED 0 4 0 2 5 0
PTEN WILD-TYPE 40 83 54 121 51 8
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.632 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PTEN MUTATED 1 2 2 1 0 4 0
PTEN WILD-TYPE 43 52 69 16 52 78 23
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.81

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 CLUS_6
ALL 131 49 73 39 47 4
PTEN MUTATED 4 3 0 0 3 0
PTEN WILD-TYPE 127 46 73 39 44 4
'ARID2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.58 (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 99 131 136
ARID2 MUTATED 4 7 10
ARID2 WILD-TYPE 95 124 126
'ARID2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.71 (Fisher's exact test), Q value = 1

Table S110.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
ARID2 MUTATED 3 11 7 1
ARID2 WILD-TYPE 57 152 96 46
'ARID2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.664 (Fisher's exact test), Q value = 1

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 = 0.763 (Fisher's exact test), Q value = 1

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 = 0.274 (Fisher's exact test), Q value = 0.88

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 127 90 49 72 29
ARID2 MUTATED 6 3 2 8 2
ARID2 WILD-TYPE 121 87 47 64 27
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.683 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
ARID2 MUTATED 7 9 5 0
ARID2 WILD-TYPE 146 137 56 7
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.375 (Fisher's exact test), Q value = 0.95

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 CLUS_7
ALL 44 60 103 45 63 40 13
ARID2 MUTATED 1 1 10 2 5 2 1
ARID2 WILD-TYPE 43 59 93 43 58 38 12
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.267 (Fisher's exact test), Q value = 0.88

Table S116.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
ARID2 MUTATED 1 4 2 7 7 1
ARID2 WILD-TYPE 39 83 52 116 49 7
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 0.99

Table S117.  Gene #12: 'ARID2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
ARID2 MUTATED 5 1 4 1 2 7 1
ARID2 WILD-TYPE 39 53 67 16 50 75 22
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.216 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
ARID2 MUTATED 6 2 5 1 7 0
ARID2 WILD-TYPE 125 47 68 38 40 4
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S119.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
RBM10 MUTATED 1 4 2
RBM10 WILD-TYPE 98 127 134
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.951 (Fisher's exact test), Q value = 1

Table S120.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
RBM10 MUTATED 1 3 3 1
RBM10 WILD-TYPE 59 160 100 46
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.887 (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 = 0.786 (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 = 0.19 (Fisher's exact test), Q value = 0.85

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 127 90 49 72 29
RBM10 MUTATED 2 3 1 0 2
RBM10 WILD-TYPE 125 87 48 72 27
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.638 (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
ALL 153 146 61 7
RBM10 MUTATED 4 4 0 0
RBM10 WILD-TYPE 149 142 61 7
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.461 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
RBM10 MUTATED 0 2 1 1 2 1 1
RBM10 WILD-TYPE 44 58 102 44 61 39 12
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.638 (Fisher's exact test), Q value = 1

Table S126.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
RBM10 MUTATED 0 2 1 5 0 0
RBM10 WILD-TYPE 40 85 53 118 56 8
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.78 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
RBM10 MUTATED 0 0 2 0 1 3 0
RBM10 WILD-TYPE 44 54 69 17 51 79 23
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.459 (Fisher's exact test), Q value = 0.96

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 CLUS_6
ALL 131 49 73 39 47 4
RBM10 MUTATED 3 2 0 0 1 0
RBM10 WILD-TYPE 128 47 73 39 46 4
'ZNF512B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.89

Table S129.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
ZNF512B MUTATED 0 3 4
ZNF512B WILD-TYPE 99 128 132
'ZNF512B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.563 (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 CLUS_4
ALL 60 163 103 47
ZNF512B MUTATED 1 3 4 0
ZNF512B WILD-TYPE 59 160 99 47
'ZNF512B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0447 (Fisher's exact test), Q value = 0.56

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 S41.  Get High-res Image Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'ZNF512B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.95

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 = 0.677 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
ZNF512B MUTATED 2 3 2 1 0
ZNF512B WILD-TYPE 125 87 47 71 29
'ZNF512B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.87

Table S134.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
ZNF512B MUTATED 2 6 0 0
ZNF512B WILD-TYPE 151 140 61 7
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.819 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
ZNF512B MUTATED 1 1 2 0 2 2 0
ZNF512B WILD-TYPE 43 59 101 45 61 38 13
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.96

Table S136.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
ZNF512B MUTATED 1 1 3 3 0 0
ZNF512B WILD-TYPE 39 86 51 120 56 8
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0555 (Fisher's exact test), Q value = 0.6

Table S137.  Gene #14: 'ZNF512B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
ZNF512B MUTATED 4 1 0 0 0 2 1
ZNF512B WILD-TYPE 40 53 71 17 52 80 22
'ZNF512B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.848 (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 CLUS_6
ALL 131 49 73 39 47 4
ZNF512B MUTATED 2 2 2 1 1 0
ZNF512B WILD-TYPE 129 47 71 38 46 4
'KCNN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0346 (Fisher's exact test), Q value = 0.54

Table S139.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
KCNN3 MUTATED 1 2 9
KCNN3 WILD-TYPE 98 129 127

Figure S42.  Get High-res Image Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KCNN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S140.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
KCNN3 MUTATED 1 5 5 1
KCNN3 WILD-TYPE 59 158 98 46
'KCNN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.016

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 S43.  Get High-res Image Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KCNN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00511 (Fisher's exact test), Q value = 0.15

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 S44.  Get High-res Image Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.88

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 127 90 49 72 29
KCNN3 MUTATED 4 1 2 5 0
KCNN3 WILD-TYPE 123 89 47 67 29
'KCNN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.569 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
KCNN3 MUTATED 6 3 3 0
KCNN3 WILD-TYPE 147 143 58 7
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.948 (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 CLUS_7
ALL 44 60 103 45 63 40 13
KCNN3 MUTATED 1 1 5 1 3 1 0
KCNN3 WILD-TYPE 43 59 98 44 60 39 13
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.754 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
KCNN3 MUTATED 1 2 3 3 3 0
KCNN3 WILD-TYPE 39 85 51 120 53 8
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.951 (Fisher's exact test), Q value = 1

Table S147.  Gene #15: 'KCNN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
KCNN3 MUTATED 2 1 2 0 2 4 0
KCNN3 WILD-TYPE 42 53 69 17 50 78 23
'KCNN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.86

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 CLUS_6
ALL 131 49 73 39 47 4
KCNN3 MUTATED 5 0 1 1 4 0
KCNN3 WILD-TYPE 126 49 72 38 43 4
'KRT10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.918 (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 99 131 136
KRT10 MUTATED 3 3 3
KRT10 WILD-TYPE 96 128 133
'KRT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0725 (Fisher's exact test), Q value = 0.61

Table S150.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
KRT10 MUTATED 0 2 6 1
KRT10 WILD-TYPE 60 161 97 46
'KRT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.86

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 127 90 49 72 29
KRT10 MUTATED 1 2 3 2 1
KRT10 WILD-TYPE 126 88 46 70 28
'KRT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.468 (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
ALL 153 146 61 7
KRT10 MUTATED 6 2 1 0
KRT10 WILD-TYPE 147 144 60 7
'KRT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.7

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 CLUS_7
ALL 44 60 103 45 63 40 13
KRT10 MUTATED 0 0 2 3 4 0 0
KRT10 WILD-TYPE 44 60 101 42 59 40 13
'KRT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.483 (Fisher's exact test), Q value = 0.97

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
KRT10 MUTATED 0 2 1 6 0 0
KRT10 WILD-TYPE 40 85 53 117 56 8
'KRT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 0.96

Table S155.  Gene #16: 'KRT10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
KRT10 MUTATED 0 0 3 0 3 3 0
KRT10 WILD-TYPE 44 54 68 17 49 79 23
'KRT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.76

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 CLUS_6
ALL 131 49 73 39 47 4
KRT10 MUTATED 1 2 5 0 1 0
KRT10 WILD-TYPE 130 47 68 39 46 4
'APOB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.184 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
APOB MUTATED 15 10 13
APOB WILD-TYPE 84 121 123
'APOB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.81

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
APOB MUTATED 5 20 6 8
APOB WILD-TYPE 55 143 97 39
'APOB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.734 (Fisher's exact test), Q value = 1

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 = 0.964 (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 = 0.0476 (Fisher's exact test), Q value = 0.56

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 127 90 49 72 29
APOB MUTATED 8 7 4 14 4
APOB WILD-TYPE 119 83 45 58 25

Figure S45.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'APOB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0185 (Fisher's exact test), Q value = 0.41

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
APOB MUTATED 11 12 13 1
APOB WILD-TYPE 142 134 48 6

Figure S46.  Get High-res Image Gene #17: 'APOB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'APOB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.84 (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 CLUS_7
ALL 44 60 103 45 63 40 13
APOB MUTATED 5 7 14 5 5 2 1
APOB WILD-TYPE 39 53 89 40 58 38 12
'APOB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
APOB MUTATED 5 13 3 9 9 0
APOB WILD-TYPE 35 74 51 114 47 8
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
APOB MUTATED 3 6 5 2 4 14 2
APOB WILD-TYPE 41 48 66 15 48 68 21
'APOB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.246 (Fisher's exact test), Q value = 0.86

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 CLUS_6
ALL 131 49 73 39 47 4
APOB MUTATED 12 6 4 5 9 0
APOB WILD-TYPE 119 43 69 34 38 4
'MLL4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.178 (Fisher's exact test), Q value = 0.85

Table S167.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
MLL4 MUTATED 4 4 11
MLL4 WILD-TYPE 95 127 125
'MLL4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.86

Table S168.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
MLL4 MUTATED 4 11 4 0
MLL4 WILD-TYPE 56 152 99 47
'MLL4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.74

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 = 0.74

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 = 0.924 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
MLL4 MUTATED 6 4 3 5 1
MLL4 WILD-TYPE 121 86 46 67 28
'MLL4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.666 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
MLL4 MUTATED 7 7 5 0
MLL4 WILD-TYPE 146 139 56 7
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
MLL4 MUTATED 3 4 5 2 1 3 1
MLL4 WILD-TYPE 41 56 98 43 62 37 12
'MLL4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S174.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
MLL4 MUTATED 3 3 3 6 4 0
MLL4 WILD-TYPE 37 84 51 117 52 8
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.696 (Fisher's exact test), Q value = 1

Table S175.  Gene #18: 'MLL4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
MLL4 MUTATED 1 2 4 0 2 7 2
MLL4 WILD-TYPE 43 52 67 17 50 75 21
'MLL4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.885 (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 CLUS_6
ALL 131 49 73 39 47 4
MLL4 MUTATED 6 3 3 3 3 0
MLL4 WILD-TYPE 125 46 70 36 44 4
'ALB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.407 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
ALB MUTATED 9 14 20
ALB WILD-TYPE 90 117 116
'ALB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
ALB MUTATED 6 25 10 2
ALB WILD-TYPE 54 138 93 45
'ALB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.96

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 = 0.29 (Fisher's exact test), Q value = 0.88

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 = 0.182 (Fisher's exact test), Q value = 0.85

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 127 90 49 72 29
ALB MUTATED 8 11 6 11 5
ALB WILD-TYPE 119 79 43 61 24
'ALB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.241 (Fisher's exact test), Q value = 0.86

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
ALB MUTATED 12 20 9 0
ALB WILD-TYPE 141 126 52 7
'ALB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0645 (Fisher's exact test), Q value = 0.6

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 CLUS_7
ALL 44 60 103 45 63 40 13
ALB MUTATED 5 6 19 5 3 1 2
ALB WILD-TYPE 39 54 84 40 60 39 11
'ALB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
ALB MUTATED 4 10 4 12 11 0
ALB WILD-TYPE 36 77 50 111 45 8
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0941 (Fisher's exact test), Q value = 0.68

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
ALB MUTATED 5 5 5 0 5 17 1
ALB WILD-TYPE 39 49 66 17 47 65 22
'ALB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
ALB MUTATED 15 6 4 3 10 0
ALB WILD-TYPE 116 43 69 36 37 4
'TSC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0412 (Fisher's exact test), Q value = 0.56

Table S187.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
TSC2 MUTATED 0 7 5
TSC2 WILD-TYPE 99 124 131

Figure S47.  Get High-res Image Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TSC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00379 (Fisher's exact test), Q value = 0.13

Table S188.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
TSC2 MUTATED 7 3 1 1
TSC2 WILD-TYPE 53 160 102 46

Figure S48.  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 = 0.87

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 = 0.318 (Fisher's exact test), Q value = 0.92

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 = 0.0967 (Fisher's exact test), Q value = 0.68

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 127 90 49 72 29
TSC2 MUTATED 9 2 0 1 0
TSC2 WILD-TYPE 118 88 49 71 29
'TSC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.96

Table S192.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
TSC2 MUTATED 8 3 1 0
TSC2 WILD-TYPE 145 143 60 7
'TSC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.995 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
TSC2 MUTATED 1 2 4 1 3 1 0
TSC2 WILD-TYPE 43 58 99 44 60 39 13
'TSC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.964 (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 CLUS_6
ALL 40 87 54 123 56 8
TSC2 MUTATED 1 4 2 4 1 0
TSC2 WILD-TYPE 39 83 52 119 55 8
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0605 (Fisher's exact test), Q value = 0.6

Table S195.  Gene #20: 'TSC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
TSC2 MUTATED 6 1 1 0 1 3 0
TSC2 WILD-TYPE 38 53 70 17 51 79 23
'TSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.991 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
TSC2 MUTATED 5 2 2 1 2 0
TSC2 WILD-TYPE 126 47 71 38 45 4
'IL6ST MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.54

Table S197.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
IL6ST MUTATED 7 2 2
IL6ST WILD-TYPE 92 129 134

Figure S49.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'IL6ST MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0297 (Fisher's exact test), Q value = 0.53

Table S198.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
IL6ST MUTATED 0 4 3 5
IL6ST WILD-TYPE 60 159 100 42

Figure S50.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'IL6ST MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.854 (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 = 0.619 (Fisher's exact test), Q value = 1

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 = 0.06 (Fisher's exact test), Q value = 0.6

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 127 90 49 72 29
IL6ST MUTATED 2 1 1 4 3
IL6ST WILD-TYPE 125 89 48 68 26
'IL6ST MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.6 (Fisher's exact test), Q value = 1

Table S202.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
IL6ST MUTATED 5 3 3 0
IL6ST WILD-TYPE 148 143 58 7
'IL6ST MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0175 (Fisher's exact test), Q value = 0.4

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 CLUS_7
ALL 44 60 103 45 63 40 13
IL6ST MUTATED 0 2 3 1 0 4 2
IL6ST WILD-TYPE 44 58 100 44 63 36 11

Figure S51.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IL6ST MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0123 (Fisher's exact test), Q value = 0.31

Table S204.  Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
IL6ST MUTATED 0 0 2 6 2 2
IL6ST WILD-TYPE 40 87 52 117 54 6

Figure S52.  Get High-res Image Gene #21: 'IL6ST MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.545 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
IL6ST MUTATED 2 0 2 1 1 4 0
IL6ST WILD-TYPE 42 54 69 16 51 78 23
'IL6ST MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0872 (Fisher's exact test), Q value = 0.66

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 CLUS_6
ALL 131 49 73 39 47 4
IL6ST MUTATED 4 0 2 0 3 1
IL6ST WILD-TYPE 127 49 71 39 44 3
'C19ORF55 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.88

Table S207.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
C19ORF55 MUTATED 0 3 3
C19ORF55 WILD-TYPE 99 128 133
'C19ORF55 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.688 (Fisher's exact test), Q value = 1

Table S208.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
C19ORF55 MUTATED 1 2 3 0
C19ORF55 WILD-TYPE 59 161 100 47
'C19ORF55 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

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 = 0.96 (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 = 0.746 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
C19ORF55 MUTATED 3 1 1 0 0
C19ORF55 WILD-TYPE 124 89 48 72 29
'C19ORF55 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.96

Table S212.  Gene #22: 'C19ORF55 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
C19ORF55 MUTATED 4 1 0 0
C19ORF55 WILD-TYPE 149 145 61 7
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.968 (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 CLUS_7
ALL 44 60 103 45 63 40 13
C19ORF55 MUTATED 1 1 1 1 1 1 0
C19ORF55 WILD-TYPE 43 59 102 44 62 39 13
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.834 (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 CLUS_6
ALL 40 87 54 123 56 8
C19ORF55 MUTATED 1 1 1 3 0 0
C19ORF55 WILD-TYPE 39 86 53 120 56 8
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0791 (Fisher's exact test), Q value = 0.63

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
C19ORF55 MUTATED 0 0 3 1 1 0 1
C19ORF55 WILD-TYPE 44 54 68 16 51 82 22
'C19ORF55 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.725 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
C19ORF55 MUTATED 4 0 1 1 0 0
C19ORF55 WILD-TYPE 127 49 72 38 47 4
'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 99 131 136
PIK3CA MUTATED 3 4 5
PIK3CA WILD-TYPE 96 127 131
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 0.95

Table S218.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PIK3CA MUTATED 0 7 4 2
PIK3CA WILD-TYPE 60 156 99 45
'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 = 0.86

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 = 0.64 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
PIK3CA MUTATED 3 4 1 2 2
PIK3CA WILD-TYPE 124 86 48 70 27
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PIK3CA MUTATED 3 7 2 0
PIK3CA WILD-TYPE 150 139 59 7
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.556 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
PIK3CA MUTATED 0 3 4 2 1 3 0
PIK3CA WILD-TYPE 44 57 99 43 62 37 13
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S224.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PIK3CA MUTATED 0 5 1 5 2 0
PIK3CA WILD-TYPE 40 82 53 118 54 8
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.472 (Fisher's exact test), Q value = 0.97

Table S225.  Gene #23: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PIK3CA MUTATED 1 0 3 1 1 5 1
PIK3CA WILD-TYPE 43 54 68 16 51 77 22
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 0.97

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 CLUS_6
ALL 131 49 73 39 47 4
PIK3CA MUTATED 3 3 4 0 2 0
PIK3CA WILD-TYPE 128 46 69 39 45 4
'CELA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 0.95

Table S227.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CELA1 MUTATED 1 1 4
CELA1 WILD-TYPE 98 130 132
'CELA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.573 (Fisher's exact test), Q value = 1

Table S228.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CELA1 MUTATED 0 3 3 0
CELA1 WILD-TYPE 60 160 100 47
'CELA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

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 = 0.51 (Fisher's exact test), Q value = 0.99

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 = 0.934 (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 127 90 49 72 29
CELA1 MUTATED 3 2 0 1 0
CELA1 WILD-TYPE 124 88 49 71 29
'CELA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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
ALL 153 146 61 7
CELA1 MUTATED 3 2 1 0
CELA1 WILD-TYPE 150 144 60 7
'CELA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
CELA1 MUTATED 0 3 2 0 1 0 0
CELA1 WILD-TYPE 44 57 101 45 62 40 13
'CELA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.606 (Fisher's exact test), Q value = 1

Table S234.  Gene #24: 'CELA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CELA1 MUTATED 0 2 2 1 1 0
CELA1 WILD-TYPE 40 85 52 122 55 8
'CELA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.791 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CELA1 MUTATED 0 2 2 0 0 2 0
CELA1 WILD-TYPE 44 52 69 17 52 80 23
'CELA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.739 (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 CLUS_6
ALL 131 49 73 39 47 4
CELA1 MUTATED 2 2 1 0 1 0
CELA1 WILD-TYPE 129 47 72 39 46 4
'RPS6KA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.86

Table S237.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
RPS6KA3 MUTATED 5 2 7
RPS6KA3 WILD-TYPE 94 129 129
'RPS6KA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.95

Table S238.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
RPS6KA3 MUTATED 1 9 4 0
RPS6KA3 WILD-TYPE 59 154 99 47
'RPS6KA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.85

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 = 0.583 (Fisher's exact test), Q value = 1

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 = 0.776 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
RPS6KA3 MUTATED 7 3 1 3 0
RPS6KA3 WILD-TYPE 120 87 48 69 29
'RPS6KA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.716 (Fisher's exact test), Q value = 1

Table S242.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
RPS6KA3 MUTATED 7 4 3 0
RPS6KA3 WILD-TYPE 146 142 58 7
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.616 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
RPS6KA3 MUTATED 2 1 5 0 4 2 0
RPS6KA3 WILD-TYPE 42 59 98 45 59 38 13
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.695 (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 CLUS_6
ALL 40 87 54 123 56 8
RPS6KA3 MUTATED 2 2 4 4 2 0
RPS6KA3 WILD-TYPE 38 85 50 119 54 8
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.97

Table S245.  Gene #25: 'RPS6KA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
RPS6KA3 MUTATED 2 2 3 0 0 5 2
RPS6KA3 WILD-TYPE 42 52 68 17 52 77 21
'RPS6KA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.854 (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 CLUS_6
ALL 131 49 73 39 47 4
RPS6KA3 MUTATED 4 3 3 2 2 0
RPS6KA3 WILD-TYPE 127 46 70 37 45 4
'NRD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (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 99 131 136
NRD1 MUTATED 3 5 5
NRD1 WILD-TYPE 96 126 131
'NRD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.782 (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 CLUS_4
ALL 60 163 103 47
NRD1 MUTATED 1 6 5 1
NRD1 WILD-TYPE 59 157 98 46
'NRD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0711 (Fisher's exact test), Q value = 0.61

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 = 0.958 (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 = 0.764 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
NRD1 MUTATED 4 3 3 3 0
NRD1 WILD-TYPE 123 87 46 69 29
'NRD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 0.99

Table S252.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
NRD1 MUTATED 8 3 2 0
NRD1 WILD-TYPE 145 143 59 7
'NRD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
NRD1 MUTATED 2 3 3 3 2 0 0
NRD1 WILD-TYPE 42 57 100 42 61 40 13
'NRD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S254.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
NRD1 MUTATED 2 3 0 5 3 0
NRD1 WILD-TYPE 38 84 54 118 53 8
'NRD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S255.  Gene #26: 'NRD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
NRD1 MUTATED 0 2 3 0 4 4 0
NRD1 WILD-TYPE 44 52 68 17 48 78 23
'NRD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.536 (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 CLUS_6
ALL 131 49 73 39 47 4
NRD1 MUTATED 3 3 2 2 3 0
NRD1 WILD-TYPE 128 46 71 37 44 4
'EEF1A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0422 (Fisher's exact test), Q value = 0.56

Table S257.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
EEF1A1 MUTATED 6 2 1
EEF1A1 WILD-TYPE 93 129 135

Figure S53.  Get High-res Image Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'EEF1A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.95

Table S258.  Gene #27: 'EEF1A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
EEF1A1 MUTATED 2 6 1 0
EEF1A1 WILD-TYPE 58 157 102 47
'EEF1A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.938 (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 = 0.831 (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 = 0.0698 (Fisher's exact test), Q value = 0.61

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 127 90 49 72 29
EEF1A1 MUTATED 0 4 2 2 1
EEF1A1 WILD-TYPE 127 86 47 70 28
'EEF1A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.22 (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
ALL 153 146 61 7
EEF1A1 MUTATED 1 6 2 0
EEF1A1 WILD-TYPE 152 140 59 7
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.539 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
EEF1A1 MUTATED 1 3 2 1 1 0 1
EEF1A1 WILD-TYPE 43 57 101 44 62 40 12
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0831 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
EEF1A1 MUTATED 1 5 2 0 1 0
EEF1A1 WILD-TYPE 39 82 52 123 55 8
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.163 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
EEF1A1 MUTATED 1 3 1 2 0 2 0
EEF1A1 WILD-TYPE 43 51 70 15 52 80 23
'EEF1A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
EEF1A1 MUTATED 5 3 0 1 0 0
EEF1A1 WILD-TYPE 126 46 73 38 47 4
'TCHH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00328 (Fisher's exact test), Q value = 0.12

Table S267.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
TCHH MUTATED 3 1 12
TCHH WILD-TYPE 96 130 124

Figure S54.  Get High-res Image Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'TCHH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.85

Table S268.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
TCHH MUTATED 1 6 9 1
TCHH WILD-TYPE 59 157 94 46
'TCHH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.85

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 = 0.0176 (Fisher's exact test), Q value = 0.4

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 S55.  Get High-res Image Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'TCHH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
TCHH MUTATED 7 2 3 3 2
TCHH WILD-TYPE 120 88 46 69 27
'TCHH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.89 (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
ALL 153 146 61 7
TCHH MUTATED 7 8 2 0
TCHH WILD-TYPE 146 138 59 7
'TCHH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.853 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
TCHH MUTATED 1 2 6 3 2 2 1
TCHH WILD-TYPE 43 58 97 42 61 38 12
'TCHH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.947 (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 CLUS_6
ALL 40 87 54 123 56 8
TCHH MUTATED 1 3 3 7 3 0
TCHH WILD-TYPE 39 84 51 116 53 8
'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.96

Table S275.  Gene #28: 'TCHH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
TCHH MUTATED 1 1 6 0 4 3 0
TCHH WILD-TYPE 43 53 65 17 48 79 23
'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.973 (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 CLUS_6
ALL 131 49 73 39 47 4
TCHH MUTATED 6 2 3 1 3 0
TCHH WILD-TYPE 125 47 70 38 44 4
'COG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 1

Table S277.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
COG2 MUTATED 0 2 2
COG2 WILD-TYPE 99 129 134
'COG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.85

Table S278.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
COG2 MUTATED 2 2 0 0
COG2 WILD-TYPE 58 161 103 47
'COG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
COG2 MUTATED 1 0 1 1 0
COG2 WILD-TYPE 126 90 48 71 29
'COG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.597 (Fisher's exact test), Q value = 1

Table S280.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
COG2 MUTATED 1 1 1 0
COG2 WILD-TYPE 152 145 60 7
'COG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.036 (Fisher's exact test), Q value = 0.54

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 CLUS_7
ALL 44 60 103 45 63 40 13
COG2 MUTATED 1 2 0 0 0 0 1
COG2 WILD-TYPE 43 58 103 45 63 40 12

Figure S56.  Get High-res Image Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'COG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 0.94

Table S282.  Gene #29: 'COG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
COG2 MUTATED 1 1 1 0 1 0
COG2 WILD-TYPE 39 86 53 123 55 8
'COG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.567 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
COG2 MUTATED 0 1 1 1 0 1 0
COG2 WILD-TYPE 44 53 70 16 52 81 23
'COG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.97

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 CLUS_6
ALL 131 49 73 39 47 4
COG2 MUTATED 2 0 0 1 1 0
COG2 WILD-TYPE 129 49 73 38 46 4
'ATXN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.661 (Fisher's exact test), Q value = 1

Table S285.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
ATXN1 MUTATED 4 3 3
ATXN1 WILD-TYPE 95 128 133
'ATXN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.459 (Fisher's exact test), Q value = 0.96

Table S286.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
ATXN1 MUTATED 1 6 1 2
ATXN1 WILD-TYPE 59 157 102 45
'ATXN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.888 (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 = 0.531 (Fisher's exact test), Q value = 1

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 = 0.75 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
ATXN1 MUTATED 2 3 1 3 1
ATXN1 WILD-TYPE 125 87 48 69 28
'ATXN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 0.96

Table S290.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
ATXN1 MUTATED 2 6 2 0
ATXN1 WILD-TYPE 151 140 59 7
'ATXN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.81

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 CLUS_7
ALL 44 60 103 45 63 40 13
ATXN1 MUTATED 1 0 6 1 0 1 1
ATXN1 WILD-TYPE 43 60 97 44 63 39 12
'ATXN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.735 (Fisher's exact test), Q value = 1

Table S292.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
ATXN1 MUTATED 1 3 1 2 3 0
ATXN1 WILD-TYPE 39 84 53 121 53 8
'ATXN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.85

Table S293.  Gene #30: 'ATXN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
ATXN1 MUTATED 1 1 1 1 0 6 0
ATXN1 WILD-TYPE 43 53 70 16 52 76 23
'ATXN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.88

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 CLUS_6
ALL 131 49 73 39 47 4
ATXN1 MUTATED 2 3 1 1 3 0
ATXN1 WILD-TYPE 129 46 72 38 44 4
'KCTD20 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.64 (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 99 131 136
KCTD20 MUTATED 1 1 3
KCTD20 WILD-TYPE 98 130 133
'KCTD20 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.608 (Fisher's exact test), Q value = 1

Table S296.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
KCTD20 MUTATED 0 4 1 0
KCTD20 WILD-TYPE 60 159 102 47
'KCTD20 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

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 = 0.435 (Fisher's exact test), Q value = 0.96

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 127 90 49 72 29
KCTD20 MUTATED 3 0 0 2 0
KCTD20 WILD-TYPE 124 90 49 70 29
'KCTD20 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.183 (Fisher's exact test), Q value = 0.85

Table S300.  Gene #31: 'KCTD20 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
KCTD20 MUTATED 3 0 2 0
KCTD20 WILD-TYPE 150 146 59 7
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.94

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 CLUS_7
ALL 44 60 103 45 63 40 13
KCTD20 MUTATED 0 0 2 1 0 2 0
KCTD20 WILD-TYPE 44 60 101 44 63 38 13
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
KCTD20 MUTATED 0 0 0 3 2 0
KCTD20 WILD-TYPE 40 87 54 120 54 8
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.789 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
KCTD20 MUTATED 1 0 2 0 0 1 0
KCTD20 WILD-TYPE 43 54 69 17 52 81 23
'KCTD20 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.509 (Fisher's exact test), Q value = 0.99

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 CLUS_6
ALL 131 49 73 39 47 4
KCTD20 MUTATED 1 0 2 0 1 0
KCTD20 WILD-TYPE 130 49 71 39 46 4
'GPR110 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.883 (Fisher's exact test), Q value = 1

Table S305.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
GPR110 MUTATED 1 2 3
GPR110 WILD-TYPE 98 129 133
'GPR110 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.729 (Fisher's exact test), Q value = 1

Table S306.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
GPR110 MUTATED 0 4 2 0
GPR110 WILD-TYPE 60 159 101 47
'GPR110 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.94

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 = 0.605 (Fisher's exact test), Q value = 1

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 = 0.0661 (Fisher's exact test), Q value = 0.6

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 127 90 49 72 29
GPR110 MUTATED 1 0 1 4 0
GPR110 WILD-TYPE 126 90 48 68 29
'GPR110 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0279 (Fisher's exact test), Q value = 0.52

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
GPR110 MUTATED 1 1 4 0
GPR110 WILD-TYPE 152 145 57 7

Figure S57.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'GPR110 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.29 (Fisher's exact test), Q value = 0.88

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 CLUS_7
ALL 44 60 103 45 63 40 13
GPR110 MUTATED 0 0 5 0 1 0 0
GPR110 WILD-TYPE 44 60 98 45 62 40 13
'GPR110 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0467 (Fisher's exact test), Q value = 0.56

Table S312.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
GPR110 MUTATED 0 0 1 1 4 0
GPR110 WILD-TYPE 40 87 53 122 52 8

Figure S58.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'GPR110 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.96

Table S313.  Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
GPR110 MUTATED 1 0 1 0 0 4 0
GPR110 WILD-TYPE 43 54 70 17 52 78 23
'GPR110 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0357 (Fisher's exact test), Q value = 0.54

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 CLUS_6
ALL 131 49 73 39 47 4
GPR110 MUTATED 2 0 0 0 4 0
GPR110 WILD-TYPE 129 49 73 39 43 4

Figure S59.  Get High-res Image Gene #32: 'GPR110 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CEP164 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.96

Table S315.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CEP164 MUTATED 1 3 5
CEP164 WILD-TYPE 98 128 131
'CEP164 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.887 (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 CLUS_4
ALL 60 163 103 47
CEP164 MUTATED 2 3 3 1
CEP164 WILD-TYPE 58 160 100 46
'CEP164 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 0.99

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 = 0.696 (Fisher's exact test), Q value = 1

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 = 0.846 (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 127 90 49 72 29
CEP164 MUTATED 4 1 1 2 1
CEP164 WILD-TYPE 123 89 48 70 28
'CEP164 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.66 (Fisher's exact test), Q value = 1

Table S320.  Gene #33: 'CEP164 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CEP164 MUTATED 5 2 2 0
CEP164 WILD-TYPE 148 144 59 7
'CEP164 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 0.97

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 CLUS_7
ALL 44 60 103 45 63 40 13
CEP164 MUTATED 1 2 1 2 1 1 1
CEP164 WILD-TYPE 43 58 102 43 62 39 12
'CEP164 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.73 (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 CLUS_6
ALL 40 87 54 123 56 8
CEP164 MUTATED 0 1 2 4 2 0
CEP164 WILD-TYPE 40 86 52 119 54 8
'CEP164 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.641 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CEP164 MUTATED 1 0 2 1 1 3 1
CEP164 WILD-TYPE 43 54 69 16 51 79 22
'CEP164 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1 (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 CLUS_6
ALL 131 49 73 39 47 4
CEP164 MUTATED 4 1 2 1 1 0
CEP164 WILD-TYPE 127 48 71 38 46 4
'TCEAL6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S325.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
TCEAL6 MUTATED 0 2 2
TCEAL6 WILD-TYPE 99 129 134
'TCEAL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.85

Table S326.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
TCEAL6 MUTATED 2 2 0 0
TCEAL6 WILD-TYPE 58 161 103 47
'TCEAL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.609 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
TCEAL6 MUTATED 1 0 1 1 0
TCEAL6 WILD-TYPE 126 90 48 71 29
'TCEAL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.593 (Fisher's exact test), Q value = 1

Table S328.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
TCEAL6 MUTATED 1 1 1 0
TCEAL6 WILD-TYPE 152 145 60 7
'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0367 (Fisher's exact test), Q value = 0.54

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 CLUS_7
ALL 44 60 103 45 63 40 13
TCEAL6 MUTATED 1 2 0 0 0 0 1
TCEAL6 WILD-TYPE 43 58 103 45 63 40 12

Figure S60.  Get High-res Image Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 0.94

Table S330.  Gene #34: 'TCEAL6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
TCEAL6 MUTATED 1 1 1 0 1 0
TCEAL6 WILD-TYPE 39 86 53 123 55 8
'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.57 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
TCEAL6 MUTATED 0 1 1 1 0 1 0
TCEAL6 WILD-TYPE 44 53 70 16 52 81 23
'TCEAL6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.97

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 CLUS_6
ALL 131 49 73 39 47 4
TCEAL6 MUTATED 2 0 0 1 1 0
TCEAL6 WILD-TYPE 129 49 73 38 46 4
'DNAJC28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.95

Table S333.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
DNAJC28 MUTATED 0 3 1
DNAJC28 WILD-TYPE 99 128 135
'DNAJC28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.638 (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 CLUS_4
ALL 60 163 103 47
DNAJC28 MUTATED 1 1 2 0
DNAJC28 WILD-TYPE 59 162 101 47
'DNAJC28 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0661 (Fisher's exact test), Q value = 0.6

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 = 0.95

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 = 0.78 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
DNAJC28 MUTATED 2 2 0 0 0
DNAJC28 WILD-TYPE 125 88 49 72 29
'DNAJC28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S338.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
DNAJC28 MUTATED 2 2 0 0
DNAJC28 WILD-TYPE 151 144 61 7
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.951 (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 CLUS_7
ALL 44 60 103 45 63 40 13
DNAJC28 MUTATED 1 1 1 0 1 0 0
DNAJC28 WILD-TYPE 43 59 102 45 62 40 13
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.596 (Fisher's exact test), Q value = 1

Table S340.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
DNAJC28 MUTATED 1 2 0 1 0 0
DNAJC28 WILD-TYPE 39 85 54 122 56 8
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S341.  Gene #35: 'DNAJC28 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
DNAJC28 MUTATED 0 1 1 0 1 1 0
DNAJC28 WILD-TYPE 44 53 70 17 51 81 23
'DNAJC28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.658 (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 CLUS_6
ALL 131 49 73 39 47 4
DNAJC28 MUTATED 3 1 0 0 0 0
DNAJC28 WILD-TYPE 128 48 73 39 47 4
'FOXI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.447 (Fisher's exact test), Q value = 0.96

Table S343.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
FOXI1 MUTATED 0 2 3
FOXI1 WILD-TYPE 99 129 133
'FOXI1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S344.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
FOXI1 MUTATED 0 3 2 0
FOXI1 WILD-TYPE 60 160 101 47
'FOXI1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.96

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 = 0.496 (Fisher's exact test), Q value = 0.98

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 127 90 49 72 29
FOXI1 MUTATED 2 0 0 2 0
FOXI1 WILD-TYPE 125 90 49 70 29
'FOXI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.85

Table S348.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
FOXI1 MUTATED 2 0 2 0
FOXI1 WILD-TYPE 151 146 59 7
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.88

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 CLUS_7
ALL 44 60 103 45 63 40 13
FOXI1 MUTATED 0 1 2 0 0 1 1
FOXI1 WILD-TYPE 44 59 101 45 63 39 12
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.587 (Fisher's exact test), Q value = 1

Table S350.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
FOXI1 MUTATED 0 1 1 1 2 0
FOXI1 WILD-TYPE 40 86 53 122 54 8
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.396 (Fisher's exact test), Q value = 0.95

Table S351.  Gene #36: 'FOXI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
FOXI1 MUTATED 0 0 2 1 0 2 0
FOXI1 WILD-TYPE 44 54 69 16 52 80 23
'FOXI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.563 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
FOXI1 MUTATED 2 0 1 0 2 0
FOXI1 WILD-TYPE 129 49 72 39 45 4
'KRTAP5-7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.95

Table S353.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
KRTAP5-7 MUTATED 0 3 1
KRTAP5-7 WILD-TYPE 99 128 135
'KRTAP5-7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 0.93

Table S354.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
KRTAP5-7 MUTATED 2 1 1 0
KRTAP5-7 WILD-TYPE 58 162 102 47
'KRTAP5-7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0843 (Fisher's exact test), Q value = 0.65

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 = 0.95

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 = 0.825 (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 127 90 49 72 29
KRTAP5-7 MUTATED 2 1 1 0 0
KRTAP5-7 WILD-TYPE 125 89 48 72 29
'KRTAP5-7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S358.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
KRTAP5-7 MUTATED 2 2 0 0
KRTAP5-7 WILD-TYPE 151 144 61 7
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0467 (Fisher's exact test), Q value = 0.56

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 CLUS_7
ALL 44 60 103 45 63 40 13
KRTAP5-7 MUTATED 1 0 0 0 0 2 0
KRTAP5-7 WILD-TYPE 43 60 103 45 63 38 13

Figure S61.  Get High-res Image Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.487 (Fisher's exact test), Q value = 0.97

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 CLUS_6
ALL 40 87 54 123 56 8
KRTAP5-7 MUTATED 1 0 0 2 0 0
KRTAP5-7 WILD-TYPE 39 87 54 121 56 8
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.327 (Fisher's exact test), Q value = 0.94

Table S361.  Gene #37: 'KRTAP5-7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
KRTAP5-7 MUTATED 0 0 1 0 1 0 1
KRTAP5-7 WILD-TYPE 44 54 70 17 51 82 22
'KRTAP5-7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.17 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
KRTAP5-7 MUTATED 0 0 2 1 0 0
KRTAP5-7 WILD-TYPE 131 49 71 38 47 4
'JAK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.94

Table S363.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
JAK1 MUTATED 6 5 3
JAK1 WILD-TYPE 93 126 133
'JAK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0303 (Fisher's exact test), Q value = 0.54

Table S364.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
JAK1 MUTATED 3 5 1 5
JAK1 WILD-TYPE 57 158 102 42

Figure S62.  Get High-res Image Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'JAK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.968 (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 = 0.99

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 = 0.228 (Fisher's exact test), Q value = 0.86

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 127 90 49 72 29
JAK1 MUTATED 2 3 4 4 1
JAK1 WILD-TYPE 125 87 45 68 28
'JAK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.628 (Fisher's exact test), Q value = 1

Table S368.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
JAK1 MUTATED 4 7 3 0
JAK1 WILD-TYPE 149 139 58 7
'JAK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.774 (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 CLUS_7
ALL 44 60 103 45 63 40 13
JAK1 MUTATED 2 2 5 2 2 0 1
JAK1 WILD-TYPE 42 58 98 43 61 40 12
'JAK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.946 (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 CLUS_6
ALL 40 87 54 123 56 8
JAK1 MUTATED 2 3 2 4 3 0
JAK1 WILD-TYPE 38 84 52 119 53 8
'JAK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S371.  Gene #38: 'JAK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
JAK1 MUTATED 2 2 2 0 2 6 0
JAK1 WILD-TYPE 42 52 69 17 50 76 23
'JAK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
JAK1 MUTATED 7 1 1 2 3 0
JAK1 WILD-TYPE 124 48 72 37 44 4
'DENND4B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.77

Table S373.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
DENND4B MUTATED 1 3 8
DENND4B WILD-TYPE 98 128 128
'DENND4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 0.95

Table S374.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
DENND4B MUTATED 2 8 1 1
DENND4B WILD-TYPE 58 155 102 46
'DENND4B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0591 (Fisher's exact test), Q value = 0.6

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 = 0.364 (Fisher's exact test), Q value = 0.95

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 = 0.363 (Fisher's exact test), Q value = 0.95

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 127 90 49 72 29
DENND4B MUTATED 3 5 1 1 2
DENND4B WILD-TYPE 124 85 48 71 27
'DENND4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.95

Table S378.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
DENND4B MUTATED 3 8 1 0
DENND4B WILD-TYPE 150 138 60 7
'DENND4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.95

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 CLUS_7
ALL 44 60 103 45 63 40 13
DENND4B MUTATED 2 3 5 0 1 0 1
DENND4B WILD-TYPE 42 57 98 45 62 40 12
'DENND4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S380.  Gene #39: 'DENND4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
DENND4B MUTATED 2 3 2 3 2 0
DENND4B WILD-TYPE 38 84 52 120 54 8
'DENND4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.562 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
DENND4B MUTATED 0 2 2 1 1 5 0
DENND4B WILD-TYPE 44 52 69 16 51 77 23
'DENND4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 0.86

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 CLUS_6
ALL 131 49 73 39 47 4
DENND4B MUTATED 2 3 1 2 3 0
DENND4B WILD-TYPE 129 46 72 37 44 4
'BRD7 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.364 (Fisher's exact test), Q value = 0.95

Table S383.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
BRD7 MUTATED 2 2 6
BRD7 WILD-TYPE 97 129 130
'BRD7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.88

Table S384.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
BRD7 MUTATED 2 2 5 1
BRD7 WILD-TYPE 58 161 98 46
'BRD7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

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 = 0.679 (Fisher's exact test), Q value = 1

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 = 0.369 (Fisher's exact test), Q value = 0.95

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 127 90 49 72 29
BRD7 MUTATED 5 1 1 1 2
BRD7 WILD-TYPE 122 89 48 71 27
'BRD7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.95

Table S388.  Gene #40: 'BRD7 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
BRD7 MUTATED 7 2 1 0
BRD7 WILD-TYPE 146 144 60 7
'BRD7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.587 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
BRD7 MUTATED 1 0 3 3 2 1 0
BRD7 WILD-TYPE 43 60 100 42 61 39 13
'BRD7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
BRD7 MUTATED 1 0 2 5 2 0
BRD7 WILD-TYPE 39 87 52 118 54 8
'BRD7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.963 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
BRD7 MUTATED 1 1 3 0 2 2 1
BRD7 WILD-TYPE 43 53 68 17 50 80 22
'BRD7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.234 (Fisher's exact test), Q value = 0.86

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 CLUS_6
ALL 131 49 73 39 47 4
BRD7 MUTATED 2 0 4 1 3 0
BRD7 WILD-TYPE 129 49 69 38 44 4
'IDH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 0.95

Table S393.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
IDH1 MUTATED 1 5 2
IDH1 WILD-TYPE 98 126 134
'IDH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0955 (Fisher's exact test), Q value = 0.68

Table S394.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
IDH1 MUTATED 4 3 1 0
IDH1 WILD-TYPE 56 160 102 47
'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 = 0.39 (Fisher's exact test), Q value = 0.95

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 = 0.405 (Fisher's exact test), Q value = 0.95

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 127 90 49 72 29
IDH1 MUTATED 3 1 3 1 0
IDH1 WILD-TYPE 124 89 46 71 29
'IDH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S398.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
IDH1 MUTATED 4 3 1 0
IDH1 WILD-TYPE 149 143 60 7
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.221 (Fisher's exact test), Q value = 0.86

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 CLUS_7
ALL 44 60 103 45 63 40 13
IDH1 MUTATED 2 0 1 2 3 0 0
IDH1 WILD-TYPE 42 60 102 43 60 40 13
'IDH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0653 (Fisher's exact test), Q value = 0.6

Table S400.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
IDH1 MUTATED 2 0 0 4 1 1
IDH1 WILD-TYPE 38 87 54 119 55 7
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S401.  Gene #41: 'IDH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
IDH1 MUTATED 1 2 1 0 3 1 0
IDH1 WILD-TYPE 43 52 70 17 49 81 23
'IDH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.81

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 CLUS_6
ALL 131 49 73 39 47 4
IDH1 MUTATED 1 0 4 2 1 0
IDH1 WILD-TYPE 130 49 69 37 46 4
'CNGA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.95

Table S403.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CNGA3 MUTATED 1 5 4
CNGA3 WILD-TYPE 98 126 132
'CNGA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.816 (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 CLUS_4
ALL 60 163 103 47
CNGA3 MUTATED 2 5 2 2
CNGA3 WILD-TYPE 58 158 101 45
'CNGA3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00372 (Fisher's exact test), Q value = 0.13

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 S63.  Get High-res Image Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CNGA3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 1

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 = 0.424 (Fisher's exact test), Q value = 0.96

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 127 90 49 72 29
CNGA3 MUTATED 2 2 2 4 0
CNGA3 WILD-TYPE 125 88 47 68 29
'CNGA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.88

Table S408.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CNGA3 MUTATED 3 3 4 0
CNGA3 WILD-TYPE 150 143 57 7
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
CNGA3 MUTATED 2 1 4 1 3 0 0
CNGA3 WILD-TYPE 42 59 99 44 60 40 13
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.542 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CNGA3 MUTATED 1 4 0 3 3 0
CNGA3 WILD-TYPE 39 83 54 120 53 8
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.85

Table S411.  Gene #42: 'CNGA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CNGA3 MUTATED 4 0 1 0 1 3 1
CNGA3 WILD-TYPE 40 54 70 17 51 79 22
'CNGA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.154 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
CNGA3 MUTATED 6 0 0 1 3 0
CNGA3 WILD-TYPE 125 49 73 38 44 4
'PLA2G3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.88

Table S413.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
PLA2G3 MUTATED 0 3 3
PLA2G3 WILD-TYPE 99 128 133
'PLA2G3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.239 (Fisher's exact test), Q value = 0.86

Table S414.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PLA2G3 MUTATED 1 5 0 0
PLA2G3 WILD-TYPE 59 158 103 47
'PLA2G3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.88

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 = 0.143 (Fisher's exact test), Q value = 0.81

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 = 0.376 (Fisher's exact test), Q value = 0.95

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 127 90 49 72 29
PLA2G3 MUTATED 1 2 0 3 0
PLA2G3 WILD-TYPE 126 88 49 69 29
'PLA2G3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.85

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PLA2G3 MUTATED 1 2 3 0
PLA2G3 WILD-TYPE 152 144 58 7
'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
PLA2G3 MUTATED 0 1 4 1 0 0 0
PLA2G3 WILD-TYPE 44 59 99 44 63 40 13
'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0759 (Fisher's exact test), Q value = 0.62

Table S420.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PLA2G3 MUTATED 0 1 0 1 4 0
PLA2G3 WILD-TYPE 40 86 54 122 52 8
'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S421.  Gene #43: 'PLA2G3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PLA2G3 MUTATED 1 1 0 0 1 3 0
PLA2G3 WILD-TYPE 43 53 71 17 51 79 23
'PLA2G3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.36

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 CLUS_6
ALL 131 49 73 39 47 4
PLA2G3 MUTATED 0 1 1 0 4 0
PLA2G3 WILD-TYPE 131 48 72 39 43 4

Figure S64.  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 = 0.838 (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 99 131 136
HLA-DPB1 MUTATED 1 2 1
HLA-DPB1 WILD-TYPE 98 129 135
'HLA-DPB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S424.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
HLA-DPB1 MUTATED 0 3 2 0
HLA-DPB1 WILD-TYPE 60 160 101 47
'HLA-DPB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.954 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
HLA-DPB1 MUTATED 2 2 0 1 0
HLA-DPB1 WILD-TYPE 125 88 49 71 29
'HLA-DPB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S426.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
HLA-DPB1 MUTATED 2 2 1 0
HLA-DPB1 WILD-TYPE 151 144 60 7
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.628 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
HLA-DPB1 MUTATED 0 2 2 0 0 1 0
HLA-DPB1 WILD-TYPE 44 58 101 45 63 39 13
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.87

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 CLUS_6
ALL 40 87 54 123 56 8
HLA-DPB1 MUTATED 0 2 2 0 1 0
HLA-DPB1 WILD-TYPE 40 85 52 123 55 8
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.758 (Fisher's exact test), Q value = 1

Table S429.  Gene #44: 'HLA-DPB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
HLA-DPB1 MUTATED 0 2 1 0 0 1 0
HLA-DPB1 WILD-TYPE 44 52 70 17 52 81 23
'HLA-DPB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.763 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
HLA-DPB1 MUTATED 1 1 1 0 1 0
HLA-DPB1 WILD-TYPE 130 48 72 39 46 4
'ALMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S431.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
ALMS1 MUTATED 6 7 11
ALMS1 WILD-TYPE 93 124 125
'ALMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 1

Table S432.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
ALMS1 MUTATED 4 9 9 2
ALMS1 WILD-TYPE 56 154 94 45
'ALMS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

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 = 0.818 (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 = 0.932 (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 127 90 49 72 29
ALMS1 MUTATED 7 6 4 5 1
ALMS1 WILD-TYPE 120 84 45 67 28
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.274 (Fisher's exact test), Q value = 0.88

Table S436.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
ALMS1 MUTATED 11 6 5 1
ALMS1 WILD-TYPE 142 140 56 6
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.85

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 CLUS_7
ALL 44 60 103 45 63 40 13
ALMS1 MUTATED 2 3 11 5 1 1 1
ALMS1 WILD-TYPE 42 57 92 40 62 39 12
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.78

Table S438.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
ALMS1 MUTATED 2 9 5 3 4 1
ALMS1 WILD-TYPE 38 78 49 120 52 7
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S439.  Gene #45: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
ALMS1 MUTATED 3 2 4 2 4 8 1
ALMS1 WILD-TYPE 41 52 67 15 48 74 22
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 0.96

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 CLUS_6
ALL 131 49 73 39 47 4
ALMS1 MUTATED 9 4 3 2 5 1
ALMS1 WILD-TYPE 122 45 70 37 42 3
'NUCB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S441.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
NUCB2 MUTATED 0 1 2
NUCB2 WILD-TYPE 99 130 134
'NUCB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.722 (Fisher's exact test), Q value = 1

Table S442.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
NUCB2 MUTATED 0 1 2 0
NUCB2 WILD-TYPE 60 162 101 47
'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 = 0.456 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
NUCB2 MUTATED 0 1 0 1 1 0 0
NUCB2 WILD-TYPE 44 59 103 44 62 40 13
'NUCB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S446.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
NUCB2 MUTATED 0 1 0 2 0 0
NUCB2 WILD-TYPE 40 86 54 121 56 8
'NUCB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0427 (Fisher's exact test), Q value = 0.56

Table S447.  Gene #46: 'NUCB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
NUCB2 MUTATED 0 0 0 1 2 0 0
NUCB2 WILD-TYPE 44 54 71 16 50 82 23

Figure S65.  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 = 1 (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 CLUS_6
ALL 131 49 73 39 47 4
NUCB2 MUTATED 2 0 1 0 0 0
NUCB2 WILD-TYPE 129 49 72 39 47 4
'BAZ2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.346 (Fisher's exact test), Q value = 0.94

Table S449.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
BAZ2A MUTATED 1 4 6
BAZ2A WILD-TYPE 98 127 130
'BAZ2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S450.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
BAZ2A MUTATED 2 5 3 1
BAZ2A WILD-TYPE 58 158 100 46
'BAZ2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.889 (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 = 1

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 = 0.978 (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 127 90 49 72 29
BAZ2A MUTATED 5 2 1 2 1
BAZ2A WILD-TYPE 122 88 48 70 28
'BAZ2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S454.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
BAZ2A MUTATED 4 5 2 0
BAZ2A WILD-TYPE 149 141 59 7
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.7

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 CLUS_7
ALL 44 60 103 45 63 40 13
BAZ2A MUTATED 0 3 2 1 3 0 2
BAZ2A WILD-TYPE 44 57 101 44 60 40 11
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.756 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
BAZ2A MUTATED 0 2 3 4 2 0
BAZ2A WILD-TYPE 40 85 51 119 54 8
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.746 (Fisher's exact test), Q value = 1

Table S457.  Gene #47: 'BAZ2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
BAZ2A MUTATED 0 1 4 0 2 3 0
BAZ2A WILD-TYPE 44 53 67 17 50 79 23
'BAZ2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.875 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
BAZ2A MUTATED 5 1 2 0 2 0
BAZ2A WILD-TYPE 126 48 71 39 45 4
'TAF1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.246 (Fisher's exact test), Q value = 0.86

Table S459.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
TAF1B MUTATED 0 2 4
TAF1B WILD-TYPE 99 129 132
'TAF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.85

Table S460.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
TAF1B MUTATED 2 4 0 0
TAF1B WILD-TYPE 58 159 103 47
'TAF1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 1

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 = 0.25 (Fisher's exact test), Q value = 0.86

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 = 0.521 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
TAF1B MUTATED 1 1 2 1 0
TAF1B WILD-TYPE 126 89 47 71 29
'TAF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S464.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
TAF1B MUTATED 2 2 1 0
TAF1B WILD-TYPE 151 144 60 7
'TAF1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0558 (Fisher's exact test), Q value = 0.6

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 CLUS_7
ALL 44 60 103 45 63 40 13
TAF1B MUTATED 1 3 0 0 1 0 1
TAF1B WILD-TYPE 43 57 103 45 62 40 12
'TAF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.88

Table S466.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
TAF1B MUTATED 1 3 1 0 1 0
TAF1B WILD-TYPE 39 84 53 123 55 8
'TAF1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.96

Table S467.  Gene #48: 'TAF1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
TAF1B MUTATED 2 1 1 1 0 1 0
TAF1B WILD-TYPE 42 53 70 16 52 81 23
'TAF1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.691 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
TAF1B MUTATED 3 1 0 1 1 0
TAF1B WILD-TYPE 128 48 73 38 46 4
'C1ORF125 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.347 (Fisher's exact test), Q value = 0.94

Table S469.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
C1ORF125 MUTATED 1 4 6
C1ORF125 WILD-TYPE 98 127 130
'C1ORF125 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.85

Table S470.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
C1ORF125 MUTATED 0 8 3 0
C1ORF125 WILD-TYPE 60 155 100 47
'C1ORF125 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.56

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 S66.  Get High-res Image Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'C1ORF125 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.76

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 = 0.396 (Fisher's exact test), Q value = 0.95

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 127 90 49 72 29
C1ORF125 MUTATED 2 4 3 2 0
C1ORF125 WILD-TYPE 125 86 46 70 29
'C1ORF125 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.938 (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
ALL 153 146 61 7
C1ORF125 MUTATED 4 5 2 0
C1ORF125 WILD-TYPE 149 141 59 7
'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0406 (Fisher's exact test), Q value = 0.56

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 CLUS_7
ALL 44 60 103 45 63 40 13
C1ORF125 MUTATED 0 6 1 2 2 0 0
C1ORF125 WILD-TYPE 44 54 102 43 61 40 13

Figure S67.  Get High-res Image Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.95

Table S476.  Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
C1ORF125 MUTATED 0 6 1 3 1 0
C1ORF125 WILD-TYPE 40 81 53 120 55 8
'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
C1ORF125 MUTATED 1 1 2 1 2 4 0
C1ORF125 WILD-TYPE 43 53 69 16 50 78 23
'C1ORF125 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0471 (Fisher's exact test), Q value = 0.56

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 CLUS_6
ALL 131 49 73 39 47 4
C1ORF125 MUTATED 4 5 0 0 2 0
C1ORF125 WILD-TYPE 127 44 73 39 45 4

Figure S68.  Get High-res Image Gene #49: 'C1ORF125 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'AR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.96

Table S479.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
AR MUTATED 4 4 2
AR WILD-TYPE 95 127 134
'AR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.774 (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 CLUS_4
ALL 60 163 103 47
AR MUTATED 2 5 3 0
AR WILD-TYPE 58 158 100 47
'AR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.94

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 = 0.6 (Fisher's exact test), Q value = 1

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 = 0.842 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
AR MUTATED 4 3 2 1 0
AR WILD-TYPE 123 87 47 71 29
'AR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S484.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
AR MUTATED 5 4 1 0
AR WILD-TYPE 148 142 60 7
'AR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.94

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 CLUS_7
ALL 44 60 103 45 63 40 13
AR MUTATED 3 0 3 1 3 0 0
AR WILD-TYPE 41 60 100 44 60 40 13
'AR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.426 (Fisher's exact test), Q value = 0.96

Table S486.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
AR MUTATED 1 2 4 2 1 0
AR WILD-TYPE 39 85 50 121 55 8
'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.94

Table S487.  Gene #50: 'AR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
AR MUTATED 0 3 4 0 0 2 0
AR WILD-TYPE 44 51 67 17 52 80 23
'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 0.98

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 CLUS_6
ALL 131 49 73 39 47 4
AR MUTATED 5 2 0 1 1 0
AR WILD-TYPE 126 47 73 38 46 4
'SPHK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.88

Table S489.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
SPHK1 MUTATED 0 3 3
SPHK1 WILD-TYPE 99 128 133
'SPHK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S490.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
SPHK1 MUTATED 2 3 1 0
SPHK1 WILD-TYPE 58 160 102 47
'SPHK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.773 (Fisher's exact test), Q value = 1

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 = 0.127 (Fisher's exact test), Q value = 0.78

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 127 90 49 72 29
SPHK1 MUTATED 1 0 0 3 0
SPHK1 WILD-TYPE 126 90 49 69 29
'SPHK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0452 (Fisher's exact test), Q value = 0.56

Table S494.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
SPHK1 MUTATED 1 0 3 0
SPHK1 WILD-TYPE 152 146 58 7

Figure S69.  Get High-res Image Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SPHK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.85

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 CLUS_7
ALL 44 60 103 45 63 40 13
SPHK1 MUTATED 2 1 2 0 0 0 1
SPHK1 WILD-TYPE 42 59 101 45 63 40 12
'SPHK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0782 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
SPHK1 MUTATED 1 2 0 0 3 0
SPHK1 WILD-TYPE 39 85 54 123 53 8
'SPHK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.85

Table S497.  Gene #51: 'SPHK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
SPHK1 MUTATED 0 1 0 1 0 3 1
SPHK1 WILD-TYPE 44 53 71 16 52 79 22
'SPHK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.81

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 CLUS_6
ALL 131 49 73 39 47 4
SPHK1 MUTATED 2 0 0 1 3 0
SPHK1 WILD-TYPE 129 49 73 38 44 4
'CREB3L3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.88

Table S499.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CREB3L3 MUTATED 2 0 3
CREB3L3 WILD-TYPE 97 131 133
'CREB3L3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S500.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CREB3L3 MUTATED 1 1 2 1
CREB3L3 WILD-TYPE 59 162 101 46
'CREB3L3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.185 (Fisher's exact test), Q value = 0.85

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 127 90 49 72 29
CREB3L3 MUTATED 1 0 1 3 0
CREB3L3 WILD-TYPE 126 90 48 69 29
'CREB3L3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 0.85

Table S502.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CREB3L3 MUTATED 3 0 2 0
CREB3L3 WILD-TYPE 150 146 59 7
'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.68 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
CREB3L3 MUTATED 0 1 3 0 0 1 0
CREB3L3 WILD-TYPE 44 59 100 45 63 39 13
'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.86

Table S504.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CREB3L3 MUTATED 0 1 0 1 3 0
CREB3L3 WILD-TYPE 40 86 54 122 53 8
'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0132 (Fisher's exact test), Q value = 0.33

Table S505.  Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CREB3L3 MUTATED 3 0 0 0 0 0 0
CREB3L3 WILD-TYPE 41 54 71 17 52 82 23

Figure S70.  Get High-res Image Gene #52: 'CREB3L3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CREB3L3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.707 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
CREB3L3 MUTATED 2 0 0 0 1 0
CREB3L3 WILD-TYPE 129 49 73 39 46 4
'LFNG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S507.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
LFNG MUTATED 1 2 4
LFNG WILD-TYPE 98 129 132
'LFNG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.897 (Fisher's exact test), Q value = 1

Table S508.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
LFNG MUTATED 1 4 1 1
LFNG WILD-TYPE 59 159 102 46
'LFNG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.88 (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 = 0.39 (Fisher's exact test), Q value = 0.95

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 = 0.332 (Fisher's exact test), Q value = 0.94

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 127 90 49 72 29
LFNG MUTATED 1 1 2 2 1
LFNG WILD-TYPE 126 89 47 70 28
'LFNG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.596 (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
ALL 153 146 61 7
LFNG MUTATED 2 3 2 0
LFNG WILD-TYPE 151 143 59 7
'LFNG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.95

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 CLUS_7
ALL 44 60 103 45 63 40 13
LFNG MUTATED 2 1 1 1 1 0 1
LFNG WILD-TYPE 42 59 102 44 62 40 12
'LFNG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.86

Table S514.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
LFNG MUTATED 2 0 0 4 1 0
LFNG WILD-TYPE 38 87 54 119 55 8
'LFNG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S515.  Gene #53: 'LFNG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
LFNG MUTATED 1 2 0 0 1 1 0
LFNG WILD-TYPE 43 52 71 17 51 81 23
'LFNG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.81

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 CLUS_6
ALL 131 49 73 39 47 4
LFNG MUTATED 0 1 1 2 1 0
LFNG WILD-TYPE 131 48 72 37 46 4
'FZR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S517.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
FZR1 MUTATED 1 3 2
FZR1 WILD-TYPE 98 128 134
'FZR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.777 (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 CLUS_4
ALL 60 163 103 47
FZR1 MUTATED 0 3 2 1
FZR1 WILD-TYPE 60 160 101 46
'FZR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.97

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 = 0.181 (Fisher's exact test), Q value = 0.85

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 127 90 49 72 29
FZR1 MUTATED 0 2 1 2 1
FZR1 WILD-TYPE 127 88 48 70 28
'FZR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.92

Table S522.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
FZR1 MUTATED 1 3 2 0
FZR1 WILD-TYPE 152 143 59 7
'FZR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.597 (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 CLUS_7
ALL 44 60 103 45 63 40 13
FZR1 MUTATED 0 1 4 1 0 0 0
FZR1 WILD-TYPE 44 59 99 44 63 40 13
'FZR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.95

Table S524.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
FZR1 MUTATED 0 3 0 1 2 0
FZR1 WILD-TYPE 40 84 54 122 54 8
'FZR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.252 (Fisher's exact test), Q value = 0.86

Table S525.  Gene #54: 'FZR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
FZR1 MUTATED 0 0 0 0 1 4 0
FZR1 WILD-TYPE 44 54 71 17 51 78 23
'FZR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 0.96

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 CLUS_6
ALL 131 49 73 39 47 4
FZR1 MUTATED 2 2 0 0 1 0
FZR1 WILD-TYPE 129 47 73 39 46 4
'TRIOBP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.926 (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 99 131 136
TRIOBP MUTATED 3 3 5
TRIOBP WILD-TYPE 96 128 131
'TRIOBP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.96

Table S528.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
TRIOBP MUTATED 0 6 3 2
TRIOBP WILD-TYPE 60 157 100 45
'TRIOBP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.939 (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 = 0.182 (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 127 90 49 72 29
TRIOBP MUTATED 4 1 0 4 2
TRIOBP WILD-TYPE 123 89 49 68 27
'TRIOBP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.95

Table S532.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
TRIOBP MUTATED 4 3 4 0
TRIOBP WILD-TYPE 149 143 57 7
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.85

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 CLUS_7
ALL 44 60 103 45 63 40 13
TRIOBP MUTATED 1 1 3 0 3 1 2
TRIOBP WILD-TYPE 43 59 100 45 60 39 11
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 0.94

Table S534.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
TRIOBP MUTATED 0 1 1 5 4 0
TRIOBP WILD-TYPE 40 86 53 118 52 8
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.7

Table S535.  Gene #55: 'TRIOBP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
TRIOBP MUTATED 0 0 1 2 2 4 0
TRIOBP WILD-TYPE 44 54 70 15 50 78 23
'TRIOBP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0682 (Fisher's exact test), Q value = 0.61

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 CLUS_6
ALL 131 49 73 39 47 4
TRIOBP MUTATED 1 1 3 1 2 1
TRIOBP WILD-TYPE 130 48 70 38 45 3
'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 99 131 136
GJB1 MUTATED 1 1 1
GJB1 WILD-TYPE 98 130 135
'GJB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (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 CLUS_4
ALL 60 163 103 47
GJB1 MUTATED 0 2 1 0
GJB1 WILD-TYPE 60 161 102 47
'GJB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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 127 90 49 72 29
GJB1 MUTATED 2 1 0 0 0
GJB1 WILD-TYPE 125 89 49 72 29
'GJB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S540.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
GJB1 MUTATED 2 1 0 0
GJB1 WILD-TYPE 151 145 61 7
'GJB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
GJB1 MUTATED 0 0 1 0 1 1 0
GJB1 WILD-TYPE 44 60 102 45 62 39 13
'GJB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.846 (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 CLUS_6
ALL 40 87 54 123 56 8
GJB1 MUTATED 0 1 1 1 0 0
GJB1 WILD-TYPE 40 86 53 122 56 8
'GJB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S543.  Gene #56: 'GJB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
GJB1 MUTATED 0 0 2 0 0 1 0
GJB1 WILD-TYPE 44 54 69 17 52 81 23
'GJB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.906 (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 CLUS_6
ALL 131 49 73 39 47 4
GJB1 MUTATED 1 1 1 0 0 0
GJB1 WILD-TYPE 130 48 72 39 47 4
'DYRK1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0757 (Fisher's exact test), Q value = 0.62

Table S545.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
DYRK1A MUTATED 2 0 5
DYRK1A WILD-TYPE 97 131 131
'DYRK1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.944 (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 CLUS_4
ALL 60 163 103 47
DYRK1A MUTATED 1 4 2 0
DYRK1A WILD-TYPE 59 159 101 47
'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 = 0.399 (Fisher's exact test), Q value = 0.95

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 = 0.779 (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 127 90 49 72 29
DYRK1A MUTATED 2 2 2 1 0
DYRK1A WILD-TYPE 125 88 47 71 29
'DYRK1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.809 (Fisher's exact test), Q value = 1

Table S550.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
DYRK1A MUTATED 2 4 1 0
DYRK1A WILD-TYPE 151 142 60 7
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
DYRK1A MUTATED 2 0 4 0 1 0 0
DYRK1A WILD-TYPE 42 60 99 45 62 40 13
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.545 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
DYRK1A MUTATED 2 2 1 1 1 0
DYRK1A WILD-TYPE 38 85 53 122 55 8
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S553.  Gene #57: 'DYRK1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
DYRK1A MUTATED 0 1 1 0 1 2 1
DYRK1A WILD-TYPE 44 53 70 17 51 80 22
'DYRK1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
DYRK1A MUTATED 1 2 1 2 0 0
DYRK1A WILD-TYPE 130 47 72 37 47 4
'TNPO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.88

Table S555.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
TNPO1 MUTATED 1 2 6
TNPO1 WILD-TYPE 98 129 130
'TNPO1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.8 (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 CLUS_4
ALL 60 163 103 47
TNPO1 MUTATED 2 4 3 0
TNPO1 WILD-TYPE 58 159 100 47
'TNPO1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.503 (Fisher's exact test), Q value = 0.99

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 = 0.86

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 = 0.621 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
TNPO1 MUTATED 2 2 2 3 0
TNPO1 WILD-TYPE 125 88 47 69 29
'TNPO1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.506 (Fisher's exact test), Q value = 0.99

Table S560.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
TNPO1 MUTATED 3 3 3 0
TNPO1 WILD-TYPE 150 143 58 7
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
TNPO1 MUTATED 0 2 3 2 2 0 0
TNPO1 WILD-TYPE 44 58 100 43 61 40 13
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S562.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
TNPO1 MUTATED 0 2 1 3 3 0
TNPO1 WILD-TYPE 40 85 53 120 53 8
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 0.96

Table S563.  Gene #58: 'TNPO1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
TNPO1 MUTATED 1 0 1 0 2 5 0
TNPO1 WILD-TYPE 43 54 70 17 50 77 23
'TNPO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 0.95

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 CLUS_6
ALL 131 49 73 39 47 4
TNPO1 MUTATED 2 2 2 0 3 0
TNPO1 WILD-TYPE 129 47 71 39 44 4
'PDZD4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.96

Table S565.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
PDZD4 MUTATED 0 1 3
PDZD4 WILD-TYPE 99 130 133
'PDZD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.95

Table S566.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PDZD4 MUTATED 1 2 0 1
PDZD4 WILD-TYPE 59 161 103 46
'PDZD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.88

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 127 90 49 72 29
PDZD4 MUTATED 0 1 1 2 0
PDZD4 WILD-TYPE 127 89 48 70 29
'PDZD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.239 (Fisher's exact test), Q value = 0.86

Table S568.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PDZD4 MUTATED 0 3 1 0
PDZD4 WILD-TYPE 153 143 60 7
'PDZD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.86

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 CLUS_7
ALL 44 60 103 45 63 40 13
PDZD4 MUTATED 1 1 1 0 0 0 1
PDZD4 WILD-TYPE 43 59 102 45 63 40 12
'PDZD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.182 (Fisher's exact test), Q value = 0.85

Table S570.  Gene #59: 'PDZD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PDZD4 MUTATED 1 1 0 0 2 0
PDZD4 WILD-TYPE 39 86 54 123 54 8
'CCNA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.95

Table S571.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CCNA2 MUTATED 0 3 2
CCNA2 WILD-TYPE 99 128 134
'CCNA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0961 (Fisher's exact test), Q value = 0.68

Table S572.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CCNA2 MUTATED 3 1 1 0
CCNA2 WILD-TYPE 57 162 102 47
'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 = 0.317 (Fisher's exact test), Q value = 0.92

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 127 90 49 72 29
CCNA2 MUTATED 1 1 2 0 0
CCNA2 WILD-TYPE 126 89 47 72 29
'CCNA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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
ALL 153 146 61 7
CCNA2 MUTATED 2 2 0 0
CCNA2 WILD-TYPE 151 144 61 7
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.125 (Fisher's exact test), Q value = 0.77

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 CLUS_7
ALL 44 60 103 45 63 40 13
CCNA2 MUTATED 2 2 0 1 0 0 0
CCNA2 WILD-TYPE 42 58 103 44 63 40 13
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.94

Table S578.  Gene #60: 'CCNA2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CCNA2 MUTATED 2 1 1 1 0 0
CCNA2 WILD-TYPE 38 86 53 122 56 8
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.249 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CCNA2 MUTATED 0 2 1 1 1 0 0
CCNA2 WILD-TYPE 44 52 70 16 51 82 23
'CCNA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
CCNA2 MUTATED 3 0 0 2 0 0
CCNA2 WILD-TYPE 128 49 73 37 47 4
'AHCTF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S581.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
AHCTF1 MUTATED 3 2 3
AHCTF1 WILD-TYPE 96 129 133
'AHCTF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (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 CLUS_4
ALL 60 163 103 47
AHCTF1 MUTATED 1 4 2 1
AHCTF1 WILD-TYPE 59 159 101 46
'AHCTF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
AHCTF1 MUTATED 4 2 0 2 0
AHCTF1 WILD-TYPE 123 88 49 70 29
'AHCTF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S584.  Gene #61: 'AHCTF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
AHCTF1 MUTATED 4 2 2 0
AHCTF1 WILD-TYPE 149 144 59 7
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
AHCTF1 MUTATED 1 0 5 0 2 0 0
AHCTF1 WILD-TYPE 43 60 98 45 61 40 13
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.742 (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 CLUS_6
ALL 40 87 54 123 56 8
AHCTF1 MUTATED 1 1 2 2 2 0
AHCTF1 WILD-TYPE 39 86 52 121 54 8
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.761 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
AHCTF1 MUTATED 1 1 2 1 0 2 0
AHCTF1 WILD-TYPE 43 53 69 16 52 80 23
'AHCTF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.9 (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 CLUS_6
ALL 131 49 73 39 47 4
AHCTF1 MUTATED 3 0 2 1 1 0
AHCTF1 WILD-TYPE 128 49 71 38 46 4
'RXRB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.542 (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 99 131 136
RXRB MUTATED 1 4 3
RXRB WILD-TYPE 98 127 133
'RXRB MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.85

Table S590.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
RXRB MUTATED 1 5 0 2
RXRB WILD-TYPE 59 158 103 45
'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 = 0.677 (Fisher's exact test), Q value = 1

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 = 0.664 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
RXRB MUTATED 2 1 1 3 0
RXRB WILD-TYPE 125 89 48 69 29
'RXRB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.73 (Fisher's exact test), Q value = 1

Table S594.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
RXRB MUTATED 3 2 2 0
RXRB WILD-TYPE 150 144 59 7
'RXRB MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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 CLUS_7
ALL 44 60 103 45 63 40 13
RXRB MUTATED 1 1 3 0 1 2 0
RXRB WILD-TYPE 43 59 100 45 62 38 13
'RXRB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.843 (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 CLUS_6
ALL 40 87 54 123 56 8
RXRB MUTATED 1 3 0 3 1 0
RXRB WILD-TYPE 39 84 54 120 55 8
'RXRB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0952 (Fisher's exact test), Q value = 0.68

Table S597.  Gene #62: 'RXRB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
RXRB MUTATED 0 1 1 2 0 4 0
RXRB WILD-TYPE 44 53 70 15 52 78 23
'RXRB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.847 (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 CLUS_6
ALL 131 49 73 39 47 4
RXRB MUTATED 2 2 2 1 1 0
RXRB WILD-TYPE 129 47 71 38 46 4
'PARP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S599.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
PARP1 MUTATED 1 1 3
PARP1 WILD-TYPE 98 130 133
'PARP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.96

Table S600.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PARP1 MUTATED 1 3 0 1
PARP1 WILD-TYPE 59 160 103 46
'PARP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
PARP1 MUTATED 1 2 1 1 0
PARP1 WILD-TYPE 126 88 48 71 29
'PARP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S602.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PARP1 MUTATED 1 3 1 0
PARP1 WILD-TYPE 152 143 60 7
'PARP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.95

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 CLUS_7
ALL 44 60 103 45 63 40 13
PARP1 MUTATED 1 0 2 0 1 0 1
PARP1 WILD-TYPE 43 60 101 45 62 40 12
'PARP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S604.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PARP1 MUTATED 1 1 1 1 1 0
PARP1 WILD-TYPE 39 86 53 122 55 8
'PARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.85

Table S605.  Gene #63: 'PARP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PARP1 MUTATED 0 1 0 1 0 3 0
PARP1 WILD-TYPE 44 53 71 16 52 79 23
'PARP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.172 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
PARP1 MUTATED 0 2 1 1 1 0
PARP1 WILD-TYPE 131 47 72 38 46 4
'NBEA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S607.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
NBEA MUTATED 6 6 9
NBEA WILD-TYPE 93 125 127
'NBEA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.97

Table S608.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
NBEA MUTATED 1 12 6 2
NBEA WILD-TYPE 59 151 97 45
'NBEA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0318 (Fisher's exact test), Q value = 0.54

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 S71.  Get High-res Image Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NBEA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 0.85

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 = 0.556 (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 127 90 49 72 29
NBEA MUTATED 8 8 1 3 1
NBEA WILD-TYPE 119 82 48 69 28
'NBEA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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
ALL 153 146 61 7
NBEA MUTATED 9 9 3 0
NBEA WILD-TYPE 144 137 58 7
'NBEA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
NBEA MUTATED 2 5 9 1 2 1 1
NBEA WILD-TYPE 42 55 94 44 61 39 12
'NBEA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S614.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
NBEA MUTATED 2 5 5 6 3 0
NBEA WILD-TYPE 38 82 49 117 53 8
'NBEA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.96

Table S615.  Gene #64: 'NBEA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
NBEA MUTATED 1 1 7 1 2 7 1
NBEA WILD-TYPE 43 53 64 16 50 75 22
'NBEA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
NBEA MUTATED 7 6 3 2 2 0
NBEA WILD-TYPE 124 43 70 37 45 4
'H6PD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S617.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
H6PD MUTATED 1 1 3
H6PD WILD-TYPE 98 130 133
'H6PD MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S618.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
H6PD MUTATED 0 3 2 0
H6PD WILD-TYPE 60 160 101 47
'H6PD MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.541 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
H6PD MUTATED 2 0 1 2 0
H6PD WILD-TYPE 125 90 48 70 29
'H6PD MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 0.85

Table S620.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
H6PD MUTATED 3 0 2 0
H6PD WILD-TYPE 150 146 59 7
'H6PD MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
H6PD MUTATED 0 2 2 0 0 1 0
H6PD WILD-TYPE 44 58 101 45 63 39 13
'H6PD MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S622.  Gene #65: 'H6PD MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
H6PD MUTATED 0 1 1 1 2 0
H6PD WILD-TYPE 40 86 53 122 54 8
'H6PD MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.821 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
H6PD MUTATED 1 0 2 0 0 2 0
H6PD WILD-TYPE 43 54 69 17 52 80 23
'H6PD MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
H6PD MUTATED 2 0 1 0 2 0
H6PD WILD-TYPE 129 49 72 39 45 4
'VPS4B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S625.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
VPS4B MUTATED 2 2 1
VPS4B WILD-TYPE 97 129 135
'VPS4B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.84

Table S626.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
VPS4B MUTATED 0 5 0 0
VPS4B WILD-TYPE 60 158 103 47
'VPS4B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.224 (Fisher's exact test), Q value = 0.86

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 127 90 49 72 29
VPS4B MUTATED 0 2 0 2 0
VPS4B WILD-TYPE 127 88 49 70 29
'VPS4B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.81

Table S628.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
VPS4B MUTATED 0 2 2 0
VPS4B WILD-TYPE 153 144 59 7
'VPS4B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.546 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
VPS4B MUTATED 0 2 3 0 0 0 0
VPS4B WILD-TYPE 44 58 100 45 63 40 13
'VPS4B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.77

Table S630.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
VPS4B MUTATED 0 3 0 0 2 0
VPS4B WILD-TYPE 40 84 54 123 54 8
'VPS4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.218 (Fisher's exact test), Q value = 0.85

Table S631.  Gene #66: 'VPS4B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
VPS4B MUTATED 0 1 0 1 0 3 0
VPS4B WILD-TYPE 44 53 71 16 52 79 23
'VPS4B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.95

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 CLUS_6
ALL 131 49 73 39 47 4
VPS4B MUTATED 2 1 0 0 2 0
VPS4B WILD-TYPE 129 48 73 39 45 4
'HNRNPL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S633.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
HNRNPL MUTATED 3 2 3
HNRNPL WILD-TYPE 96 129 133
'HNRNPL MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S634.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
HNRNPL MUTATED 1 5 2 0
HNRNPL WILD-TYPE 59 158 101 47
'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 = 0.85

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

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 127 90 49 72 29
HNRNPL MUTATED 4 1 1 1 0
HNRNPL WILD-TYPE 123 89 48 71 29
'HNRNPL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S638.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
HNRNPL MUTATED 4 2 1 0
HNRNPL WILD-TYPE 149 144 60 7
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.86

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 CLUS_7
ALL 44 60 103 45 63 40 13
HNRNPL MUTATED 0 4 3 1 0 0 0
HNRNPL WILD-TYPE 44 56 100 44 63 40 13
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S640.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
HNRNPL MUTATED 0 3 2 2 1 0
HNRNPL WILD-TYPE 40 84 52 121 55 8
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.853 (Fisher's exact test), Q value = 1

Table S641.  Gene #67: 'HNRNPL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
HNRNPL MUTATED 1 2 1 1 1 2 0
HNRNPL WILD-TYPE 43 52 70 16 51 80 23
'HNRNPL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.826 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
HNRNPL MUTATED 4 2 1 0 1 0
HNRNPL WILD-TYPE 127 47 72 39 46 4
'FILIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.774 (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 99 131 136
FILIP1 MUTATED 3 6 4
FILIP1 WILD-TYPE 96 125 132
'FILIP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 0.89

Table S644.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
FILIP1 MUTATED 3 8 1 1
FILIP1 WILD-TYPE 57 155 102 46
'FILIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.706 (Fisher's exact test), Q value = 1

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 = 1

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 = 0.783 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
FILIP1 MUTATED 3 3 1 4 1
FILIP1 WILD-TYPE 124 87 48 68 28
'FILIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0984 (Fisher's exact test), Q value = 0.69

Table S648.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
FILIP1 MUTATED 4 3 4 1
FILIP1 WILD-TYPE 149 143 57 6
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.656 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
FILIP1 MUTATED 2 4 4 2 1 0 0
FILIP1 WILD-TYPE 42 56 99 43 62 40 13
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.81

Table S650.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
FILIP1 MUTATED 2 4 2 1 3 1
FILIP1 WILD-TYPE 38 83 52 122 53 7
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0905 (Fisher's exact test), Q value = 0.67

Table S651.  Gene #68: 'FILIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
FILIP1 MUTATED 0 4 2 2 0 3 0
FILIP1 WILD-TYPE 44 50 69 15 52 79 23
'FILIP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.34 (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 CLUS_6
ALL 131 49 73 39 47 4
FILIP1 MUTATED 7 1 0 1 2 0
FILIP1 WILD-TYPE 124 48 73 38 45 4
'FAM22F MUTATION STATUS' versus 'CN_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.85

Table S653.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
FAM22F MUTATED 1 0 3
FAM22F WILD-TYPE 98 131 133
'FAM22F MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.72

Table S654.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
FAM22F MUTATED 1 0 3 0
FAM22F WILD-TYPE 59 163 100 47
'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 = 0.689 (Fisher's exact test), Q value = 1

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 = 0.252 (Fisher's exact test), Q value = 0.86

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 127 90 49 72 29
FAM22F MUTATED 1 0 2 1 0
FAM22F WILD-TYPE 126 90 47 71 29
'FAM22F MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.288 (Fisher's exact test), Q value = 0.88

Table S658.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
FAM22F MUTATED 3 0 1 0
FAM22F WILD-TYPE 150 146 60 7
'FAM22F MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
FAM22F MUTATED 0 0 1 2 1 0 0
FAM22F WILD-TYPE 44 60 102 43 62 40 13
'FAM22F MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.567 (Fisher's exact test), Q value = 1

Table S660.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
FAM22F MUTATED 0 0 0 3 1 0
FAM22F WILD-TYPE 40 87 54 120 55 8
'FAM22F MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.95

Table S661.  Gene #69: 'FAM22F MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
FAM22F MUTATED 1 0 1 0 2 0 0
FAM22F WILD-TYPE 43 54 70 17 50 82 23
'FAM22F MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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 CLUS_6
ALL 131 49 73 39 47 4
FAM22F MUTATED 2 0 1 0 1 0
FAM22F WILD-TYPE 129 49 72 39 46 4
'GPSM2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.564 (Fisher's exact test), Q value = 1

Table S663.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
GPSM2 MUTATED 0 2 2
GPSM2 WILD-TYPE 99 129 134
'GPSM2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S664.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
GPSM2 MUTATED 0 2 2 0
GPSM2 WILD-TYPE 60 161 101 47
'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 = 0.688 (Fisher's exact test), Q value = 1

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 = 0.616 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
GPSM2 MUTATED 1 2 1 0 0
GPSM2 WILD-TYPE 126 88 48 72 29
'GPSM2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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
ALL 153 146 61 7
GPSM2 MUTATED 2 2 0 0
GPSM2 WILD-TYPE 151 144 61 7
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.974 (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 CLUS_7
ALL 44 60 103 45 63 40 13
GPSM2 MUTATED 0 1 1 1 1 0 0
GPSM2 WILD-TYPE 44 59 102 44 62 40 13
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S670.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
GPSM2 MUTATED 0 1 0 2 1 0
GPSM2 WILD-TYPE 40 86 54 121 55 8
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S671.  Gene #70: 'GPSM2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
GPSM2 MUTATED 0 0 2 0 0 2 0
GPSM2 WILD-TYPE 44 54 69 17 52 80 23
'GPSM2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.726 (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 CLUS_6
ALL 131 49 73 39 47 4
GPSM2 MUTATED 2 1 0 0 1 0
GPSM2 WILD-TYPE 129 48 73 39 46 4
'RCCD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.85

Table S673.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
RCCD1 MUTATED 0 4 1
RCCD1 WILD-TYPE 99 127 135
'RCCD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (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 CLUS_4
ALL 60 163 103 47
RCCD1 MUTATED 1 3 1 0
RCCD1 WILD-TYPE 59 160 102 47
'RCCD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.617 (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 127 90 49 72 29
RCCD1 MUTATED 1 2 1 0 0
RCCD1 WILD-TYPE 126 88 48 72 29
'RCCD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.45 (Fisher's exact test), Q value = 0.96

Table S676.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
RCCD1 MUTATED 1 3 0 0
RCCD1 WILD-TYPE 152 143 61 7
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
RCCD1 MUTATED 1 1 2 0 0 1 0
RCCD1 WILD-TYPE 43 59 101 45 63 39 13
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.96

Table S678.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
RCCD1 MUTATED 1 1 2 1 0 0
RCCD1 WILD-TYPE 39 86 52 122 56 8
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.98

Table S679.  Gene #71: 'RCCD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
RCCD1 MUTATED 0 1 2 1 0 1 0
RCCD1 WILD-TYPE 44 53 69 16 52 81 23
'RCCD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.393 (Fisher's exact test), Q value = 0.95

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 CLUS_6
ALL 131 49 73 39 47 4
RCCD1 MUTATED 4 0 0 1 0 0
RCCD1 WILD-TYPE 127 49 73 38 47 4
'PTGR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.85

Table S681.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
PTGR1 MUTATED 2 3 0
PTGR1 WILD-TYPE 97 128 136
'PTGR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S682.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PTGR1 MUTATED 1 2 2 0
PTGR1 WILD-TYPE 59 161 101 47
'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 = 0.655 (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 127 90 49 72 29
PTGR1 MUTATED 2 0 1 1 0
PTGR1 WILD-TYPE 125 90 48 71 29
'PTGR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.835 (Fisher's exact test), Q value = 1

Table S686.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PTGR1 MUTATED 2 1 1 0
PTGR1 WILD-TYPE 151 145 60 7
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.856 (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 CLUS_7
ALL 44 60 103 45 63 40 13
PTGR1 MUTATED 0 2 2 0 1 0 0
PTGR1 WILD-TYPE 44 58 101 45 62 40 13
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S688.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PTGR1 MUTATED 0 1 2 1 1 0
PTGR1 WILD-TYPE 40 86 52 122 55 8
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.85

Table S689.  Gene #72: 'PTGR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PTGR1 MUTATED 0 0 3 1 0 1 0
PTGR1 WILD-TYPE 44 54 68 16 52 81 23
'PTGR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.478 (Fisher's exact test), Q value = 0.97

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 CLUS_6
ALL 131 49 73 39 47 4
PTGR1 MUTATED 4 0 0 0 1 0
PTGR1 WILD-TYPE 127 49 73 39 46 4
'SAMM50 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S691.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
SAMM50 MUTATED 0 1 2
SAMM50 WILD-TYPE 99 130 134
'SAMM50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.85

Table S692.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
SAMM50 MUTATED 2 1 0 0
SAMM50 WILD-TYPE 58 162 103 47
'SAMM50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
SAMM50 MUTATED 1 0 1 1 0
SAMM50 WILD-TYPE 126 90 48 71 29
'SAMM50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S694.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
SAMM50 MUTATED 1 1 1 0
SAMM50 WILD-TYPE 152 145 60 7
'SAMM50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.56

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 CLUS_7
ALL 44 60 103 45 63 40 13
SAMM50 MUTATED 1 1 0 0 0 0 1
SAMM50 WILD-TYPE 43 59 103 45 63 40 12

Figure S72.  Get High-res Image Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SAMM50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.85

Table S696.  Gene #73: 'SAMM50 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
SAMM50 MUTATED 1 0 1 0 1 0
SAMM50 WILD-TYPE 39 87 53 123 55 8
'SAMM50 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
SAMM50 MUTATED 0 1 1 0 0 1 0
SAMM50 WILD-TYPE 44 53 70 17 52 81 23
'SAMM50 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.94

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 CLUS_6
ALL 131 49 73 39 47 4
SAMM50 MUTATED 1 0 0 1 1 0
SAMM50 WILD-TYPE 130 49 73 38 46 4
'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.88

Table S699.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
PBRM1 MUTATED 1 2 6
PBRM1 WILD-TYPE 98 129 130
'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S700.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PBRM1 MUTATED 0 5 3 1
PBRM1 WILD-TYPE 60 158 100 46
'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.432 (Fisher's exact test), Q value = 0.96

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 = 0.604 (Fisher's exact test), Q value = 1

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 = 0.0395 (Fisher's exact test), Q value = 0.56

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 127 90 49 72 29
PBRM1 MUTATED 3 0 0 5 0
PBRM1 WILD-TYPE 124 90 49 67 29

Figure S73.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.44

Table S704.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PBRM1 MUTATED 1 2 5 0
PBRM1 WILD-TYPE 152 144 56 7

Figure S74.  Get High-res Image Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.417 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
PBRM1 MUTATED 0 1 5 0 3 0 0
PBRM1 WILD-TYPE 44 59 98 45 60 40 13
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0699 (Fisher's exact test), Q value = 0.61

Table S706.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PBRM1 MUTATED 0 1 0 3 5 0
PBRM1 WILD-TYPE 40 86 54 120 51 8
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.95

Table S707.  Gene #74: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PBRM1 MUTATED 0 0 2 1 1 4 0
PBRM1 WILD-TYPE 44 54 69 16 51 78 23
'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.133 (Fisher's exact test), Q value = 0.8

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 CLUS_6
ALL 131 49 73 39 47 4
PBRM1 MUTATED 3 0 1 0 4 0
PBRM1 WILD-TYPE 128 49 72 39 43 4
'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 99 131 136
SGK269 MUTATED 2 3 3
SGK269 WILD-TYPE 97 128 133
'SGK269 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.74

Table S710.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
SGK269 MUTATED 2 6 0 0
SGK269 WILD-TYPE 58 157 103 47
'SGK269 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.88

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 = 1

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 = 0.893 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
SGK269 MUTATED 2 2 1 2 1
SGK269 WILD-TYPE 125 88 48 70 28
'SGK269 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.589 (Fisher's exact test), Q value = 1

Table S714.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
SGK269 MUTATED 2 4 2 0
SGK269 WILD-TYPE 151 142 59 7
'SGK269 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.85

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 CLUS_7
ALL 44 60 103 45 63 40 13
SGK269 MUTATED 2 0 4 0 1 0 1
SGK269 WILD-TYPE 42 60 99 45 62 40 12
'SGK269 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.94

Table S716.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
SGK269 MUTATED 2 1 2 1 2 0
SGK269 WILD-TYPE 38 86 52 122 54 8
'SGK269 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0562 (Fisher's exact test), Q value = 0.6

Table S717.  Gene #75: 'SGK269 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
SGK269 MUTATED 0 1 0 1 0 5 1
SGK269 WILD-TYPE 44 53 71 16 52 77 22
'SGK269 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.057 (Fisher's exact test), Q value = 0.6

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 CLUS_6
ALL 131 49 73 39 47 4
SGK269 MUTATED 1 2 0 2 3 0
SGK269 WILD-TYPE 130 47 73 37 44 4
'LEO1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.227 (Fisher's exact test), Q value = 0.86

Table S719.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
LEO1 MUTATED 0 1 4
LEO1 WILD-TYPE 99 130 132
'LEO1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.97

Table S720.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
LEO1 MUTATED 0 2 3 0
LEO1 WILD-TYPE 60 161 100 47
'LEO1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.77

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 = 0.718 (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 127 90 49 72 29
LEO1 MUTATED 1 1 1 2 0
LEO1 WILD-TYPE 126 89 48 70 29
'LEO1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.95

Table S724.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
LEO1 MUTATED 2 1 2 0
LEO1 WILD-TYPE 151 145 59 7
'LEO1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.629 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
LEO1 MUTATED 0 2 2 0 0 1 0
LEO1 WILD-TYPE 44 58 101 45 63 39 13
'LEO1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.51 (Fisher's exact test), Q value = 0.99

Table S726.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
LEO1 MUTATED 0 2 0 1 2 0
LEO1 WILD-TYPE 40 85 54 122 54 8
'LEO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S727.  Gene #76: 'LEO1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
LEO1 MUTATED 1 0 1 0 0 3 0
LEO1 WILD-TYPE 43 54 70 17 52 79 23
'LEO1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.439 (Fisher's exact test), Q value = 0.96

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 CLUS_6
ALL 131 49 73 39 47 4
LEO1 MUTATED 1 1 1 0 2 0
LEO1 WILD-TYPE 130 48 72 39 45 4
'CD97 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.448 (Fisher's exact test), Q value = 0.96

Table S729.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CD97 MUTATED 0 2 3
CD97 WILD-TYPE 99 129 133
'CD97 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (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 CLUS_4
ALL 60 163 103 47
CD97 MUTATED 1 3 1 0
CD97 WILD-TYPE 59 160 102 47
'CD97 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 0.98

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 127 90 49 72 29
CD97 MUTATED 2 0 0 2 0
CD97 WILD-TYPE 125 90 49 70 29
'CD97 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.168 (Fisher's exact test), Q value = 0.85

Table S732.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CD97 MUTATED 2 0 2 0
CD97 WILD-TYPE 151 146 59 7
'CD97 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.389 (Fisher's exact test), Q value = 0.95

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 CLUS_7
ALL 44 60 103 45 63 40 13
CD97 MUTATED 0 1 1 0 1 1 1
CD97 WILD-TYPE 44 59 102 45 62 39 12
'CD97 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.672 (Fisher's exact test), Q value = 1

Table S734.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CD97 MUTATED 0 1 0 2 2 0
CD97 WILD-TYPE 40 86 54 121 54 8
'CD97 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.96

Table S735.  Gene #77: 'CD97 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CD97 MUTATED 1 0 1 1 0 2 0
CD97 WILD-TYPE 43 54 70 16 52 80 23
'CD97 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.88

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 CLUS_6
ALL 131 49 73 39 47 4
CD97 MUTATED 1 0 2 0 2 0
CD97 WILD-TYPE 130 49 71 39 45 4
'SKA3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.565 (Fisher's exact test), Q value = 1

Table S737.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
SKA3 MUTATED 0 2 2
SKA3 WILD-TYPE 99 129 134
'SKA3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.88

Table S738.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
SKA3 MUTATED 0 1 3 0
SKA3 WILD-TYPE 60 162 100 47
'SKA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
SKA3 MUTATED 2 0 1 1 0
SKA3 WILD-TYPE 125 90 48 71 29
'SKA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S740.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
SKA3 MUTATED 2 1 1 0
SKA3 WILD-TYPE 151 145 60 7
'SKA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.58 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
SKA3 MUTATED 0 0 1 1 2 0 0
SKA3 WILD-TYPE 44 60 102 44 61 40 13
'SKA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.569 (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 CLUS_6
ALL 40 87 54 123 56 8
SKA3 MUTATED 0 0 0 3 1 0
SKA3 WILD-TYPE 40 87 54 120 55 8
'SKA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S743.  Gene #78: 'SKA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
SKA3 MUTATED 1 0 2 0 1 0 0
SKA3 WILD-TYPE 43 54 69 17 51 82 23
'SKA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.946 (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 CLUS_6
ALL 131 49 73 39 47 4
SKA3 MUTATED 2 0 1 0 1 0
SKA3 WILD-TYPE 129 49 72 39 46 4
'CBX4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.85

Table S745.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CBX4 MUTATED 0 4 2
CBX4 WILD-TYPE 99 127 134
'CBX4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.019 (Fisher's exact test), Q value = 0.41

Table S746.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CBX4 MUTATED 3 0 3 0
CBX4 WILD-TYPE 57 163 100 47

Figure S75.  Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'CBX4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.211 (Fisher's exact test), Q value = 0.85

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 = 0.191 (Fisher's exact test), Q value = 0.85

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 = 0.162 (Fisher's exact test), Q value = 0.85

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 127 90 49 72 29
CBX4 MUTATED 5 0 1 0 0
CBX4 WILD-TYPE 122 90 48 72 29
'CBX4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0367 (Fisher's exact test), Q value = 0.54

Table S750.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CBX4 MUTATED 6 0 0 0
CBX4 WILD-TYPE 147 146 61 7

Figure S76.  Get High-res Image Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CBX4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.86

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 CLUS_7
ALL 44 60 103 45 63 40 13
CBX4 MUTATED 2 1 0 0 2 1 0
CBX4 WILD-TYPE 42 59 103 45 61 39 13
'CBX4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.88

Table S752.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CBX4 MUTATED 2 0 1 3 0 0
CBX4 WILD-TYPE 38 87 53 120 56 8
'CBX4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0583 (Fisher's exact test), Q value = 0.6

Table S753.  Gene #79: 'CBX4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CBX4 MUTATED 0 2 2 0 0 0 2
CBX4 WILD-TYPE 44 52 69 17 52 82 21
'CBX4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 0.95

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 CLUS_6
ALL 131 49 73 39 47 4
CBX4 MUTATED 2 0 2 2 0 0
CBX4 WILD-TYPE 129 49 71 37 47 4
'MTA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.881 (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 99 131 136
MTA1 MUTATED 1 2 3
MTA1 WILD-TYPE 98 129 133
'MTA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.065 (Fisher's exact test), Q value = 0.6

Table S756.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
MTA1 MUTATED 3 2 0 1
MTA1 WILD-TYPE 57 161 103 46
'MTA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
MTA1 MUTATED 2 3 1 0 0
MTA1 WILD-TYPE 125 87 48 72 29
'MTA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.541 (Fisher's exact test), Q value = 1

Table S758.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
MTA1 MUTATED 2 4 0 0
MTA1 WILD-TYPE 151 142 61 7
'MTA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.85

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 CLUS_7
ALL 44 60 103 45 63 40 13
MTA1 MUTATED 2 3 1 0 0 0 0
MTA1 WILD-TYPE 42 57 102 45 63 40 13
'MTA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.85

Table S760.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
MTA1 MUTATED 2 2 1 0 1 0
MTA1 WILD-TYPE 38 85 53 123 55 8
'MTA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S761.  Gene #80: 'MTA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
MTA1 MUTATED 1 2 1 0 1 1 0
MTA1 WILD-TYPE 43 52 70 17 51 81 23
'MTA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
MTA1 MUTATED 2 2 0 2 0 0
MTA1 WILD-TYPE 129 47 73 37 47 4
'CRIP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.052 (Fisher's exact test), Q value = 0.59

Table S763.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
CRIP3 MUTATED 1 0 5
CRIP3 WILD-TYPE 98 131 131
'CRIP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.85

Table S764.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
CRIP3 MUTATED 0 5 0 1
CRIP3 WILD-TYPE 60 158 103 46
'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 = 0.685 (Fisher's exact test), Q value = 1

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 = 0.462 (Fisher's exact test), Q value = 0.96

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 127 90 49 72 29
CRIP3 MUTATED 1 2 0 2 1
CRIP3 WILD-TYPE 126 88 49 70 28
'CRIP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.316 (Fisher's exact test), Q value = 0.92

Table S768.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
CRIP3 MUTATED 1 3 2 0
CRIP3 WILD-TYPE 152 143 59 7
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.771 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
CRIP3 MUTATED 1 1 3 0 0 1 0
CRIP3 WILD-TYPE 43 59 100 45 63 39 13
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.257 (Fisher's exact test), Q value = 0.87

Table S770.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
CRIP3 MUTATED 1 1 0 1 3 0
CRIP3 WILD-TYPE 39 86 54 122 53 8
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S771.  Gene #81: 'CRIP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
CRIP3 MUTATED 0 1 1 0 0 4 0
CRIP3 WILD-TYPE 44 53 70 17 52 78 23
'CRIP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.6

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 CLUS_6
ALL 131 49 73 39 47 4
CRIP3 MUTATED 0 1 1 1 3 0
CRIP3 WILD-TYPE 131 48 72 38 44 4
'NR4A2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.773 (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 99 131 136
NR4A2 MUTATED 1 3 2
NR4A2 WILD-TYPE 98 128 134
'NR4A2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.612 (Fisher's exact test), Q value = 1

Table S774.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
NR4A2 MUTATED 2 3 1 0
NR4A2 WILD-TYPE 58 160 102 47
'NR4A2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.848 (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 = 0.962 (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 = 0.435 (Fisher's exact test), Q value = 0.96

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 127 90 49 72 29
NR4A2 MUTATED 3 0 0 2 0
NR4A2 WILD-TYPE 124 90 49 70 29
'NR4A2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.186 (Fisher's exact test), Q value = 0.85

Table S778.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
NR4A2 MUTATED 3 0 2 0
NR4A2 WILD-TYPE 150 146 59 7
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.649 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
NR4A2 MUTATED 1 2 3 0 0 0 0
NR4A2 WILD-TYPE 43 58 100 45 63 40 13
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.163 (Fisher's exact test), Q value = 0.85

Table S780.  Gene #82: 'NR4A2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
NR4A2 MUTATED 1 1 2 0 2 0
NR4A2 WILD-TYPE 39 86 52 123 54 8
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.68 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
NR4A2 MUTATED 1 1 1 1 0 2 0
NR4A2 WILD-TYPE 43 53 70 16 52 80 23
'NR4A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.88

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 CLUS_6
ALL 131 49 73 39 47 4
NR4A2 MUTATED 4 0 0 0 2 0
NR4A2 WILD-TYPE 127 49 73 39 45 4
'HNF1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.41

Table S783.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
HNF1A MUTATED 5 3 0
HNF1A WILD-TYPE 94 128 136

Figure S77.  Get High-res Image Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HNF1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.586 (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 CLUS_4
ALL 60 163 103 47
HNF1A MUTATED 1 4 1 2
HNF1A WILD-TYPE 59 159 102 45
'HNF1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.95

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 = 0.395 (Fisher's exact test), Q value = 0.95

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 = 0.093 (Fisher's exact test), Q value = 0.68

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 127 90 49 72 29
HNF1A MUTATED 1 4 0 1 2
HNF1A WILD-TYPE 126 86 49 71 27
'HNF1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.85

Table S788.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
HNF1A MUTATED 1 6 1 0
HNF1A WILD-TYPE 152 140 60 7
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.058 (Fisher's exact test), Q value = 0.6

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 CLUS_7
ALL 44 60 103 45 63 40 13
HNF1A MUTATED 1 2 1 0 0 3 1
HNF1A WILD-TYPE 43 58 102 45 63 37 12
'HNF1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.85

Table S790.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
HNF1A MUTATED 1 5 0 2 0 0
HNF1A WILD-TYPE 39 82 54 121 56 8
'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.84

Table S791.  Gene #83: 'HNF1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
HNF1A MUTATED 1 2 0 0 0 2 2
HNF1A WILD-TYPE 43 52 71 17 52 80 21
'HNF1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.761 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
HNF1A MUTATED 3 2 1 1 0 0
HNF1A WILD-TYPE 128 47 72 38 47 4
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 0.99

Table S793.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
KRAS MUTATED 3 1 2
KRAS WILD-TYPE 96 130 134
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.54

Table S794.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
KRAS MUTATED 1 0 3 2
KRAS WILD-TYPE 59 163 100 45

Figure S78.  Get High-res Image Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 1

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 = 0.532 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
KRAS MUTATED 3 0 1 2 0
KRAS WILD-TYPE 124 90 48 70 29
'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 0.88

Table S798.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
KRAS MUTATED 5 1 0 0
KRAS WILD-TYPE 148 145 61 7
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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 CLUS_7
ALL 44 60 103 45 63 40 13
KRAS MUTATED 0 1 2 1 2 0 0
KRAS WILD-TYPE 44 59 101 44 61 40 13
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.158 (Fisher's exact test), Q value = 0.85

Table S800.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
KRAS MUTATED 0 0 3 3 0 0
KRAS WILD-TYPE 40 87 51 120 56 8
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.97

Table S801.  Gene #84: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
KRAS MUTATED 0 0 3 0 0 1 0
KRAS WILD-TYPE 44 54 68 17 52 81 23
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

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 CLUS_6
ALL 131 49 73 39 47 4
KRAS MUTATED 2 0 1 0 1 0
KRAS WILD-TYPE 129 49 72 39 46 4
'PGBD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.632 (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 99 131 136
PGBD1 MUTATED 0 2 1
PGBD1 WILD-TYPE 99 129 135
'PGBD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (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 CLUS_4
ALL 60 163 103 47
PGBD1 MUTATED 0 2 1 0
PGBD1 WILD-TYPE 60 161 102 47
'PGBD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

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 = 0.731 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
PGBD1 MUTATED 1 1 0 1 0
PGBD1 WILD-TYPE 126 89 49 71 29
'PGBD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S808.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PGBD1 MUTATED 1 1 1 0
PGBD1 WILD-TYPE 152 145 60 7
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

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 CLUS_7
ALL 44 60 103 45 63 40 13
PGBD1 MUTATED 0 1 1 0 1 0 0
PGBD1 WILD-TYPE 44 59 102 45 62 40 13
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.92 (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 CLUS_6
ALL 40 87 54 123 56 8
PGBD1 MUTATED 0 1 0 1 1 0
PGBD1 WILD-TYPE 40 86 54 122 55 8
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S811.  Gene #85: 'PGBD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PGBD1 MUTATED 0 0 1 0 0 2 0
PGBD1 WILD-TYPE 44 54 70 17 52 80 23
'PGBD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.92

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 CLUS_6
ALL 131 49 73 39 47 4
PGBD1 MUTATED 0 1 1 0 1 0
PGBD1 WILD-TYPE 131 48 72 39 46 4
'LATS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S813.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
LATS1 MUTATED 1 4 2
LATS1 WILD-TYPE 98 127 134
'LATS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S814.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
LATS1 MUTATED 2 4 1 0
LATS1 WILD-TYPE 58 159 102 47
'LATS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.94

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 = 0.395 (Fisher's exact test), Q value = 0.95

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 = 0.418 (Fisher's exact test), Q value = 0.96

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 127 90 49 72 29
LATS1 MUTATED 1 1 2 2 0
LATS1 WILD-TYPE 126 89 47 70 29
'LATS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S818.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
LATS1 MUTATED 2 2 2 0
LATS1 WILD-TYPE 151 144 59 7
'LATS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (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 CLUS_7
ALL 44 60 103 45 63 40 13
LATS1 MUTATED 1 1 2 1 1 1 0
LATS1 WILD-TYPE 43 59 101 44 62 39 13
'LATS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S820.  Gene #86: 'LATS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
LATS1 MUTATED 1 3 1 1 1 0
LATS1 WILD-TYPE 39 84 53 122 55 8
'LATS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.797 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
LATS1 MUTATED 0 1 2 1 1 2 0
LATS1 WILD-TYPE 44 53 69 16 51 80 23
'LATS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.647 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
LATS1 MUTATED 4 1 0 1 1 0
LATS1 WILD-TYPE 127 48 73 38 46 4
'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.293 (Fisher's exact test), Q value = 0.88

Table S823.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
KEAP1 MUTATED 4 9 4
KEAP1 WILD-TYPE 95 122 132
'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.74

Table S824.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
KEAP1 MUTATED 6 8 2 1
KEAP1 WILD-TYPE 54 155 101 46
'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.96

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 = 0.934 (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 = 0.138 (Fisher's exact test), Q value = 0.81

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 127 90 49 72 29
KEAP1 MUTATED 4 6 0 4 3
KEAP1 WILD-TYPE 123 84 49 68 26
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1 (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
ALL 153 146 61 7
KEAP1 MUTATED 7 7 3 0
KEAP1 WILD-TYPE 146 139 58 7
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00414 (Fisher's exact test), Q value = 0.14

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 CLUS_7
ALL 44 60 103 45 63 40 13
KEAP1 MUTATED 4 5 1 0 5 0 2
KEAP1 WILD-TYPE 40 55 102 45 58 40 11

Figure S79.  Get High-res Image Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.96

Table S830.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
KEAP1 MUTATED 4 5 3 4 1 0
KEAP1 WILD-TYPE 36 82 51 119 55 8
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S831.  Gene #87: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
KEAP1 MUTATED 3 4 2 1 1 3 1
KEAP1 WILD-TYPE 41 50 69 16 51 79 22
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0759 (Fisher's exact test), Q value = 0.62

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 CLUS_6
ALL 131 49 73 39 47 4
KEAP1 MUTATED 5 3 1 4 1 1
KEAP1 WILD-TYPE 126 46 72 35 46 3
'SENP6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.22 (Fisher's exact test), Q value = 0.85

Table S833.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
SENP6 MUTATED 2 2 7
SENP6 WILD-TYPE 97 129 129
'SENP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S834.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
SENP6 MUTATED 1 4 4 2
SENP6 WILD-TYPE 59 159 99 45
'SENP6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00239 (Fisher's exact test), Q value = 0.1

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 S80.  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 = 0.88

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 = 0.861 (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 127 90 49 72 29
SENP6 MUTATED 5 2 1 3 0
SENP6 WILD-TYPE 122 88 48 69 29
'SENP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.727 (Fisher's exact test), Q value = 1

Table S838.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
SENP6 MUTATED 6 3 2 0
SENP6 WILD-TYPE 147 143 59 7
'SENP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.86

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 CLUS_7
ALL 44 60 103 45 63 40 13
SENP6 MUTATED 0 4 2 2 2 0 1
SENP6 WILD-TYPE 44 56 101 43 61 40 12
'SENP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S840.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
SENP6 MUTATED 0 3 1 4 3 0
SENP6 WILD-TYPE 40 84 53 119 53 8
'SENP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.96

Table S841.  Gene #88: 'SENP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
SENP6 MUTATED 1 0 3 0 4 3 0
SENP6 WILD-TYPE 43 54 68 17 48 79 23
'SENP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.645 (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 CLUS_6
ALL 131 49 73 39 47 4
SENP6 MUTATED 4 3 2 0 2 0
SENP6 WILD-TYPE 127 46 71 39 45 4
'FKBP4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.95

Table S843.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
FKBP4 MUTATED 0 3 1
FKBP4 WILD-TYPE 99 128 135
'FKBP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.95

Table S844.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
FKBP4 MUTATED 0 3 0 1
FKBP4 WILD-TYPE 60 160 103 46
'FKBP4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.678 (Fisher's exact test), Q value = 1

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 = 0.0995 (Fisher's exact test), Q value = 0.69

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 = 0.346 (Fisher's exact test), Q value = 0.94

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 127 90 49 72 29
FKBP4 MUTATED 0 2 0 1 0
FKBP4 WILD-TYPE 127 88 49 71 29
'FKBP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.339 (Fisher's exact test), Q value = 0.94

Table S848.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
FKBP4 MUTATED 0 2 1 0
FKBP4 WILD-TYPE 153 144 60 7
'FKBP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.22

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 CLUS_7
ALL 44 60 103 45 63 40 13
FKBP4 MUTATED 0 3 0 0 0 0 1
FKBP4 WILD-TYPE 44 57 103 45 63 40 12

Figure S81.  Get High-res Image Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FKBP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.218 (Fisher's exact test), Q value = 0.85

Table S850.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
FKBP4 MUTATED 0 3 0 0 1 0
FKBP4 WILD-TYPE 40 84 54 123 55 8
'FKBP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.85

Table S851.  Gene #89: 'FKBP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
FKBP4 MUTATED 1 0 0 1 0 1 0
FKBP4 WILD-TYPE 43 54 71 16 52 81 23
'FKBP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.435 (Fisher's exact test), Q value = 0.96

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 CLUS_6
ALL 131 49 73 39 47 4
FKBP4 MUTATED 1 1 0 0 1 0
FKBP4 WILD-TYPE 130 48 73 39 46 4
'FOXK2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.773 (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 99 131 136
FOXK2 MUTATED 1 3 2
FOXK2 WILD-TYPE 98 128 134
'FOXK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.96

Table S854.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
FOXK2 MUTATED 0 5 1 0
FOXK2 WILD-TYPE 60 158 102 47
'FOXK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.95

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 127 90 49 72 29
FOXK2 MUTATED 1 2 0 3 0
FOXK2 WILD-TYPE 126 88 49 69 29
'FOXK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.61 (Fisher's exact test), Q value = 1

Table S856.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
FOXK2 MUTATED 2 2 2 0
FOXK2 WILD-TYPE 151 144 59 7
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.769 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
FOXK2 MUTATED 1 1 3 0 0 1 0
FOXK2 WILD-TYPE 43 59 100 45 63 39 13
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 0.99

Table S858.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
FOXK2 MUTATED 1 2 0 1 2 0
FOXK2 WILD-TYPE 39 85 54 122 54 8
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 0.96

Table S859.  Gene #90: 'FOXK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
FOXK2 MUTATED 1 1 0 0 0 3 1
FOXK2 WILD-TYPE 43 53 71 17 52 79 22
'FOXK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.71

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 CLUS_6
ALL 131 49 73 39 47 4
FOXK2 MUTATED 0 2 1 1 2 0
FOXK2 WILD-TYPE 131 47 72 38 45 4
'DSPP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.96 (Fisher's exact test), Q value = 1

Table S861.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
DSPP MUTATED 5 8 8
DSPP WILD-TYPE 94 123 128
'DSPP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.92

Table S862.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
DSPP MUTATED 6 10 4 1
DSPP WILD-TYPE 54 153 99 46
'DSPP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

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 = 0.94

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 = 0.459 (Fisher's exact test), Q value = 0.96

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 127 90 49 72 29
DSPP MUTATED 6 3 5 5 2
DSPP WILD-TYPE 121 87 44 67 27
'DSPP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S866.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
DSPP MUTATED 9 8 4 0
DSPP WILD-TYPE 144 138 57 7
'DSPP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.985 (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 CLUS_7
ALL 44 60 103 45 63 40 13
DSPP MUTATED 3 3 6 2 5 2 0
DSPP WILD-TYPE 41 57 97 43 58 38 13
'DSPP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S868.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
DSPP MUTATED 3 3 4 6 5 0
DSPP WILD-TYPE 37 84 50 117 51 8
'DSPP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.88

Table S869.  Gene #91: 'DSPP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
DSPP MUTATED 4 3 4 2 0 5 2
DSPP WILD-TYPE 40 51 67 15 52 77 21
'DSPP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.88

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 CLUS_6
ALL 131 49 73 39 47 4
DSPP MUTATED 11 0 3 3 3 0
DSPP WILD-TYPE 120 49 70 36 44 4
'C10ORF28 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.96

Table S871.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
C10ORF28 MUTATED 0 1 3
C10ORF28 WILD-TYPE 99 130 133
'C10ORF28 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.92

Table S872.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
C10ORF28 MUTATED 2 1 1 0
C10ORF28 WILD-TYPE 58 162 102 47
'C10ORF28 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.931 (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 127 90 49 72 29
C10ORF28 MUTATED 1 1 1 1 0
C10ORF28 WILD-TYPE 126 89 48 71 29
'C10ORF28 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S874.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
C10ORF28 MUTATED 1 2 1 0
C10ORF28 WILD-TYPE 152 144 60 7
'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.76

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 CLUS_7
ALL 44 60 103 45 63 40 13
C10ORF28 MUTATED 1 0 0 0 1 2 0
C10ORF28 WILD-TYPE 43 60 103 45 62 38 13
'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.402 (Fisher's exact test), Q value = 0.95

Table S876.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
C10ORF28 MUTATED 1 0 0 3 0 0
C10ORF28 WILD-TYPE 39 87 54 120 56 8
'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.88

Table S877.  Gene #92: 'C10ORF28 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
C10ORF28 MUTATED 0 1 2 0 0 0 1
C10ORF28 WILD-TYPE 44 53 69 17 52 82 22
'C10ORF28 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.429 (Fisher's exact test), Q value = 0.96

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 CLUS_6
ALL 131 49 73 39 47 4
C10ORF28 MUTATED 1 0 2 1 0 0
C10ORF28 WILD-TYPE 130 49 71 38 47 4
'PRAMEF4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.566 (Fisher's exact test), Q value = 1

Table S879.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
PRAMEF4 MUTATED 0 2 2
PRAMEF4 WILD-TYPE 99 129 134
'PRAMEF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 0.99

Table S880.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
PRAMEF4 MUTATED 1 3 0 0
PRAMEF4 WILD-TYPE 59 160 103 47
'PRAMEF4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.583 (Fisher's exact test), Q value = 1

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 = 0.707 (Fisher's exact test), Q value = 1

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

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 127 90 49 72 29
PRAMEF4 MUTATED 1 1 1 1 0
PRAMEF4 WILD-TYPE 126 89 48 71 29
'PRAMEF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S884.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
PRAMEF4 MUTATED 2 1 1 0
PRAMEF4 WILD-TYPE 151 145 60 7
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.76 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
PRAMEF4 MUTATED 0 1 1 0 2 0 0
PRAMEF4 WILD-TYPE 44 59 102 45 61 40 13
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.86

Table S886.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
PRAMEF4 MUTATED 0 1 2 0 1 0
PRAMEF4 WILD-TYPE 40 86 52 123 55 8
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S887.  Gene #93: 'PRAMEF4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
PRAMEF4 MUTATED 1 0 1 0 0 2 0
PRAMEF4 WILD-TYPE 43 54 70 17 52 80 23
'PRAMEF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.249 (Fisher's exact test), Q value = 0.86

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 CLUS_6
ALL 131 49 73 39 47 4
PRAMEF4 MUTATED 1 1 0 0 2 0
PRAMEF4 WILD-TYPE 130 48 73 39 45 4
'RPS6KA5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.638 (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 99 131 136
RPS6KA5 MUTATED 1 1 3
RPS6KA5 WILD-TYPE 98 130 133
'RPS6KA5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S890.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
RPS6KA5 MUTATED 0 3 2 0
RPS6KA5 WILD-TYPE 60 160 101 47
'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 = 0.688 (Fisher's exact test), Q value = 1

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 = 0.721 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
RPS6KA5 MUTATED 1 1 1 2 0
RPS6KA5 WILD-TYPE 126 89 48 70 29
'RPS6KA5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.163 (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
ALL 153 146 61 7
RPS6KA5 MUTATED 0 3 2 0
RPS6KA5 WILD-TYPE 153 143 59 7
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.96

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 CLUS_7
ALL 44 60 103 45 63 40 13
RPS6KA5 MUTATED 0 1 2 0 0 2 0
RPS6KA5 WILD-TYPE 44 59 101 45 63 38 13
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S896.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
RPS6KA5 MUTATED 0 1 0 2 2 0
RPS6KA5 WILD-TYPE 40 86 54 121 54 8
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0754 (Fisher's exact test), Q value = 0.62

Table S897.  Gene #94: 'RPS6KA5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
RPS6KA5 MUTATED 1 0 0 0 0 2 2
RPS6KA5 WILD-TYPE 43 54 71 17 52 80 21
'RPS6KA5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.81

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 CLUS_6
ALL 131 49 73 39 47 4
RPS6KA5 MUTATED 0 1 2 0 2 0
RPS6KA5 WILD-TYPE 131 48 71 39 45 4
'DDX42 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 0.86

Table S899.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
DDX42 MUTATED 0 2 4
DDX42 WILD-TYPE 99 129 132
'DDX42 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.85

Table S900.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
DDX42 MUTATED 2 4 0 0
DDX42 WILD-TYPE 58 159 103 47
'DDX42 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

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 = 0.46 (Fisher's exact test), Q value = 0.96

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 = 0.902 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
DDX42 MUTATED 2 1 1 2 0
DDX42 WILD-TYPE 125 89 48 70 29
'DDX42 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.609 (Fisher's exact test), Q value = 1

Table S904.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
DDX42 MUTATED 2 2 2 0
DDX42 WILD-TYPE 151 144 59 7
'DDX42 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
DDX42 MUTATED 1 2 3 0 0 0 0
DDX42 WILD-TYPE 43 58 100 45 63 40 13
'DDX42 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S906.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
DDX42 MUTATED 1 1 1 1 2 0
DDX42 WILD-TYPE 39 86 53 122 54 8
'DDX42 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S907.  Gene #95: 'DDX42 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
DDX42 MUTATED 1 1 1 0 0 3 0
DDX42 WILD-TYPE 43 53 70 17 52 79 23
'DDX42 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.95

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 CLUS_6
ALL 131 49 73 39 47 4
DDX42 MUTATED 2 1 0 1 2 0
DDX42 WILD-TYPE 129 48 73 38 45 4
'RHCG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.85

Table S909.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
RHCG MUTATED 1 0 3
RHCG WILD-TYPE 98 131 133
'RHCG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 0.95

Table S910.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
RHCG MUTATED 0 3 0 1
RHCG WILD-TYPE 60 160 103 46
'RHCG MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

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 = 0.75

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 = 0.269 (Fisher's exact test), Q value = 0.88

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 127 90 49 72 29
RHCG MUTATED 0 1 1 2 0
RHCG WILD-TYPE 127 89 48 70 29
'RHCG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.81

Table S914.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
RHCG MUTATED 0 2 2 0
RHCG WILD-TYPE 153 144 59 7
'RHCG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
RHCG MUTATED 1 0 2 1 0 0 0
RHCG WILD-TYPE 43 60 101 44 63 40 13
'RHCG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.257 (Fisher's exact test), Q value = 0.87

Table S916.  Gene #96: 'RHCG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
RHCG MUTATED 1 0 0 1 2 0
RHCG WILD-TYPE 39 87 54 122 54 8
'RHCG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.805 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
RHCG MUTATED 0 1 0 0 1 2 0
RHCG WILD-TYPE 44 53 71 17 51 80 23
'RHCG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.125 (Fisher's exact test), Q value = 0.77

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 CLUS_6
ALL 131 49 73 39 47 4
RHCG MUTATED 0 0 1 1 2 0
RHCG WILD-TYPE 131 49 72 38 45 4
'SWAP70 MUTATION STATUS' versus 'CN_CNMF'

P value = 1 (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 99 131 136
SWAP70 MUTATED 1 2 2
SWAP70 WILD-TYPE 98 129 134
'SWAP70 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.668 (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 CLUS_4
ALL 60 163 103 47
SWAP70 MUTATED 0 2 2 1
SWAP70 WILD-TYPE 60 161 101 46
'SWAP70 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

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 = 0.465 (Fisher's exact test), Q value = 0.96

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 = 0.745 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
SWAP70 MUTATED 3 1 1 0 0
SWAP70 WILD-TYPE 124 89 48 72 29
'SWAP70 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S924.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
SWAP70 MUTATED 3 2 0 0
SWAP70 WILD-TYPE 150 144 61 7
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.523 (Fisher's exact test), Q value = 1

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 CLUS_7
ALL 44 60 103 45 63 40 13
SWAP70 MUTATED 1 1 0 1 1 1 0
SWAP70 WILD-TYPE 43 59 103 44 62 39 13
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S926.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
SWAP70 MUTATED 1 1 1 2 0 0
SWAP70 WILD-TYPE 39 86 53 121 56 8
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S927.  Gene #97: 'SWAP70 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
SWAP70 MUTATED 1 1 2 0 1 0 0
SWAP70 WILD-TYPE 43 53 69 17 51 82 23
'SWAP70 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.524 (Fisher's exact test), Q value = 1

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 CLUS_6
ALL 131 49 73 39 47 4
SWAP70 MUTATED 1 1 2 1 0 0
SWAP70 WILD-TYPE 130 48 71 38 47 4
'BIN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.96

Table S929.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
BIN1 MUTATED 0 1 3
BIN1 WILD-TYPE 99 130 133
'BIN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S930.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
BIN1 MUTATED 0 2 2 0
BIN1 WILD-TYPE 60 161 101 47
'BIN1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.54

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 S82.  Get High-res Image Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'BIN1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.86

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 = 0.695 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
BIN1 MUTATED 1 1 0 2 0
BIN1 WILD-TYPE 126 89 49 70 29
'BIN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.94

Table S934.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
BIN1 MUTATED 1 1 2 0
BIN1 WILD-TYPE 152 145 59 7
'BIN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.259 (Fisher's exact test), Q value = 0.87

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 CLUS_7
ALL 44 60 103 45 63 40 13
BIN1 MUTATED 1 0 1 0 1 0 1
BIN1 WILD-TYPE 43 60 102 45 62 40 12
'BIN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.87

Table S936.  Gene #98: 'BIN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
BIN1 MUTATED 1 0 0 1 2 0
BIN1 WILD-TYPE 39 87 54 122 54 8
'BIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.902 (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 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
BIN1 MUTATED 0 0 1 0 1 2 0
BIN1 WILD-TYPE 44 54 70 17 51 80 23
'BIN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.85

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 CLUS_6
ALL 131 49 73 39 47 4
BIN1 MUTATED 1 0 0 1 2 0
BIN1 WILD-TYPE 130 49 73 38 45 4
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.56

Table S939.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 99 131 136
SMARCA4 MUTATED 1 8 2
SMARCA4 WILD-TYPE 98 123 134

Figure S83.  Get High-res Image Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S940.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 60 163 103 47
SMARCA4 MUTATED 2 4 4 1
SMARCA4 WILD-TYPE 58 159 99 46
'SMARCA4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.88

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 = 0.0547 (Fisher's exact test), Q value = 0.6

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 = 0.779 (Fisher's exact test), Q value = 1

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 127 90 49 72 29
SMARCA4 MUTATED 5 2 2 1 0
SMARCA4 WILD-TYPE 122 88 47 71 29
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.335 (Fisher's exact test), Q value = 0.94

Table S944.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 153 146 61 7
SMARCA4 MUTATED 7 3 0 0
SMARCA4 WILD-TYPE 146 143 61 7
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 0.95

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 CLUS_7
ALL 44 60 103 45 63 40 13
SMARCA4 MUTATED 0 4 5 1 1 0 0
SMARCA4 WILD-TYPE 44 56 98 44 62 40 13
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00111 (Fisher's exact test), Q value = 0.055

Table S946.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 40 87 54 123 56 8
SMARCA4 MUTATED 0 3 6 0 1 1
SMARCA4 WILD-TYPE 40 84 48 123 55 7

Figure S84.  Get High-res Image Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.582 (Fisher's exact test), Q value = 1

Table S947.  Gene #99: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 44 54 71 17 52 82 23
SMARCA4 MUTATED 2 0 3 1 2 2 0
SMARCA4 WILD-TYPE 42 54 68 16 50 80 23
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.249 (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 CLUS_6
ALL 131 49 73 39 47 4
SMARCA4 MUTATED 8 1 1 0 0 0
SMARCA4 WILD-TYPE 123 48 72 39 47 4
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/26874154/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC/26874120/LIHC.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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