Correlation between gene mutation status and molecular subtypes
Overview
Introduction

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

Summary

Testing the association between mutation status of 70 genes and 12 molecular subtypes across 784 patients, 111 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • SETD2 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CNMF'.

  • PBRM1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • VHL mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • NF2 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

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

  • KDM5C mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • MTOR mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ZNF814 mutation correlated to 'MRNASEQ_CNMF'.

  • AR mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • KRAS mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • SLC6A14 mutation correlated to 'MIRSEQ_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • PARD6B mutation correlated to 'RPPA_CNMF',  'RPPA_CHIERARCHICAL', and 'MRNASEQ_CHIERARCHICAL'.

  • CUL3 mutation correlated to 'METHLYATION_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • PIK3CA mutation correlated to 'METHLYATION_CNMF'.

  • SMARCB1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • PCF11 mutation correlated to 'CN_CNMF',  'RPPA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CNMF'.

  • TXNIP mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • PAM mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • KDM6A mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • ARHGAP35 mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_CNMF'.

  • FAT1 mutation correlated to 'MRNASEQ_CNMF'.

  • TCEB1 mutation correlated to 'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MLL3 mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • EMG1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • SCARB2 mutation correlated to 'RPPA_CNMF'.

  • FAM20C mutation correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 70 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 111 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		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 Fisher's exact test Fisher's exact test
PBRM1 143 (18%) 641 0.00168
(0.0282) 		0.0013
(0.0223) 		1e-05
(0.00029) 		1e-05
(0.00029) 		0.0253
(0.212) 		0.00487
(0.066) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029)
VHL 196 (25%) 588 0.00057
(0.0114) 		0.00096
(0.0175) 		1e-05
(0.00029) 		1e-05
(0.00029) 		0.0105
(0.121) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029)
MTOR 34 (4%) 750 0.00014
(0.00336) 		0.00013
(0.00321) 		0.0143
(0.149) 		0.0323
(0.249) 		0.0176
(0.166) 		0.0148
(0.15) 		0.00034
(0.00714) 		5e-05
(0.00135) 		0.132
(0.598) 		0.00092
(0.0172)
TP53 38 (5%) 746 0.0005
(0.0102) 		1e-05
(0.00029) 		0.819
(1.00) 		0.0399
(0.284) 		1e-05
(0.00029) 		1e-05
(0.00029) 		2e-05
(0.00056) 		1e-05
(0.00029) 		1e-05
(0.00029) 		1e-05
(0.00029)
MET 25 (3%) 759 8e-05
(0.0021) 		0.00028
(0.00603) 		0.102
(0.514) 		0.41
(0.961) 		1e-05
(0.00029) 		1e-05
(0.00029) 		0.00011
(0.0028) 		1e-05
(0.00029) 		0.00214
(0.0346) 		0.0111
(0.125)
KDM5C 27 (3%) 757 0.00282
(0.0431) 		0.00799
(0.0959) 		0.431
(0.973) 		0.303
(0.851) 		0.00019
(0.00431) 		0.00019
(0.00431) 		1e-05
(0.00029) 		0.00549
(0.0721) 		0.313
(0.859) 		0.501
(0.997)
KDM6A 13 (2%) 771 0.00499
(0.0665) 		0.0164
(0.158) 		0.584
(1.00) 		0.371
(0.932) 		0.0241
(0.209) 		0.029
(0.232) 		0.0074
(0.0914) 		0.0124
(0.136) 		0.312
(0.859) 		0.201
(0.741)
SETD2 61 (8%) 723 0.547
(1.00) 		0.566
(1.00) 		0.00383
(0.0564) 		1e-05
(0.00029) 		0.425
(0.973) 		0.473
(0.987) 		0.0777
(0.427) 		1e-05
(0.00029) 		0.107
(0.527) 		0.00587
(0.0759) 		0.0279
(0.225) 		0.0577
(0.348)
AR 15 (2%) 769 0.00112
(0.02) 		0.0684
(0.386) 		0.832
(1.00) 		0.513
(1.00) 		0.00022
(0.00486) 		0.0148
(0.15) 		0.00876
(0.102) 		0.00756
(0.092) 		0.0644
(0.373) 		0.178
(0.706)
PCF11 13 (2%) 771 0.00454
(0.0625) 		0.496
(0.996) 		0.589
(1.00) 		0.00059
(0.0115) 		0.00614
(0.0781) 		0.037
(0.271) 		0.00452
(0.0625) 		0.199
(0.741) 		0.033
(0.25) 		0.275
(0.837)
EMG1 4 (1%) 780 0.00444
(0.0625) 		0.00428
(0.062) 		0.273
(0.837) 		0.00856
(0.101) 		0.0326
(0.249) 		1
(1.00) 		0.0009
(0.0172)
PTEN 28 (4%) 756 0.188
(0.729) 		0.0903
(0.477) 		0.772
(1.00) 		0.665
(1.00) 		0.0201
(0.184) 		0.0135
(0.144) 		0.619
(1.00) 		0.0121
(0.134) 		0.0632
(0.371) 		0.0447
(0.305)
PARD6B 8 (1%) 776 1
(1.00) 		0.339
(0.883) 		0.0107
(0.122) 		0.00737
(0.0914) 		0.0937
(0.479) 		0.0252
(0.212) 		0.216
(0.762) 		0.0403
(0.284) 		0.489
(0.994) 		0.164
(0.665)
TCEB1 4 (1%) 780 0.269
(0.837) 		0.147
(0.637) 		0.307
(0.857) 		0.266
(0.837) 		0.00237
(0.0372) 		0.0152
(0.152) 		0.188
(0.729) 		0.148
(0.637) 		0.00202
(0.0333)
NF2 16 (2%) 768 0.267
(0.837) 		0.645
(1.00) 		0.44
(0.973) 		0.141
(0.616) 		0.0229
(0.205) 		0.00239
(0.0372) 		0.219
(0.77) 		0.0941
(0.479) 		0.0587
(0.35) 		0.408
(0.961)
SLC6A14 4 (1%) 780 0.84
(1.00) 		0.806
(1.00) 		0.0718
(0.397) 		0.237
(0.796) 		0.366
(0.927) 		0.0319
(0.248) 		0.373
(0.932) 		0.0206
(0.186) 		0.378
(0.936)
CUL3 16 (2%) 768 1
(1.00) 		0.0128
(0.138) 		0.877
(1.00) 		0.0916
(0.479) 		0.0886
(0.471) 		0.00371
(0.0556) 		0.579
(1.00) 		0.191
(0.729) 		0.321
(0.859) 		0.733
(1.00)
ARHGAP35 7 (1%) 777 0.623
(1.00) 		0.0232
(0.205) 		0.76
(1.00) 		0.795
(1.00) 		0.704
(1.00) 		0.481
(0.987) 		0.0268
(0.22) 		0.229
(0.782)
MLL3 42 (5%) 742 0.78
(1.00) 		0.658
(1.00) 		0.161
(0.665) 		0.428
(0.973) 		0.291
(0.849) 		0.913
(1.00) 		0.014
(0.148) 		0.221
(0.77) 		0.0377
(0.273) 		0.0161
(0.157) 		0.442
(0.973) 		0.336
(0.882)
FAM20C 5 (1%) 779 0.0265
(0.22) 		0.203
(0.746) 		0.879
(1.00) 		0.786
(1.00) 		0.0651
(0.375) 		0.341
(0.883) 		0.0407
(0.285) 		0.0168
(0.161) 		0.403
(0.96) 		0.323
(0.862)
ZNF814 14 (2%) 770 0.537
(1.00) 		0.0675
(0.383) 		0.808
(1.00) 		0.727
(1.00) 		0.0247
(0.212) 		0.115
(0.548) 		0.0463
(0.314) 		0.0921
(0.479) 		0.517
(1.00) 		0.584
(1.00)
STAG2 15 (2%) 769 0.893
(1.00) 		0.0343
(0.255) 		0.511
(1.00) 		0.164
(0.665) 		0.575
(1.00) 		0.0304
(0.241) 		0.524
(1.00) 		0.427
(0.973) 		0.212
(0.761) 		0.449
(0.973)
KRAS 6 (1%) 778 0.226
(0.779) 		0.192
(0.729) 		0.569
(1.00) 		0.453
(0.976) 		0.0498
(0.325) 		0.301
(0.851) 		0.127
(0.584) 		0.471
(0.987) 		0.11
(0.536) 		0.00127
(0.0222)
PIK3CA 15 (2%) 769 0.275
(0.837) 		0.0235
(0.206) 		0.928
(1.00) 		0.785
(1.00) 		0.758
(1.00) 		0.508
(1.00) 		0.631
(1.00) 		0.297
(0.851) 		0.554
(1.00) 		0.714
(1.00)
SMARCB1 9 (1%) 775 0.0817
(0.443) 		0.818
(1.00) 		0.864
(1.00) 		0.738
(1.00) 		0.257
(0.826) 		0.0312
(0.245) 		0.462
(0.98) 		0.537
(1.00) 		0.2
(0.741) 		0.198
(0.741)
TXNIP 8 (1%) 776 0.278
(0.843) 		0.149
(0.637) 		0.0496
(0.325) 		0.2
(0.741) 		0.0473
(0.318) 		0.0199
(0.183) 		0.428
(0.973) 		0.153
(0.644) 		0.109
(0.536) 		0.181
(0.712)
PAM 4 (1%) 780 0.24
(0.799) 		0.145
(0.631) 		0.1
(0.509) 		0.0937
(0.479) 		0.0524
(0.334) 		0.529
(1.00) 		0.0812
(0.443) 		0.0189
(0.176)
FAT1 20 (3%) 764 0.127
(0.584) 		0.568
(1.00) 		0.952
(1.00) 		0.471
(0.987) 		0.027
(0.22) 		0.0509
(0.327) 		0.111
(0.537) 		0.314
(0.859) 		0.519
(1.00) 		0.319
(0.859)
SCARB2 4 (1%) 780 0.216
(0.762) 		0.122
(0.572) 		0.0154
(0.153) 		0.828
(1.00) 		0.265
(0.837) 		0.626
(1.00) 		0.0488
(0.325) 		0.477
(0.987)
NEFH 12 (2%) 772 0.389
(0.953) 		0.694
(1.00) 		0.0673
(0.383) 		0.844
(1.00) 		0.522
(1.00) 		0.385
(0.945) 		0.932
(1.00) 		0.299
(0.851) 		0.429
(0.973) 		0.275
(0.837)
SMARCA4 20 (3%) 764 0.433
(0.973) 		0.544
(1.00) 		0.863
(1.00) 		0.536
(1.00) 		0.245
(0.813) 		0.578
(1.00) 		0.229
(0.782) 		0.254
(0.826) 		0.618
(1.00) 		0.444
(0.973)
NFE2L2 12 (2%) 772 0.135
(0.602) 		0.0935
(0.479) 		0.668
(1.00) 		0.0504
(0.325) 		0.286
(0.843) 		0.255
(0.826) 		0.609
(1.00) 		0.37
(0.932) 		0.676
(1.00) 		0.751
(1.00)
ARID1A 18 (2%) 766 0.825
(1.00) 		0.287
(0.843) 		0.475
(0.987) 		0.498
(0.996) 		0.31
(0.859) 		0.85
(1.00) 		0.586
(1.00) 		0.637
(1.00) 		0.457
(0.976) 		0.803
(1.00)
BCLAF1 10 (1%) 774 0.222
(0.77) 		0.495
(0.996) 		0.725
(1.00) 		0.97
(1.00) 		0.165
(0.665) 		0.815
(1.00) 		0.0637
(0.372) 		0.293
(0.851) 		0.396
(0.954) 		0.82
(1.00)
ATM 20 (3%) 764 0.516
(1.00) 		0.482
(0.988) 		0.829
(1.00) 		0.984
(1.00) 		0.412
(0.964) 		0.0543
(0.343) 		0.373
(0.932) 		0.213
(0.761) 		0.834
(1.00) 		0.553
(1.00)
CACNA1C 15 (2%) 769 0.469
(0.987) 		0.0552
(0.346) 		0.87
(1.00) 		0.206
(0.748) 		0.531
(1.00) 		0.0564
(0.348) 		0.351
(0.903) 		0.121
(0.572) 		0.24
(0.799) 		0.703
(1.00)
WASL 8 (1%) 776 1
(1.00) 		0.917
(1.00) 		0.441
(0.973) 		0.851
(1.00) 		1
(1.00) 		0.88
(1.00) 		0.89
(1.00) 		0.904
(1.00) 		0.94
(1.00) 		0.395
(0.954)
DNMT3A 11 (1%) 773 0.456
(0.976) 		0.663
(1.00) 		0.164
(0.665) 		0.253
(0.826) 		0.317
(0.859) 		0.272
(0.837) 		0.918
(1.00) 		0.431
(0.973) 		0.517
(1.00) 		0.286
(0.843)
KIAA0922 7 (1%) 777 0.0841
(0.45) 		0.317
(0.859) 		0.658
(1.00) 		0.974
(1.00) 		0.133
(0.6) 		0.418
(0.971) 		0.0579
(0.348) 		0.321
(0.859) 		0.48
(0.987) 		0.409
(0.961)
GPR50 5 (1%) 779 0.74
(1.00) 		0.694
(1.00) 		0.0384
(0.276) 		0.35
(0.902) 		0.437
(0.973) 		0.748
(1.00) 		0.366
(0.927) 		0.765
(1.00)
ACSF2 11 (1%) 773 0.793
(1.00) 		0.87
(1.00) 		0.196
(0.741) 		0.15
(0.637) 		0.787
(1.00) 		0.35
(0.902) 		0.796
(1.00) 		0.742
(1.00) 		0.465
(0.985) 		0.399
(0.956)
WDR52 9 (1%) 775 1
(1.00) 		0.362
(0.926) 		0.96
(1.00) 		0.605
(1.00) 		0.878
(1.00) 		0.916
(1.00) 		0.513
(1.00) 		0.398
(0.954) 		0.446
(0.973) 		0.894
(1.00)
ALMS1 14 (2%) 770 0.377
(0.936) 		0.944
(1.00) 		0.777
(1.00) 		0.433
(0.973) 		0.912
(1.00) 		0.816
(1.00) 		0.253
(0.826) 		0.0423
(0.292) 		0.363
(0.926) 		0.82
(1.00)
NUDT11 5 (1%) 779 0.455
(0.976) 		0.285
(0.843) 		0.666
(1.00) 		0.904
(1.00) 		0.703
(1.00) 		0.264
(0.837) 		0.538
(1.00) 		0.842
(1.00)
PCK1 9 (1%) 775 0.752
(1.00) 		0.589
(1.00) 		0.656
(1.00) 		0.667
(1.00) 		0.48
(0.987) 		0.565
(1.00) 		0.757
(1.00) 		0.124
(0.575) 		0.284
(0.843) 		0.456
(0.976)
RAI1 11 (1%) 773 0.061
(0.361) 		0.701
(1.00) 		0.27
(0.837) 		0.699
(1.00) 		0.722
(1.00) 		0.318
(0.859) 		0.424
(0.973) 		0.529
(1.00) 		0.282
(0.843) 		0.67
(1.00)
GLS 9 (1%) 775 0.38
(0.94) 		0.254
(0.826) 		0.192
(0.729) 		0.0714
(0.397) 		1
(1.00) 		0.763
(1.00) 		0.34
(0.883) 		0.929
(1.00) 		0.497
(0.996) 		0.471
(0.987)
EPS15L1 10 (1%) 774 0.786
(1.00) 		0.556
(1.00) 		0.165
(0.665) 		0.895
(1.00) 		0.867
(1.00) 		0.461
(0.98) 		0.0502
(0.325) 		0.775
(1.00) 		0.393
(0.954) 		0.687
(1.00)
NOM1 6 (1%) 778 0.332
(0.88) 		0.801
(1.00) 		0.45
(0.973) 		0.891
(1.00) 		0.943
(1.00) 		0.67
(1.00) 		0.76
(1.00) 		0.937
(1.00) 		0.905
(1.00) 		0.644
(1.00)
CDK12 8 (1%) 776 0.479
(0.987) 		0.656
(1.00) 		0.533
(1.00) 		0.139
(0.611) 		0.828
(1.00) 		0.726
(1.00) 		0.731
(1.00) 		0.11
(0.536) 		0.645
(1.00) 		0.546
(1.00)
RIMBP3 5 (1%) 779 1
(1.00) 		0.522
(1.00) 		0.607
(1.00) 		0.786
(1.00) 		0.222
(0.77) 		0.0371
(0.271) 		0.434
(0.973) 		0.295
(0.851)
FAM178A 8 (1%) 776 0.0837
(0.45) 		1
(1.00) 		0.57
(1.00) 		0.733
(1.00) 		0.398
(0.954) 		0.823
(1.00) 		0.814
(1.00) 		1
(1.00)
PODXL 6 (1%) 778 0.225
(0.778) 		0.315
(0.859) 		0.214
(0.761) 		0.863
(1.00) 		1
(1.00) 		0.237
(0.796) 		1
(1.00) 		0.68
(1.00) 		0.265
(0.837) 		0.364
(0.926)
DNAJA3 3 (0%) 781 1
(1.00) 		0.512
(1.00) 		0.27
(0.837) 		0.438
(0.973) 		0.843
(1.00) 		0.865
(1.00) 		0.161
(0.665)
NASP 5 (1%) 779 0.646
(1.00) 		0.302
(0.851) 		0.155
(0.651) 		0.621
(1.00) 		0.106
(0.527) 		0.415
(0.969) 		0.291
(0.849) 		0.121
(0.572) 		0.0339
(0.254) 		0.176
(0.702)
SLC23A1 6 (1%) 778 0.877
(1.00) 		0.614
(1.00) 		0.298
(0.851) 		0.417
(0.971) 		0.269
(0.837) 		0.41
(0.961) 		0.869
(1.00) 		0.0571
(0.348)
RILPL1 5 (1%) 779 0.846
(1.00) 		0.41
(0.961) 		0.49
(0.994) 		0.248
(0.822) 		0.28
(0.843) 		0.306
(0.856) 		0.848
(1.00) 		0.206
(0.748)
NIPBL 15 (2%) 769 0.133
(0.6) 		0.521
(1.00) 		0.639
(1.00) 		0.489
(0.994) 		0.51
(1.00) 		0.505
(1.00) 		0.164
(0.665) 		0.447
(0.973) 		0.816
(1.00) 		0.971
(1.00)
FAM47A 6 (1%) 778 0.333
(0.88) 		0.556
(1.00) 		0.31
(0.859) 		0.949
(1.00) 		1
(1.00) 		0.0718
(0.397) 		0.321
(0.859) 		0.68
(1.00)
RHEB 3 (0%) 781 0.334
(0.881) 		0.237
(0.796) 		0.207
(0.748) 		1
(1.00) 		0.52
(1.00) 		0.106
(0.527) 		0.727
(1.00) 		0.149
(0.637) 		0.527
(1.00)
BRAF 5 (1%) 779 1
(1.00) 		0.444
(0.973) 		1
(1.00) 		0.753
(1.00) 		0.19
(0.729) 		0.478
(0.987) 		0.847
(1.00) 		0.258
(0.826) 		0.403
(0.96) 		0.883
(1.00)
ANK3 22 (3%) 762 0.302
(0.851) 		0.842
(1.00) 		0.284
(0.843) 		0.617
(1.00) 		0.764
(1.00) 		0.491
(0.994) 		0.384
(0.945) 		0.629
(1.00) 		0.817
(1.00) 		0.88
(1.00) 		0.761
(1.00) 		0.297
(0.851)
LHX1 4 (1%) 780 1
(1.00) 		0.377
(0.936) 		0.901
(1.00) 		0.601
(1.00) 		0.569
(1.00) 		0.617
(1.00) 		0.832
(1.00) 		0.123
(0.572)
C1ORF25 6 (1%) 778 0.59
(1.00) 		0.487
(0.994) 		0.43
(0.973) 		0.942
(1.00) 		0.762
(1.00) 		0.138
(0.611) 		0.87
(1.00) 		0.595
(1.00) 		0.449
(0.973) 		0.327
(0.868)
KDELR3 7 (1%) 777 0.23
(0.782) 		0.212
(0.761) 		0.182
(0.715) 		0.458
(0.976) 		0.112
(0.538) 		0.296
(0.851) 		0.258
(0.826) 		0.397
(0.954) 		0.201
(0.741) 		0.806
(1.00)
TTLL6 4 (1%) 780 0.165
(0.665) 		0.136
(0.602) 		0.611
(1.00) 		0.391
(0.954) 		0.042
(0.292) 		0.338
(0.883) 		0.832
(1.00) 		0.0574
(0.348)
STXBP3 5 (1%) 779 0.641
(1.00) 		0.543
(1.00) 		0.499
(0.996) 		0.667
(1.00) 		0.849
(1.00) 		0.499
(0.996)
CCBL2 3 (0%) 781 0.439
(0.973) 		0.847
(1.00) 		0.861
(1.00) 		0.795
(1.00) 		1
(1.00) 		0.282
(0.843)
B3GNT6 3 (0%) 781 0.177
(0.704) 		0.917
(1.00) 		0.714
(1.00) 		1
(1.00) 		0.86
(1.00) 		0.663
(1.00) 		1
(1.00) 		1
(1.00)
HNF1B 4 (1%) 780 0.686
(1.00) 		0.74
(1.00) 		0.0577
(0.348) 		0.19
(0.729) 		0.571
(1.00) 		0.131
(0.596) 		0.834
(1.00) 		0.595
(1.00) 		0.866
(1.00) 		0.425
(0.973)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-04 (Fisher's exact test), Q value = 0.01

Table S1.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
TP53 MUTATED 27 3 8
TP53 WILD-TYPE 286 165 290

Figure S1.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S2.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
TP53 MUTATED 25 3 3 3 2
TP53 WILD-TYPE 70 108 139 60 183

Figure S2.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S3.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
TP53 MUTATED 10 7 8 7
TP53 WILD-TYPE 153 154 162 168
'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0399 (Fisher's exact test), Q value = 0.28

Table S4.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
TP53 MUTATED 10 4 11 4 1 0 2
TP53 WILD-TYPE 168 58 94 125 51 61 80

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
TP53 MUTATED 26 5 2 5
TP53 WILD-TYPE 81 174 231 257

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S6.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
TP53 MUTATED 24 5 1 3 1 1 1 1 1
TP53 WILD-TYPE 60 45 121 74 106 31 89 51 166

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00056

Table S7.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
TP53 MUTATED 30 3 5
TP53 WILD-TYPE 299 161 277

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S8.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
TP53 MUTATED 24 9 2 3
TP53 WILD-TYPE 49 291 196 201

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

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S9.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
TP53 MUTATED 2 19 3 2
TP53 WILD-TYPE 153 47 53 94

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
TP53 MUTATED 0 3 1 0 2 2 18
TP53 WILD-TYPE 90 70 49 19 35 56 28

Figure S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.188 (Fisher's exact test), Q value = 0.73

Table S11.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PTEN MUTATED 13 2 11
PTEN WILD-TYPE 300 166 287
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0903 (Fisher's exact test), Q value = 0.48

Table S12.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PTEN MUTATED 6 6 2 0 8
PTEN WILD-TYPE 89 105 140 63 177
'PTEN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.772 (Fisher's exact test), Q value = 1

Table S13.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PTEN MUTATED 6 8 5 8
PTEN WILD-TYPE 157 153 165 167
'PTEN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.665 (Fisher's exact test), Q value = 1

Table S14.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PTEN MUTATED 7 2 5 9 1 1 2
PTEN WILD-TYPE 171 60 100 120 51 60 80
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0201 (Fisher's exact test), Q value = 0.18

Table S15.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PTEN MUTATED 7 10 3 7
PTEN WILD-TYPE 100 169 230 255

Figure S10.  Get High-res Image Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0135 (Fisher's exact test), Q value = 0.14

Table S16.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PTEN MUTATED 7 0 1 1 8 0 1 3 6
PTEN WILD-TYPE 77 50 121 76 99 32 89 49 161

Figure S11.  Get High-res Image Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S17.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PTEN MUTATED 14 4 10
PTEN WILD-TYPE 315 160 272
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0121 (Fisher's exact test), Q value = 0.13

Table S18.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PTEN MUTATED 7 11 2 8
PTEN WILD-TYPE 66 289 196 196

Figure S12.  Get High-res Image Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0632 (Fisher's exact test), Q value = 0.37

Table S19.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
PTEN MUTATED 6 5 0 1
PTEN WILD-TYPE 149 61 56 95
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0447 (Fisher's exact test), Q value = 0.31

Table S20.  Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
PTEN MUTATED 4 0 2 0 0 1 5
PTEN WILD-TYPE 86 73 48 19 37 57 41

Figure S13.  Get High-res Image Gene #2: 'PTEN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.547 (Fisher's exact test), Q value = 1

Table S21.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 15
SETD2 MUTATED 1 2 0 0
SETD2 WILD-TYPE 16 14 10 15
'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S22.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 16 10 9
SETD2 MUTATED 0 2 0 1 0
SETD2 WILD-TYPE 7 14 16 9 9
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00383 (Fisher's exact test), Q value = 0.056

Table S23.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
SETD2 MUTATED 13 15 33
SETD2 WILD-TYPE 300 153 265

Figure S14.  Get High-res Image Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S24.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
SETD2 MUTATED 3 4 13 25 3
SETD2 WILD-TYPE 92 107 129 38 182

Figure S15.  Get High-res Image Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.97

Table S25.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
SETD2 MUTATED 13 13 10 19
SETD2 WILD-TYPE 150 148 160 156
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.473 (Fisher's exact test), Q value = 0.99

Table S26.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
SETD2 MUTATED 19 6 10 6 3 3 8
SETD2 WILD-TYPE 159 56 95 123 49 58 74
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0777 (Fisher's exact test), Q value = 0.43

Table S27.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
SETD2 MUTATED 3 16 24 18
SETD2 WILD-TYPE 104 163 209 244
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S28.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
SETD2 MUTATED 2 3 20 14 12 0 5 3 2
SETD2 WILD-TYPE 82 47 102 63 95 32 85 49 165

Figure S16.  Get High-res Image Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.53

Table S29.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
SETD2 MUTATED 19 11 29
SETD2 WILD-TYPE 310 153 253
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00587 (Fisher's exact test), Q value = 0.076

Table S30.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
SETD2 MUTATED 2 31 19 7
SETD2 WILD-TYPE 71 269 179 197

Figure S17.  Get High-res Image Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0279 (Fisher's exact test), Q value = 0.23

Table S31.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
SETD2 MUTATED 9 1 4 13
SETD2 WILD-TYPE 146 65 52 83

Figure S18.  Get High-res Image Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0577 (Fisher's exact test), Q value = 0.35

Table S32.  Gene #3: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
SETD2 MUTATED 5 7 1 0 4 9 1
SETD2 WILD-TYPE 85 66 49 19 33 49 45
'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00168 (Fisher's exact test), Q value = 0.028

Table S33.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 15
PBRM1 MUTATED 9 3 1 0
PBRM1 WILD-TYPE 8 13 9 15

Figure S19.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0013 (Fisher's exact test), Q value = 0.022

Table S34.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 16 10 9
PBRM1 MUTATED 5 3 0 4 1
PBRM1 WILD-TYPE 2 13 16 6 8

Figure S20.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S35.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PBRM1 MUTATED 10 46 87
PBRM1 WILD-TYPE 303 122 211

Figure S21.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PBRM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S36.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PBRM1 MUTATED 1 12 60 27 3
PBRM1 WILD-TYPE 94 99 82 36 182

Figure S22.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.21

Table S37.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PBRM1 MUTATED 23 37 28 45
PBRM1 WILD-TYPE 140 124 142 130

Figure S23.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PBRM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00487 (Fisher's exact test), Q value = 0.066

Table S38.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PBRM1 MUTATED 44 6 13 35 12 13 10
PBRM1 WILD-TYPE 134 56 92 94 40 48 72

Figure S24.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S39.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PBRM1 MUTATED 3 40 87 12
PBRM1 WILD-TYPE 104 139 146 250

Figure S25.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S40.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PBRM1 MUTATED 2 0 57 9 26 1 31 13 3
PBRM1 WILD-TYPE 82 50 65 68 81 31 59 39 164

Figure S26.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S41.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PBRM1 MUTATED 12 26 101
PBRM1 WILD-TYPE 317 138 181

Figure S27.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S42.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PBRM1 MUTATED 1 52 79 7
PBRM1 WILD-TYPE 72 248 119 197

Figure S28.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S43.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
PBRM1 MUTATED 8 1 1 31
PBRM1 WILD-TYPE 147 65 55 65

Figure S29.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S44.  Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
PBRM1 MUTATED 5 4 0 0 4 27 1
PBRM1 WILD-TYPE 85 69 50 19 33 31 45

Figure S30.  Get High-res Image Gene #4: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'CN_CNMF'

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

Table S45.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
NEFH MUTATED 7 1 4
NEFH WILD-TYPE 306 167 294
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S46.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
NEFH MUTATED 1 1 2 2 5
NEFH WILD-TYPE 94 110 140 61 180
'NEFH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0673 (Fisher's exact test), Q value = 0.38

Table S47.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
NEFH MUTATED 2 2 0 6
NEFH WILD-TYPE 161 159 170 169
'NEFH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S48.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
NEFH MUTATED 4 0 1 1 1 1 2
NEFH WILD-TYPE 174 62 104 128 51 60 80
'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 1

Table S49.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
NEFH MUTATED 2 1 3 6
NEFH WILD-TYPE 105 178 230 256
'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.94

Table S50.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
NEFH MUTATED 0 0 3 2 1 1 0 0 5
NEFH WILD-TYPE 84 50 119 75 106 31 90 52 162
'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.932 (Fisher's exact test), Q value = 1

Table S51.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
NEFH MUTATED 6 2 4
NEFH WILD-TYPE 323 162 278
'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.299 (Fisher's exact test), Q value = 0.85

Table S52.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
NEFH MUTATED 0 3 3 6
NEFH WILD-TYPE 73 297 195 198
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.97

Table S53.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
NEFH MUTATED 4 0 0 3
NEFH WILD-TYPE 151 66 56 93
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.84

Table S54.  Gene #5: 'NEFH MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
NEFH MUTATED 2 0 2 1 0 2 0
NEFH WILD-TYPE 88 73 48 18 37 56 46
'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.011

Table S55.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 15
VHL MUTATED 10 5 1 0
VHL WILD-TYPE 7 11 9 15

Figure S31.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00096 (Fisher's exact test), Q value = 0.018

Table S56.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 16 10 9
VHL MUTATED 4 5 0 6 1
VHL WILD-TYPE 3 11 16 4 8

Figure S32.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S57.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
VHL MUTATED 2 81 113
VHL WILD-TYPE 311 87 185

Figure S33.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'VHL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S58.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
VHL MUTATED 1 30 73 19 0
VHL WILD-TYPE 94 81 69 44 185

Figure S34.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'VHL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0105 (Fisher's exact test), Q value = 0.12

Table S59.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
VHL MUTATED 50 47 30 55
VHL WILD-TYPE 113 114 140 120

Figure S35.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'VHL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S60.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
VHL MUTATED 49 0 23 49 17 20 24
VHL WILD-TYPE 129 62 82 80 35 41 58

Figure S36.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S61.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
VHL MUTATED 5 66 121 4
VHL WILD-TYPE 102 113 112 258

Figure S37.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S62.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
VHL MUTATED 2 1 59 1 49 13 47 24 0
VHL WILD-TYPE 82 49 63 76 58 19 43 28 167

Figure S38.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S63.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
VHL MUTATED 3 59 130
VHL WILD-TYPE 326 105 152

Figure S39.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S64.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
VHL MUTATED 1 84 107 0
VHL WILD-TYPE 72 216 91 204

Figure S40.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S65.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
VHL MUTATED 1 1 2 48
VHL WILD-TYPE 154 65 54 48

Figure S41.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S66.  Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
VHL MUTATED 0 5 0 0 18 28 1
VHL WILD-TYPE 90 68 50 19 19 30 45

Figure S42.  Get High-res Image Gene #6: 'VHL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.84

Table S67.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
NF2 MUTATED 9 1 6
NF2 WILD-TYPE 304 167 292
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S68.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
NF2 MUTATED 2 3 1 2 4
NF2 WILD-TYPE 93 108 141 61 181
'NF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.97

Table S69.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
NF2 MUTATED 2 4 2 6
NF2 WILD-TYPE 161 157 168 169
'NF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.62

Table S70.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
NF2 MUTATED 3 1 4 0 3 1 2
NF2 WILD-TYPE 175 61 101 129 49 60 80
'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0229 (Fisher's exact test), Q value = 0.2

Table S71.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
NF2 MUTATED 1 3 1 11
NF2 WILD-TYPE 106 176 232 251

Figure S43.  Get High-res Image Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.037

Table S72.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
NF2 MUTATED 0 6 1 1 2 1 0 0 5
NF2 WILD-TYPE 84 44 121 76 105 31 90 52 162

Figure S44.  Get High-res Image Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.77

Table S73.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
NF2 MUTATED 10 3 3
NF2 WILD-TYPE 319 161 279
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0941 (Fisher's exact test), Q value = 0.48

Table S74.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
NF2 MUTATED 0 8 1 7
NF2 WILD-TYPE 73 292 197 197
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0587 (Fisher's exact test), Q value = 0.35

Table S75.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
NF2 MUTATED 3 0 3 0
NF2 WILD-TYPE 152 66 53 96
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.408 (Fisher's exact test), Q value = 0.96

Table S76.  Gene #7: 'NF2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
NF2 MUTATED 3 3 0 0 0 0 0
NF2 WILD-TYPE 87 70 50 19 37 58 46
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0021

Table S77.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
MET MUTATED 20 1 3
MET WILD-TYPE 293 167 295

Figure S45.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00028 (Fisher's exact test), Q value = 0.006

Table S78.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
MET MUTATED 1 3 1 1 18
MET WILD-TYPE 94 108 141 62 167

Figure S46.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.51

Table S79.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
MET MUTATED 7 9 2 4
MET WILD-TYPE 156 152 168 171
'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 0.96

Table S80.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
MET MUTATED 8 0 5 5 1 0 3
MET WILD-TYPE 170 62 100 124 51 61 79
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S81.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
MET MUTATED 0 1 1 23
MET WILD-TYPE 107 178 232 239

Figure S47.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S82.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
MET MUTATED 0 3 0 1 0 0 0 1 20
MET WILD-TYPE 84 47 122 76 107 32 90 51 147

Figure S48.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00011 (Fisher's exact test), Q value = 0.0028

Table S83.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
MET MUTATED 20 4 1
MET WILD-TYPE 309 160 281

Figure S49.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S84.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
MET MUTATED 0 5 0 20
MET WILD-TYPE 73 295 198 184

Figure S50.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00214 (Fisher's exact test), Q value = 0.035

Table S85.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
MET MUTATED 14 1 2 0
MET WILD-TYPE 141 65 54 96

Figure S51.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.12

Table S86.  Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
MET MUTATED 7 4 6 0 0 0 0
MET WILD-TYPE 83 69 44 19 37 58 46

Figure S52.  Get High-res Image Gene #8: 'MET MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00282 (Fisher's exact test), Q value = 0.043

Table S87.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
KDM5C MUTATED 3 8 16
KDM5C WILD-TYPE 310 160 282

Figure S53.  Get High-res Image Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00799 (Fisher's exact test), Q value = 0.096

Table S88.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
KDM5C MUTATED 1 7 6 4 1
KDM5C WILD-TYPE 94 104 136 59 184

Figure S54.  Get High-res Image Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM5C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.431 (Fisher's exact test), Q value = 0.97

Table S89.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
KDM5C MUTATED 4 7 4 9
KDM5C WILD-TYPE 159 154 166 166
'KDM5C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.303 (Fisher's exact test), Q value = 0.85

Table S90.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
KDM5C MUTATED 10 0 5 6 1 1 1
KDM5C WILD-TYPE 168 62 100 123 51 60 81
'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0043

Table S91.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
KDM5C MUTATED 1 12 12 1
KDM5C WILD-TYPE 106 167 221 261

Figure S55.  Get High-res Image Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.0043

Table S92.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
KDM5C MUTATED 1 0 8 0 6 0 3 7 1
KDM5C WILD-TYPE 83 50 114 77 101 32 87 45 166

Figure S56.  Get High-res Image Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00029

Table S93.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
KDM5C MUTATED 2 3 22
KDM5C WILD-TYPE 327 161 260

Figure S57.  Get High-res Image Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00549 (Fisher's exact test), Q value = 0.072

Table S94.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
KDM5C MUTATED 1 13 12 1
KDM5C WILD-TYPE 72 287 186 203

Figure S58.  Get High-res Image Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.313 (Fisher's exact test), Q value = 0.86

Table S95.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
KDM5C MUTATED 1 1 0 3
KDM5C WILD-TYPE 154 65 56 93
'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.501 (Fisher's exact test), Q value = 1

Table S96.  Gene #9: 'KDM5C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
KDM5C MUTATED 1 0 0 0 1 2 1
KDM5C WILD-TYPE 89 73 50 19 36 56 45
'MTOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00014 (Fisher's exact test), Q value = 0.0034

Table S97.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
MTOR MUTATED 3 10 21
MTOR WILD-TYPE 310 158 277

Figure S59.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00013 (Fisher's exact test), Q value = 0.0032

Table S98.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
MTOR MUTATED 6 6 10 7 0
MTOR WILD-TYPE 89 105 132 56 185

Figure S60.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0143 (Fisher's exact test), Q value = 0.15

Table S99.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
MTOR MUTATED 3 7 4 15
MTOR WILD-TYPE 160 154 166 160

Figure S61.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'MTOR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0323 (Fisher's exact test), Q value = 0.25

Table S100.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
MTOR MUTATED 13 3 2 5 5 0 1
MTOR WILD-TYPE 165 59 103 124 47 61 81

Figure S62.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.17

Table S101.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
MTOR MUTATED 4 12 14 4
MTOR WILD-TYPE 103 167 219 258

Figure S63.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.15

Table S102.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
MTOR MUTATED 3 3 4 2 8 1 9 3 1
MTOR WILD-TYPE 81 47 118 75 99 31 81 49 166

Figure S64.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00034 (Fisher's exact test), Q value = 0.0071

Table S103.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
MTOR MUTATED 4 9 21
MTOR WILD-TYPE 325 155 261

Figure S65.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0014

Table S104.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
MTOR MUTATED 0 23 10 1
MTOR WILD-TYPE 73 277 188 203

Figure S66.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.132 (Fisher's exact test), Q value = 0.6

Table S105.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
MTOR MUTATED 2 3 2 6
MTOR WILD-TYPE 153 63 54 90
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00092 (Fisher's exact test), Q value = 0.017

Table S106.  Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
MTOR MUTATED 0 4 0 3 1 5 0
MTOR WILD-TYPE 90 69 50 16 36 53 46

Figure S67.  Get High-res Image Gene #10: 'MTOR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.537 (Fisher's exact test), Q value = 1

Table S107.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
ZNF814 MUTATED 8 2 4
ZNF814 WILD-TYPE 305 166 294
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0675 (Fisher's exact test), Q value = 0.38

Table S108.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
ZNF814 MUTATED 4 2 0 3 5
ZNF814 WILD-TYPE 91 109 142 60 180
'ZNF814 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.808 (Fisher's exact test), Q value = 1

Table S109.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
ZNF814 MUTATED 4 3 3 2
ZNF814 WILD-TYPE 159 158 167 173
'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S110.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
ZNF814 MUTATED 5 2 2 1 1 0 1
ZNF814 WILD-TYPE 173 60 103 128 51 61 81
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.21

Table S111.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
ZNF814 MUTATED 4 1 1 8
ZNF814 WILD-TYPE 103 178 232 254

Figure S68.  Get High-res Image Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.115 (Fisher's exact test), Q value = 0.55

Table S112.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
ZNF814 MUTATED 4 0 1 4 1 0 0 0 4
ZNF814 WILD-TYPE 80 50 121 73 106 32 90 52 163
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0463 (Fisher's exact test), Q value = 0.31

Table S113.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
ZNF814 MUTATED 9 4 1
ZNF814 WILD-TYPE 320 160 281

Figure S69.  Get High-res Image Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0921 (Fisher's exact test), Q value = 0.48

Table S114.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
ZNF814 MUTATED 3 4 1 6
ZNF814 WILD-TYPE 70 296 197 198
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S115.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
ZNF814 MUTATED 4 3 2 1
ZNF814 WILD-TYPE 151 63 54 95
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S116.  Gene #11: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
ZNF814 MUTATED 3 3 0 1 0 1 2
ZNF814 WILD-TYPE 87 70 50 18 37 57 44
'AR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00112 (Fisher's exact test), Q value = 0.02

Table S117.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
AR MUTATED 13 0 2
AR WILD-TYPE 300 168 296

Figure S70.  Get High-res Image Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'AR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0684 (Fisher's exact test), Q value = 0.39

Table S118.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
AR MUTATED 2 1 1 1 10
AR WILD-TYPE 93 110 141 62 175
'AR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S119.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
AR MUTATED 2 2 4 2
AR WILD-TYPE 161 159 166 173
'AR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S120.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
AR MUTATED 3 3 1 1 0 1 1
AR WILD-TYPE 175 59 104 128 52 60 81
'AR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00022 (Fisher's exact test), Q value = 0.0049

Table S121.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
AR MUTATED 1 0 1 13
AR WILD-TYPE 106 179 232 249

Figure S71.  Get High-res Image Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'AR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0148 (Fisher's exact test), Q value = 0.15

Table S122.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
AR MUTATED 1 1 0 5 0 0 1 0 7
AR WILD-TYPE 83 49 122 72 107 32 89 52 160

Figure S72.  Get High-res Image Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'AR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00876 (Fisher's exact test), Q value = 0.1

Table S123.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
AR MUTATED 12 2 1
AR WILD-TYPE 317 162 281

Figure S73.  Get High-res Image Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'AR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00756 (Fisher's exact test), Q value = 0.092

Table S124.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
AR MUTATED 1 3 1 10
AR WILD-TYPE 72 297 197 194

Figure S74.  Get High-res Image Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0644 (Fisher's exact test), Q value = 0.37

Table S125.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
AR MUTATED 9 2 2 0
AR WILD-TYPE 146 64 54 96
'AR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 0.71

Table S126.  Gene #12: 'AR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
AR MUTATED 7 2 2 1 0 0 1
AR WILD-TYPE 83 71 48 18 37 58 45
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.893 (Fisher's exact test), Q value = 1

Table S127.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
STAG2 MUTATED 6 4 5
STAG2 WILD-TYPE 307 164 293
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.25

Table S128.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
STAG2 MUTATED 1 6 1 3 2
STAG2 WILD-TYPE 94 105 141 60 183

Figure S75.  Get High-res Image Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'STAG2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.511 (Fisher's exact test), Q value = 1

Table S129.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
STAG2 MUTATED 3 1 3 5
STAG2 WILD-TYPE 160 160 167 170
'STAG2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.66

Table S130.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
STAG2 MUTATED 1 3 1 3 2 0 2
STAG2 WILD-TYPE 177 59 104 126 50 61 80
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.575 (Fisher's exact test), Q value = 1

Table S131.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
STAG2 MUTATED 3 5 3 4
STAG2 WILD-TYPE 104 174 230 258
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0304 (Fisher's exact test), Q value = 0.24

Table S132.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
STAG2 MUTATED 0 3 0 3 3 1 3 1 1
STAG2 WILD-TYPE 84 47 122 74 104 31 87 51 166

Figure S76.  Get High-res Image Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.524 (Fisher's exact test), Q value = 1

Table S133.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
STAG2 MUTATED 6 5 4
STAG2 WILD-TYPE 323 159 278
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.427 (Fisher's exact test), Q value = 0.97

Table S134.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
STAG2 MUTATED 0 9 3 3
STAG2 WILD-TYPE 73 291 195 201
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.76

Table S135.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
STAG2 MUTATED 3 1 4 2
STAG2 WILD-TYPE 152 65 52 94
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 0.97

Table S136.  Gene #13: 'STAG2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
STAG2 MUTATED 2 3 1 0 3 1 0
STAG2 WILD-TYPE 88 70 49 19 34 57 46
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.226 (Fisher's exact test), Q value = 0.78

Table S137.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
KRAS MUTATED 2 3 1
KRAS WILD-TYPE 311 165 297
'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.73

Table S138.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
KRAS MUTATED 3 1 0 0 2
KRAS WILD-TYPE 92 110 142 63 183
'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S139.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
KRAS MUTATED 0 0 2 1
KRAS WILD-TYPE 163 161 168 174
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.453 (Fisher's exact test), Q value = 0.98

Table S140.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
KRAS MUTATED 0 1 1 1 0 0 0
KRAS WILD-TYPE 178 61 104 128 52 61 82
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.33

Table S141.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
KRAS MUTATED 3 1 0 2
KRAS WILD-TYPE 104 178 233 260

Figure S77.  Get High-res Image Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.301 (Fisher's exact test), Q value = 0.85

Table S142.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
KRAS MUTATED 3 0 0 0 1 0 0 0 2
KRAS WILD-TYPE 81 50 122 77 106 32 90 52 165
'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.58

Table S143.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
KRAS MUTATED 4 2 0
KRAS WILD-TYPE 325 162 282
'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.471 (Fisher's exact test), Q value = 0.99

Table S144.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
KRAS MUTATED 0 4 0 2
KRAS WILD-TYPE 73 296 198 202
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.54

Table S145.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
KRAS MUTATED 2 3 0 0
KRAS WILD-TYPE 153 63 56 96
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00127 (Fisher's exact test), Q value = 0.022

Table S146.  Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
KRAS MUTATED 1 0 1 3 0 0 0
KRAS WILD-TYPE 89 73 49 16 37 58 46

Figure S78.  Get High-res Image Gene #14: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SLC6A14 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.84 (Fisher's exact test), Q value = 1

Table S147.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
SLC6A14 MUTATED 1 1 2
SLC6A14 WILD-TYPE 312 167 296
'SLC6A14 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S148.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
SLC6A14 MUTATED 1 0 2 1
SLC6A14 WILD-TYPE 162 161 168 174
'SLC6A14 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0718 (Fisher's exact test), Q value = 0.4

Table S149.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
SLC6A14 MUTATED 0 1 0 0 1 1 1
SLC6A14 WILD-TYPE 178 61 105 129 51 60 81
'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.8

Table S150.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
SLC6A14 MUTATED 1 2 1 0
SLC6A14 WILD-TYPE 106 177 232 262
'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 0.93

Table S151.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
SLC6A14 MUTATED 1 1 0 0 1 0 1 0 0
SLC6A14 WILD-TYPE 83 49 122 77 106 32 89 52 167
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.25

Table S152.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
SLC6A14 MUTATED 1 3 0
SLC6A14 WILD-TYPE 328 161 282

Figure S79.  Get High-res Image Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.93

Table S153.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
SLC6A14 MUTATED 1 2 1 0
SLC6A14 WILD-TYPE 72 298 197 204
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0206 (Fisher's exact test), Q value = 0.19

Table S154.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
SLC6A14 MUTATED 0 1 2 0
SLC6A14 WILD-TYPE 155 65 54 96

Figure S80.  Get High-res Image Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.378 (Fisher's exact test), Q value = 0.94

Table S155.  Gene #15: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
SLC6A14 MUTATED 0 1 0 0 1 0 1
SLC6A14 WILD-TYPE 90 72 50 19 36 58 45
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.97

Table S156.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
SMARCA4 MUTATED 10 2 8
SMARCA4 WILD-TYPE 303 166 290
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.544 (Fisher's exact test), Q value = 1

Table S157.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
SMARCA4 MUTATED 3 2 2 1 8
SMARCA4 WILD-TYPE 92 109 140 62 177
'SMARCA4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S158.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
SMARCA4 MUTATED 4 3 5 6
SMARCA4 WILD-TYPE 159 158 165 169
'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.536 (Fisher's exact test), Q value = 1

Table S159.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
SMARCA4 MUTATED 7 1 4 1 2 2 1
SMARCA4 WILD-TYPE 171 61 101 128 50 59 81
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.81

Table S160.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
SMARCA4 MUTATED 2 2 5 11
SMARCA4 WILD-TYPE 105 177 228 251
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.578 (Fisher's exact test), Q value = 1

Table S161.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
SMARCA4 MUTATED 1 2 2 1 2 0 2 1 9
SMARCA4 WILD-TYPE 83 48 120 76 105 32 88 51 158
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.78

Table S162.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
SMARCA4 MUTATED 12 2 5
SMARCA4 WILD-TYPE 317 162 277
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 0.83

Table S163.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
SMARCA4 MUTATED 1 6 3 9
SMARCA4 WILD-TYPE 72 294 195 195
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.618 (Fisher's exact test), Q value = 1

Table S164.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
SMARCA4 MUTATED 6 1 1 1
SMARCA4 WILD-TYPE 149 65 55 95
'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 0.97

Table S165.  Gene #16: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
SMARCA4 MUTATED 5 0 1 0 1 1 1
SMARCA4 WILD-TYPE 85 73 49 19 36 57 45
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.6

Table S166.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
NFE2L2 MUTATED 7 0 5
NFE2L2 WILD-TYPE 306 168 293
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0935 (Fisher's exact test), Q value = 0.48

Table S167.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
NFE2L2 MUTATED 1 1 0 3 4
NFE2L2 WILD-TYPE 94 110 142 60 181
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.668 (Fisher's exact test), Q value = 1

Table S168.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
NFE2L2 MUTATED 2 2 5 3
NFE2L2 WILD-TYPE 161 159 165 172
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0504 (Fisher's exact test), Q value = 0.33

Table S169.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
NFE2L2 MUTATED 2 3 1 1 3 2 0
NFE2L2 WILD-TYPE 176 59 104 128 49 59 82
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.286 (Fisher's exact test), Q value = 0.84

Table S170.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
NFE2L2 MUTATED 1 4 1 6
NFE2L2 WILD-TYPE 106 175 232 256
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.83

Table S171.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
NFE2L2 MUTATED 0 1 1 3 4 0 0 0 3
NFE2L2 WILD-TYPE 84 49 121 74 103 32 90 52 164
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S172.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
NFE2L2 MUTATED 7 2 3
NFE2L2 WILD-TYPE 322 162 279
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.93

Table S173.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
NFE2L2 MUTATED 0 4 2 6
NFE2L2 WILD-TYPE 73 296 196 198
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.676 (Fisher's exact test), Q value = 1

Table S174.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
NFE2L2 MUTATED 4 0 1 1
NFE2L2 WILD-TYPE 151 66 55 95
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.751 (Fisher's exact test), Q value = 1

Table S175.  Gene #17: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
NFE2L2 MUTATED 3 1 1 0 1 0 0
NFE2L2 WILD-TYPE 87 72 49 19 36 58 46
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.825 (Fisher's exact test), Q value = 1

Table S176.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
ARID1A MUTATED 6 4 8
ARID1A WILD-TYPE 307 164 290
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.84

Table S177.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
ARID1A MUTATED 0 4 6 1 5
ARID1A WILD-TYPE 95 107 136 62 180
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 0.99

Table S178.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
ARID1A MUTATED 5 6 2 4
ARID1A WILD-TYPE 158 155 168 171
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.498 (Fisher's exact test), Q value = 1

Table S179.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
ARID1A MUTATED 4 0 3 2 3 2 3
ARID1A WILD-TYPE 174 62 102 127 49 59 79
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.86

Table S180.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
ARID1A MUTATED 0 5 5 8
ARID1A WILD-TYPE 107 174 228 254
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S181.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
ARID1A MUTATED 0 1 2 2 3 1 3 1 5
ARID1A WILD-TYPE 84 49 120 75 104 31 87 51 162
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.586 (Fisher's exact test), Q value = 1

Table S182.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
ARID1A MUTATED 8 2 8
ARID1A WILD-TYPE 321 162 274
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.637 (Fisher's exact test), Q value = 1

Table S183.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
ARID1A MUTATED 0 7 5 6
ARID1A WILD-TYPE 73 293 193 198
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.98

Table S184.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
ARID1A MUTATED 6 0 1 3
ARID1A WILD-TYPE 149 66 55 93
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.803 (Fisher's exact test), Q value = 1

Table S185.  Gene #18: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
ARID1A MUTATED 3 3 2 0 0 2 0
ARID1A WILD-TYPE 87 70 48 19 37 56 46
'BCLAF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 0.77

Table S186.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
BCLAF1 MUTATED 7 1 2
BCLAF1 WILD-TYPE 306 167 296
'BCLAF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.495 (Fisher's exact test), Q value = 1

Table S187.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
BCLAF1 MUTATED 2 0 2 1 5
BCLAF1 WILD-TYPE 93 111 140 62 180
'BCLAF1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S188.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
BCLAF1 MUTATED 3 2 3 1
BCLAF1 WILD-TYPE 160 159 167 174
'BCLAF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.97 (Fisher's exact test), Q value = 1

Table S189.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
BCLAF1 MUTATED 2 0 2 2 1 1 1
BCLAF1 WILD-TYPE 176 62 103 127 51 60 81
'BCLAF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.66

Table S190.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
BCLAF1 MUTATED 3 1 1 5
BCLAF1 WILD-TYPE 104 178 232 257
'BCLAF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.815 (Fisher's exact test), Q value = 1

Table S191.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
BCLAF1 MUTATED 2 1 1 1 1 0 0 0 4
BCLAF1 WILD-TYPE 82 49 121 76 106 32 90 52 163
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0637 (Fisher's exact test), Q value = 0.37

Table S192.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
BCLAF1 MUTATED 8 1 1
BCLAF1 WILD-TYPE 321 163 281
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.293 (Fisher's exact test), Q value = 0.85

Table S193.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
BCLAF1 MUTATED 2 3 1 4
BCLAF1 WILD-TYPE 71 297 197 200
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S194.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
BCLAF1 MUTATED 2 3 1 1
BCLAF1 WILD-TYPE 153 63 55 95
'BCLAF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S195.  Gene #19: 'BCLAF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
BCLAF1 MUTATED 2 2 0 0 0 1 2
BCLAF1 WILD-TYPE 88 71 50 19 37 57 44
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.516 (Fisher's exact test), Q value = 1

Table S196.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
ATM MUTATED 6 6 8
ATM WILD-TYPE 307 162 290
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.482 (Fisher's exact test), Q value = 0.99

Table S197.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
ATM MUTATED 3 4 5 2 2
ATM WILD-TYPE 92 107 137 61 183
'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.829 (Fisher's exact test), Q value = 1

Table S198.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
ATM MUTATED 5 3 4 6
ATM WILD-TYPE 158 158 166 169
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.984 (Fisher's exact test), Q value = 1

Table S199.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
ATM MUTATED 5 2 3 4 1 2 1
ATM WILD-TYPE 173 60 102 125 51 59 81
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.412 (Fisher's exact test), Q value = 0.96

Table S200.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
ATM MUTATED 3 4 9 4
ATM WILD-TYPE 104 175 224 258
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0543 (Fisher's exact test), Q value = 0.34

Table S201.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
ATM MUTATED 3 0 6 1 1 3 4 0 2
ATM WILD-TYPE 81 50 116 76 106 29 86 52 165
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.93

Table S202.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
ATM MUTATED 6 3 10
ATM WILD-TYPE 323 161 272
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.213 (Fisher's exact test), Q value = 0.76

Table S203.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
ATM MUTATED 3 7 7 2
ATM WILD-TYPE 70 293 191 202
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S204.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
ATM MUTATED 3 2 2 2
ATM WILD-TYPE 152 64 54 94
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.553 (Fisher's exact test), Q value = 1

Table S205.  Gene #20: 'ATM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
ATM MUTATED 1 4 1 0 0 1 2
ATM WILD-TYPE 89 69 49 19 37 57 44
'CACNA1C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.99

Table S206.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
CACNA1C MUTATED 4 3 8
CACNA1C WILD-TYPE 309 165 290
'CACNA1C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0552 (Fisher's exact test), Q value = 0.35

Table S207.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
CACNA1C MUTATED 3 3 2 4 1
CACNA1C WILD-TYPE 92 108 140 59 184
'CACNA1C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S208.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
CACNA1C MUTATED 4 2 4 3
CACNA1C WILD-TYPE 159 159 166 172
'CACNA1C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.75

Table S209.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
CACNA1C MUTATED 1 1 3 3 3 0 2
CACNA1C WILD-TYPE 177 61 102 126 49 61 80
'CACNA1C MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S210.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
CACNA1C MUTATED 3 5 4 3
CACNA1C WILD-TYPE 104 174 229 259
'CACNA1C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0564 (Fisher's exact test), Q value = 0.35

Table S211.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
CACNA1C MUTATED 3 1 4 0 2 3 1 0 1
CACNA1C WILD-TYPE 81 49 118 77 105 29 89 52 166
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 0.9

Table S212.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
CACNA1C MUTATED 4 3 8
CACNA1C WILD-TYPE 325 161 274
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.57

Table S213.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
CACNA1C MUTATED 3 8 3 1
CACNA1C WILD-TYPE 70 292 195 203
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.8

Table S214.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
CACNA1C MUTATED 1 2 2 1
CACNA1C WILD-TYPE 154 64 54 95
'CACNA1C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S215.  Gene #21: 'CACNA1C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
CACNA1C MUTATED 1 2 0 0 0 1 2
CACNA1C WILD-TYPE 89 71 50 19 37 57 44
'PARD6B MUTATION STATUS' versus 'CN_CNMF'

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

Table S216.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PARD6B MUTATED 3 2 3
PARD6B WILD-TYPE 310 166 295
'PARD6B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.88

Table S217.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PARD6B MUTATED 1 0 1 1 5
PARD6B WILD-TYPE 94 111 141 62 180
'PARD6B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0107 (Fisher's exact test), Q value = 0.12

Table S218.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PARD6B MUTATED 0 1 5 0
PARD6B WILD-TYPE 163 160 165 175

Figure S81.  Get High-res Image Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'PARD6B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00737 (Fisher's exact test), Q value = 0.091

Table S219.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PARD6B MUTATED 1 3 0 0 0 2 0
PARD6B WILD-TYPE 177 59 105 129 52 59 82

Figure S82.  Get High-res Image Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PARD6B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0937 (Fisher's exact test), Q value = 0.48

Table S220.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PARD6B MUTATED 1 0 1 6
PARD6B WILD-TYPE 106 179 232 256
'PARD6B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0252 (Fisher's exact test), Q value = 0.21

Table S221.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PARD6B MUTATED 0 1 0 4 0 0 0 1 2
PARD6B WILD-TYPE 84 49 122 73 107 32 90 51 165

Figure S83.  Get High-res Image Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PARD6B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.76

Table S222.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PARD6B MUTATED 6 1 1
PARD6B WILD-TYPE 323 163 281
'PARD6B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0403 (Fisher's exact test), Q value = 0.28

Table S223.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PARD6B MUTATED 0 1 1 6
PARD6B WILD-TYPE 73 299 197 198

Figure S84.  Get High-res Image Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PARD6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.489 (Fisher's exact test), Q value = 0.99

Table S224.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
PARD6B MUTATED 5 0 1 1
PARD6B WILD-TYPE 150 66 55 95
'PARD6B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.66

Table S225.  Gene #22: 'PARD6B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
PARD6B MUTATED 5 0 0 0 1 1 0
PARD6B WILD-TYPE 85 73 50 19 36 57 46
'CUL3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S226.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
CUL3 MUTATED 7 3 6
CUL3 WILD-TYPE 306 165 292
'CUL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.14

Table S227.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
CUL3 MUTATED 0 2 1 0 10
CUL3 WILD-TYPE 95 109 141 63 175

Figure S85.  Get High-res Image Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'CUL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S228.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
CUL3 MUTATED 4 2 4 4
CUL3 WILD-TYPE 159 159 166 171
'CUL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0916 (Fisher's exact test), Q value = 0.48

Table S229.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
CUL3 MUTATED 4 1 0 3 4 0 2
CUL3 WILD-TYPE 174 61 105 126 48 61 80
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0886 (Fisher's exact test), Q value = 0.47

Table S230.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
CUL3 MUTATED 0 2 4 10
CUL3 WILD-TYPE 107 177 229 252
'CUL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00371 (Fisher's exact test), Q value = 0.056

Table S231.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
CUL3 MUTATED 0 0 5 7 1 0 0 0 3
CUL3 WILD-TYPE 84 50 117 70 106 32 90 52 164

Figure S86.  Get High-res Image Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'CUL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S232.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
CUL3 MUTATED 9 2 5
CUL3 WILD-TYPE 320 162 277
'CUL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.73

Table S233.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
CUL3 MUTATED 0 5 3 8
CUL3 WILD-TYPE 73 295 195 196
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.86

Table S234.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
CUL3 MUTATED 7 0 1 2
CUL3 WILD-TYPE 148 66 55 94
'CUL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S235.  Gene #23: 'CUL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
CUL3 MUTATED 5 2 1 0 1 1 0
CUL3 WILD-TYPE 85 71 49 19 36 57 46
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.84

Table S236.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PIK3CA MUTATED 4 2 9
PIK3CA WILD-TYPE 309 166 289
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0235 (Fisher's exact test), Q value = 0.21

Table S237.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PIK3CA MUTATED 0 0 3 4 3
PIK3CA WILD-TYPE 95 111 139 59 182

Figure S87.  Get High-res Image Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.928 (Fisher's exact test), Q value = 1

Table S238.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PIK3CA MUTATED 3 2 4 4
PIK3CA WILD-TYPE 160 159 166 171
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S239.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PIK3CA MUTATED 2 1 2 3 2 2 1
PIK3CA WILD-TYPE 176 61 103 126 50 59 81
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S240.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PIK3CA MUTATED 1 4 6 4
PIK3CA WILD-TYPE 106 175 227 258
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S241.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PIK3CA MUTATED 0 1 2 2 4 1 3 0 2
PIK3CA WILD-TYPE 84 49 120 75 103 31 87 52 165
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S242.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PIK3CA MUTATED 8 3 4
PIK3CA WILD-TYPE 321 161 278
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.85

Table S243.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PIK3CA MUTATED 0 9 4 2
PIK3CA WILD-TYPE 73 291 194 202
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S244.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
PIK3CA MUTATED 2 1 1 0
PIK3CA WILD-TYPE 153 65 55 96
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S245.  Gene #24: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
PIK3CA MUTATED 2 2 0 0 0 0 0
PIK3CA WILD-TYPE 88 71 50 19 37 58 46
'SMARCB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0817 (Fisher's exact test), Q value = 0.44

Table S246.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
SMARCB1 MUTATED 7 1 1
SMARCB1 WILD-TYPE 306 167 297
'SMARCB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.818 (Fisher's exact test), Q value = 1

Table S247.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
SMARCB1 MUTATED 2 2 1 1 2
SMARCB1 WILD-TYPE 93 109 141 62 183
'SMARCB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S248.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
SMARCB1 MUTATED 2 1 2 1
SMARCB1 WILD-TYPE 161 160 168 174
'SMARCB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S249.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
SMARCB1 MUTATED 2 1 1 0 0 1 1
SMARCB1 WILD-TYPE 176 61 104 129 52 60 81
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 0.83

Table S250.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
SMARCB1 MUTATED 1 1 1 6
SMARCB1 WILD-TYPE 106 178 232 256
'SMARCB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.25

Table S251.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
SMARCB1 MUTATED 1 0 0 5 1 0 1 0 1
SMARCB1 WILD-TYPE 83 50 122 72 106 32 89 52 166

Figure S88.  Get High-res Image Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.98

Table S252.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
SMARCB1 MUTATED 6 1 2
SMARCB1 WILD-TYPE 323 163 280
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.537 (Fisher's exact test), Q value = 1

Table S253.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
SMARCB1 MUTATED 1 3 1 4
SMARCB1 WILD-TYPE 72 297 197 200
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.74

Table S254.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
SMARCB1 MUTATED 2 1 2 0
SMARCB1 WILD-TYPE 153 65 54 96
'SMARCB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.198 (Fisher's exact test), Q value = 0.74

Table S255.  Gene #25: 'SMARCB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
SMARCB1 MUTATED 0 2 1 1 0 0 1
SMARCB1 WILD-TYPE 90 71 49 18 37 58 45
'PCF11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00454 (Fisher's exact test), Q value = 0.063

Table S256.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PCF11 MUTATED 9 3 0
PCF11 WILD-TYPE 304 165 298

Figure S89.  Get High-res Image Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PCF11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S257.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PCF11 MUTATED 1 1 2 1 7
PCF11 WILD-TYPE 94 110 140 62 178
'PCF11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S258.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PCF11 MUTATED 1 2 4 2
PCF11 WILD-TYPE 162 159 166 173
'PCF11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00059 (Fisher's exact test), Q value = 0.012

Table S259.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PCF11 MUTATED 0 4 0 2 0 3 0
PCF11 WILD-TYPE 178 58 105 127 52 58 82

Figure S90.  Get High-res Image Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PCF11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00614 (Fisher's exact test), Q value = 0.078

Table S260.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PCF11 MUTATED 0 1 1 10
PCF11 WILD-TYPE 107 178 232 252

Figure S91.  Get High-res Image Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PCF11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.037 (Fisher's exact test), Q value = 0.27

Table S261.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PCF11 MUTATED 0 1 1 4 0 0 0 0 6
PCF11 WILD-TYPE 84 49 121 73 107 32 90 52 161

Figure S92.  Get High-res Image Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PCF11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00452 (Fisher's exact test), Q value = 0.063

Table S262.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PCF11 MUTATED 10 3 0
PCF11 WILD-TYPE 319 161 282

Figure S93.  Get High-res Image Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PCF11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 0.74

Table S263.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PCF11 MUTATED 0 6 1 6
PCF11 WILD-TYPE 73 294 197 198
'PCF11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.033 (Fisher's exact test), Q value = 0.25

Table S264.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
PCF11 MUTATED 6 0 3 0
PCF11 WILD-TYPE 149 66 53 96

Figure S94.  Get High-res Image Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'PCF11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.84

Table S265.  Gene #26: 'PCF11 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
PCF11 MUTATED 3 4 1 1 0 0 0
PCF11 WILD-TYPE 87 69 49 18 37 58 46
'WASL MUTATION STATUS' versus 'CN_CNMF'

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

Table S266.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
WASL MUTATED 3 2 3
WASL WILD-TYPE 310 166 295
'WASL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S267.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
WASL MUTATED 1 2 1 0 2
WASL WILD-TYPE 94 109 141 63 183
'WASL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 0.97

Table S268.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
WASL MUTATED 1 4 1 2
WASL WILD-TYPE 162 157 169 173
'WASL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S269.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
WASL MUTATED 4 0 1 1 1 0 1
WASL WILD-TYPE 174 62 104 128 51 61 81
'WASL MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S270.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
WASL MUTATED 1 2 2 3
WASL WILD-TYPE 106 177 231 259
'WASL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S271.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
WASL MUTATED 1 0 1 0 1 1 1 0 3
WASL WILD-TYPE 83 50 121 77 106 31 89 52 164
'WASL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S272.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
WASL MUTATED 3 2 2
WASL WILD-TYPE 326 162 280
'WASL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S273.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
WASL MUTATED 1 3 1 2
WASL WILD-TYPE 72 297 197 202
'WASL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S274.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
WASL MUTATED 2 1 1 2
WASL WILD-TYPE 153 65 55 94
'WASL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.395 (Fisher's exact test), Q value = 0.95

Table S275.  Gene #27: 'WASL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
WASL MUTATED 2 0 0 0 2 1 1
WASL WILD-TYPE 88 73 50 19 35 57 45
'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.456 (Fisher's exact test), Q value = 0.98

Table S276.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
DNMT3A MUTATED 4 4 3
DNMT3A WILD-TYPE 309 164 295
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S277.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
DNMT3A MUTATED 0 1 3 1 4
DNMT3A WILD-TYPE 95 110 139 62 181
'DNMT3A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.66

Table S278.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
DNMT3A MUTATED 2 4 3 0
DNMT3A WILD-TYPE 161 157 167 175
'DNMT3A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.83

Table S279.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
DNMT3A MUTATED 3 0 0 2 0 3 1
DNMT3A WILD-TYPE 175 62 105 127 52 58 81
'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.86

Table S280.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
DNMT3A MUTATED 0 1 4 6
DNMT3A WILD-TYPE 107 178 229 256
'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.272 (Fisher's exact test), Q value = 0.84

Table S281.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
DNMT3A MUTATED 0 1 2 0 0 0 3 0 5
DNMT3A WILD-TYPE 84 49 120 77 107 32 87 52 162
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S282.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
DNMT3A MUTATED 5 2 3
DNMT3A WILD-TYPE 324 162 279
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.431 (Fisher's exact test), Q value = 0.97

Table S283.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
DNMT3A MUTATED 0 3 2 5
DNMT3A WILD-TYPE 73 297 196 199
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.517 (Fisher's exact test), Q value = 1

Table S284.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
DNMT3A MUTATED 4 0 0 1
DNMT3A WILD-TYPE 151 66 56 95
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.84

Table S285.  Gene #28: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
DNMT3A MUTATED 4 0 0 0 0 1 0
DNMT3A WILD-TYPE 86 73 50 19 37 57 46
'KIAA0922 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0841 (Fisher's exact test), Q value = 0.45

Table S286.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
KIAA0922 MUTATED 6 0 1
KIAA0922 WILD-TYPE 307 168 297
'KIAA0922 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.86

Table S287.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
KIAA0922 MUTATED 0 2 0 1 3
KIAA0922 WILD-TYPE 95 109 142 62 182
'KIAA0922 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S288.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
KIAA0922 MUTATED 2 0 1 1
KIAA0922 WILD-TYPE 161 161 169 174
'KIAA0922 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S289.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
KIAA0922 MUTATED 1 0 1 1 0 0 1
KIAA0922 WILD-TYPE 177 62 104 128 52 61 81
'KIAA0922 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.6

Table S290.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
KIAA0922 MUTATED 1 1 0 5
KIAA0922 WILD-TYPE 106 178 233 257
'KIAA0922 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.418 (Fisher's exact test), Q value = 0.97

Table S291.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
KIAA0922 MUTATED 0 1 0 2 1 0 0 0 3
KIAA0922 WILD-TYPE 84 49 122 75 106 32 90 52 164
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0579 (Fisher's exact test), Q value = 0.35

Table S292.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
KIAA0922 MUTATED 4 3 0
KIAA0922 WILD-TYPE 325 161 282
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.321 (Fisher's exact test), Q value = 0.86

Table S293.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
KIAA0922 MUTATED 0 4 0 3
KIAA0922 WILD-TYPE 73 296 198 201
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.99

Table S294.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
KIAA0922 MUTATED 2 0 1 0
KIAA0922 WILD-TYPE 153 66 55 96
'KIAA0922 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.96

Table S295.  Gene #29: 'KIAA0922 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
KIAA0922 MUTATED 0 2 1 0 0 0 0
KIAA0922 WILD-TYPE 90 71 49 19 37 58 46
'GPR50 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S296.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
GPR50 MUTATED 1 1 3
GPR50 WILD-TYPE 312 167 295
'GPR50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.694 (Fisher's exact test), Q value = 1

Table S297.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
GPR50 MUTATED 2 1 1 0 1
GPR50 WILD-TYPE 93 110 141 63 184
'GPR50 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.28

Table S298.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
GPR50 MUTATED 1 0 4 0
GPR50 WILD-TYPE 162 161 166 175

Figure S95.  Get High-res Image Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'GPR50 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.9

Table S299.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
GPR50 MUTATED 0 1 1 2 0 1 0
GPR50 WILD-TYPE 178 61 104 127 52 60 82
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 0.97

Table S300.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
GPR50 MUTATED 2 1 1 1
GPR50 WILD-TYPE 105 178 232 261
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.748 (Fisher's exact test), Q value = 1

Table S301.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
GPR50 MUTATED 1 1 0 0 1 0 1 0 1
GPR50 WILD-TYPE 83 49 122 77 106 32 89 52 166
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.93

Table S302.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
GPR50 MUTATED 1 2 2
GPR50 WILD-TYPE 328 162 280
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S303.  Gene #30: 'GPR50 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
GPR50 MUTATED 1 2 1 1
GPR50 WILD-TYPE 72 298 197 203
'ACSF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S304.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
ACSF2 MUTATED 5 3 3
ACSF2 WILD-TYPE 308 165 295
'ACSF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S305.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
ACSF2 MUTATED 1 2 1 1 4
ACSF2 WILD-TYPE 94 109 141 62 181
'ACSF2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.74

Table S306.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
ACSF2 MUTATED 4 0 2 4
ACSF2 WILD-TYPE 159 161 168 171
'ACSF2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.64

Table S307.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
ACSF2 MUTATED 1 1 5 1 1 0 1
ACSF2 WILD-TYPE 177 61 100 128 51 61 81
'ACSF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S308.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
ACSF2 MUTATED 1 3 2 5
ACSF2 WILD-TYPE 106 176 231 257
'ACSF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.9

Table S309.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
ACSF2 MUTATED 0 1 1 2 1 1 0 2 3
ACSF2 WILD-TYPE 84 49 121 75 106 31 90 50 164
'ACSF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S310.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
ACSF2 MUTATED 5 3 3
ACSF2 WILD-TYPE 324 161 279
'ACSF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.742 (Fisher's exact test), Q value = 1

Table S311.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
ACSF2 MUTATED 0 5 2 4
ACSF2 WILD-TYPE 73 295 196 200
'ACSF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.465 (Fisher's exact test), Q value = 0.98

Table S312.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
ACSF2 MUTATED 3 0 0 3
ACSF2 WILD-TYPE 152 66 56 93
'ACSF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.399 (Fisher's exact test), Q value = 0.96

Table S313.  Gene #31: 'ACSF2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
ACSF2 MUTATED 3 0 0 0 1 2 0
ACSF2 WILD-TYPE 87 73 50 19 36 56 46
'WDR52 MUTATION STATUS' versus 'CN_CNMF'

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

Table S314.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
WDR52 MUTATED 4 2 3
WDR52 WILD-TYPE 309 166 295
'WDR52 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 0.93

Table S315.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
WDR52 MUTATED 2 0 2 2 2
WDR52 WILD-TYPE 93 111 140 61 183
'WDR52 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S316.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
WDR52 MUTATED 1 2 2 2
WDR52 WILD-TYPE 162 159 168 173
'WDR52 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S317.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
WDR52 MUTATED 2 1 3 1 0 0 0
WDR52 WILD-TYPE 176 61 102 128 52 61 82
'WDR52 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S318.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
WDR52 MUTATED 2 2 2 3
WDR52 WILD-TYPE 105 177 231 259
'WDR52 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S319.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
WDR52 MUTATED 2 0 2 1 2 0 0 0 2
WDR52 WILD-TYPE 82 50 120 76 105 32 90 52 165
'WDR52 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.513 (Fisher's exact test), Q value = 1

Table S320.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
WDR52 MUTATED 4 3 2
WDR52 WILD-TYPE 325 161 280
'WDR52 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.398 (Fisher's exact test), Q value = 0.95

Table S321.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
WDR52 MUTATED 2 4 1 2
WDR52 WILD-TYPE 71 296 197 202
'WDR52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.97

Table S322.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
WDR52 MUTATED 1 0 1 2
WDR52 WILD-TYPE 154 66 55 94
'WDR52 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S323.  Gene #32: 'WDR52 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
WDR52 MUTATED 1 1 0 0 1 1 0
WDR52 WILD-TYPE 89 72 50 19 36 57 46
'ALMS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.94

Table S324.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
ALMS1 MUTATED 7 4 3
ALMS1 WILD-TYPE 306 164 295
'ALMS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S325.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
ALMS1 MUTATED 1 2 4 1 4
ALMS1 WILD-TYPE 94 109 138 62 181
'ALMS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S326.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
ALMS1 MUTATED 3 2 3 5
ALMS1 WILD-TYPE 160 159 167 170
'ALMS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.433 (Fisher's exact test), Q value = 0.97

Table S327.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
ALMS1 MUTATED 3 2 2 1 3 1 1
ALMS1 WILD-TYPE 175 60 103 128 49 60 81
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S328.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
ALMS1 MUTATED 1 3 4 6
ALMS1 WILD-TYPE 106 176 229 256
'ALMS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S329.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
ALMS1 MUTATED 0 2 3 2 2 0 1 1 3
ALMS1 WILD-TYPE 84 48 119 75 105 32 89 51 164
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 0.83

Table S330.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
ALMS1 MUTATED 7 4 2
ALMS1 WILD-TYPE 322 160 280
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0423 (Fisher's exact test), Q value = 0.29

Table S331.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
ALMS1 MUTATED 0 7 0 6
ALMS1 WILD-TYPE 73 293 198 198

Figure S96.  Get High-res Image Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.93

Table S332.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
ALMS1 MUTATED 5 0 2 1
ALMS1 WILD-TYPE 150 66 54 95
'ALMS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.82 (Fisher's exact test), Q value = 1

Table S333.  Gene #33: 'ALMS1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
ALMS1 MUTATED 4 1 1 0 1 1 0
ALMS1 WILD-TYPE 86 72 49 19 36 57 46
'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.84

Table S334.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
TXNIP MUTATED 3 0 5
TXNIP WILD-TYPE 310 168 293
'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.64

Table S335.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
TXNIP MUTATED 2 3 2 1 0
TXNIP WILD-TYPE 93 108 140 62 185
'TXNIP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.33

Table S336.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
TXNIP MUTATED 3 0 0 4
TXNIP WILD-TYPE 160 161 170 171

Figure S97.  Get High-res Image Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TXNIP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.2 (Fisher's exact test), Q value = 0.74

Table S337.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
TXNIP MUTATED 2 0 2 0 2 1 0
TXNIP WILD-TYPE 176 62 103 129 50 60 82
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0473 (Fisher's exact test), Q value = 0.32

Table S338.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
TXNIP MUTATED 3 2 3 0
TXNIP WILD-TYPE 104 177 230 262

Figure S98.  Get High-res Image Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0199 (Fisher's exact test), Q value = 0.18

Table S339.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
TXNIP MUTATED 1 2 2 0 1 2 0 0 0
TXNIP WILD-TYPE 83 48 120 77 106 30 90 52 167

Figure S99.  Get High-res Image Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.97

Table S340.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
TXNIP MUTATED 2 1 5
TXNIP WILD-TYPE 327 163 277
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 0.64

Table S341.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
TXNIP MUTATED 0 6 2 0
TXNIP WILD-TYPE 73 294 196 204
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.54

Table S342.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
TXNIP MUTATED 0 2 1 1
TXNIP WILD-TYPE 155 64 55 95
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 0.71

Table S343.  Gene #34: 'TXNIP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
TXNIP MUTATED 0 2 0 1 0 1 0
TXNIP WILD-TYPE 90 71 50 18 37 57 46
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.455 (Fisher's exact test), Q value = 0.98

Table S344.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
NUDT11 MUTATED 2 2 1
NUDT11 WILD-TYPE 311 166 297
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.285 (Fisher's exact test), Q value = 0.84

Table S345.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
NUDT11 MUTATED 0 0 3 1 1
NUDT11 WILD-TYPE 95 111 139 62 184
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S346.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
NUDT11 MUTATED 0 2 1 2
NUDT11 WILD-TYPE 163 159 169 173
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.904 (Fisher's exact test), Q value = 1

Table S347.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
NUDT11 MUTATED 2 0 1 1 1 0 0
NUDT11 WILD-TYPE 176 62 104 128 51 61 82
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.703 (Fisher's exact test), Q value = 1

Table S348.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
NUDT11 MUTATED 0 2 2 1
NUDT11 WILD-TYPE 107 177 231 261
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 0.84

Table S349.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
NUDT11 MUTATED 0 0 2 0 0 1 0 1 1
NUDT11 WILD-TYPE 84 50 120 77 107 31 90 51 166
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S350.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
NUDT11 MUTATED 1 1 3
NUDT11 WILD-TYPE 328 163 279
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S351.  Gene #35: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
NUDT11 MUTATED 0 2 2 1
NUDT11 WILD-TYPE 73 298 196 203
'PCK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S352.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PCK1 MUTATED 5 1 3
PCK1 WILD-TYPE 308 167 295
'PCK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S353.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PCK1 MUTATED 0 1 1 0 4
PCK1 WILD-TYPE 95 110 141 63 181
'PCK1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S354.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PCK1 MUTATED 1 3 1 2
PCK1 WILD-TYPE 162 158 169 173
'PCK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 1

Table S355.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PCK1 MUTATED 4 0 0 1 0 1 1
PCK1 WILD-TYPE 174 62 105 128 52 60 81
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.48 (Fisher's exact test), Q value = 0.99

Table S356.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PCK1 MUTATED 0 1 3 5
PCK1 WILD-TYPE 107 178 230 257
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S357.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PCK1 MUTATED 0 0 1 0 1 0 2 0 5
PCK1 WILD-TYPE 84 50 121 77 106 32 88 52 162
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S358.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PCK1 MUTATED 5 1 3
PCK1 WILD-TYPE 324 163 279
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.57

Table S359.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PCK1 MUTATED 0 1 3 5
PCK1 WILD-TYPE 73 299 195 199
'PCK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.84

Table S360.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
PCK1 MUTATED 4 0 0 0
PCK1 WILD-TYPE 151 66 56 96
'PCK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.456 (Fisher's exact test), Q value = 0.98

Table S361.  Gene #36: 'PCK1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
PCK1 MUTATED 3 0 1 0 0 0 0
PCK1 WILD-TYPE 87 73 49 19 37 58 46
'RAI1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.061 (Fisher's exact test), Q value = 0.36

Table S362.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
RAI1 MUTATED 8 0 3
RAI1 WILD-TYPE 305 168 295
'RAI1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.701 (Fisher's exact test), Q value = 1

Table S363.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
RAI1 MUTATED 1 1 3 0 5
RAI1 WILD-TYPE 94 110 139 63 180
'RAI1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.84

Table S364.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
RAI1 MUTATED 0 2 4 2
RAI1 WILD-TYPE 163 159 166 173
'RAI1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S365.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
RAI1 MUTATED 2 2 1 2 0 1 0
RAI1 WILD-TYPE 176 60 104 127 52 60 82
'RAI1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S366.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
RAI1 MUTATED 1 1 4 5
RAI1 WILD-TYPE 106 178 229 257
'RAI1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.86

Table S367.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
RAI1 MUTATED 1 1 0 1 0 0 2 2 4
RAI1 WILD-TYPE 83 49 122 76 107 32 88 50 163
'RAI1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.97

Table S368.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
RAI1 MUTATED 6 3 2
RAI1 WILD-TYPE 323 161 280
'RAI1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S369.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
RAI1 MUTATED 1 3 2 5
RAI1 WILD-TYPE 72 297 196 199
'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.282 (Fisher's exact test), Q value = 0.84

Table S370.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
RAI1 MUTATED 4 1 2 0
RAI1 WILD-TYPE 151 65 54 96
'RAI1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S371.  Gene #37: 'RAI1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
RAI1 MUTATED 2 1 1 0 2 0 1
RAI1 WILD-TYPE 88 72 49 19 35 58 45
'PAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.8

Table S372.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PAM MUTATED 3 0 0
PAM WILD-TYPE 310 168 298
'PAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.63

Table S373.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PAM MUTATED 0 0 0 0 4
PAM WILD-TYPE 95 111 142 63 181
'PAM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.51

Table S374.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PAM MUTATED 3 0 0 1
PAM WILD-TYPE 160 161 170 174
'PAM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0937 (Fisher's exact test), Q value = 0.48

Table S375.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PAM MUTATED 1 0 0 0 2 0 1
PAM WILD-TYPE 177 62 105 129 50 61 81
'PAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0524 (Fisher's exact test), Q value = 0.33

Table S376.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PAM MUTATED 0 0 0 4
PAM WILD-TYPE 107 179 233 258
'PAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S377.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PAM MUTATED 0 0 0 1 0 0 0 0 3
PAM WILD-TYPE 84 50 122 76 107 32 90 52 164
'PAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0812 (Fisher's exact test), Q value = 0.44

Table S378.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PAM MUTATED 4 0 0
PAM WILD-TYPE 325 164 282
'PAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.18

Table S379.  Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PAM MUTATED 0 0 0 4
PAM WILD-TYPE 73 300 198 200

Figure S100.  Get High-res Image Gene #38: 'PAM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00499 (Fisher's exact test), Q value = 0.067

Table S380.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
KDM6A MUTATED 11 0 2
KDM6A WILD-TYPE 302 168 296

Figure S101.  Get High-res Image Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0164 (Fisher's exact test), Q value = 0.16

Table S381.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
KDM6A MUTATED 2 0 0 1 8
KDM6A WILD-TYPE 93 111 142 62 177

Figure S102.  Get High-res Image Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM6A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.584 (Fisher's exact test), Q value = 1

Table S382.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
KDM6A MUTATED 1 3 4 2
KDM6A WILD-TYPE 162 158 166 173
'KDM6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.371 (Fisher's exact test), Q value = 0.93

Table S383.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
KDM6A MUTATED 2 1 0 2 2 2 1
KDM6A WILD-TYPE 176 61 105 127 50 59 81
'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.21

Table S384.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
KDM6A MUTATED 2 0 2 9
KDM6A WILD-TYPE 105 179 231 253

Figure S103.  Get High-res Image Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.029 (Fisher's exact test), Q value = 0.23

Table S385.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
KDM6A MUTATED 0 2 0 3 0 1 1 0 6
KDM6A WILD-TYPE 84 48 122 74 107 31 89 52 161

Figure S104.  Get High-res Image Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0074 (Fisher's exact test), Q value = 0.091

Table S386.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
KDM6A MUTATED 11 0 2
KDM6A WILD-TYPE 318 164 280

Figure S105.  Get High-res Image Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0124 (Fisher's exact test), Q value = 0.14

Table S387.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
KDM6A MUTATED 0 3 1 9
KDM6A WILD-TYPE 73 297 197 195

Figure S106.  Get High-res Image Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.312 (Fisher's exact test), Q value = 0.86

Table S388.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
KDM6A MUTATED 5 1 1 0
KDM6A WILD-TYPE 150 65 55 96
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.74

Table S389.  Gene #39: 'KDM6A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
KDM6A MUTATED 5 2 0 0 0 0 0
KDM6A WILD-TYPE 85 71 50 19 37 58 46
'GLS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.38 (Fisher's exact test), Q value = 0.94

Table S390.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
GLS MUTATED 4 0 4
GLS WILD-TYPE 309 168 294
'GLS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 0.83

Table S391.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
GLS MUTATED 1 2 0 2 2
GLS WILD-TYPE 94 109 142 61 183
'GLS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.192 (Fisher's exact test), Q value = 0.73

Table S392.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
GLS MUTATED 1 0 4 3
GLS WILD-TYPE 162 161 166 172
'GLS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0714 (Fisher's exact test), Q value = 0.4

Table S393.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
GLS MUTATED 1 3 1 0 0 1 2
GLS WILD-TYPE 177 59 104 129 52 60 80
'GLS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S394.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
GLS MUTATED 1 2 2 3
GLS WILD-TYPE 106 177 231 259
'GLS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S395.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
GLS MUTATED 1 2 1 0 1 0 1 0 2
GLS WILD-TYPE 83 48 121 77 106 32 89 52 165
'GLS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.88

Table S396.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
GLS MUTATED 5 0 4
GLS WILD-TYPE 324 164 278
'GLS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S397.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
GLS MUTATED 1 3 2 3
GLS WILD-TYPE 72 297 196 201
'GLS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S398.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
GLS MUTATED 3 1 0 0
GLS WILD-TYPE 152 65 56 96
'GLS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.471 (Fisher's exact test), Q value = 0.99

Table S399.  Gene #40: 'GLS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
GLS MUTATED 0 2 1 0 0 0 1
GLS WILD-TYPE 90 71 49 19 37 58 45
'EPS15L1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S400.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
EPS15L1 MUTATED 4 3 3
EPS15L1 WILD-TYPE 309 165 295
'EPS15L1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S401.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
EPS15L1 MUTATED 1 1 0 1 3
EPS15L1 WILD-TYPE 94 110 142 62 182
'EPS15L1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.66

Table S402.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
EPS15L1 MUTATED 2 4 3 0
EPS15L1 WILD-TYPE 161 157 167 175
'EPS15L1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S403.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
EPS15L1 MUTATED 2 1 2 2 1 1 0
EPS15L1 WILD-TYPE 176 61 103 127 51 60 82
'EPS15L1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S404.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
EPS15L1 MUTATED 2 2 2 4
EPS15L1 WILD-TYPE 105 177 231 258
'EPS15L1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.461 (Fisher's exact test), Q value = 0.98

Table S405.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
EPS15L1 MUTATED 1 0 0 3 2 0 2 0 2
EPS15L1 WILD-TYPE 83 50 122 74 105 32 88 52 165
'EPS15L1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0502 (Fisher's exact test), Q value = 0.33

Table S406.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
EPS15L1 MUTATED 4 5 1
EPS15L1 WILD-TYPE 325 159 281
'EPS15L1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S407.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
EPS15L1 MUTATED 1 3 2 4
EPS15L1 WILD-TYPE 72 297 196 200
'EPS15L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.393 (Fisher's exact test), Q value = 0.95

Table S408.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
EPS15L1 MUTATED 4 1 0 0
EPS15L1 WILD-TYPE 151 65 56 96
'EPS15L1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S409.  Gene #41: 'EPS15L1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
EPS15L1 MUTATED 1 1 2 0 0 0 1
EPS15L1 WILD-TYPE 89 72 48 19 37 58 45
'NOM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.88

Table S410.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
NOM1 MUTATED 1 1 4
NOM1 WILD-TYPE 312 167 294
'NOM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S411.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
NOM1 MUTATED 0 2 2 0 2
NOM1 WILD-TYPE 95 109 140 63 183
'NOM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.97

Table S412.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
NOM1 MUTATED 0 2 1 3
NOM1 WILD-TYPE 163 159 169 172
'NOM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S413.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
NOM1 MUTATED 2 0 1 2 1 0 0
NOM1 WILD-TYPE 176 62 104 127 51 61 82
'NOM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.943 (Fisher's exact test), Q value = 1

Table S414.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
NOM1 MUTATED 0 2 2 2
NOM1 WILD-TYPE 107 177 231 260
'NOM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S415.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
NOM1 MUTATED 0 1 1 1 0 0 1 1 1
NOM1 WILD-TYPE 84 49 121 76 107 32 89 51 166
'NOM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.76 (Fisher's exact test), Q value = 1

Table S416.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
NOM1 MUTATED 2 2 2
NOM1 WILD-TYPE 327 162 280
'NOM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S417.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
NOM1 MUTATED 0 2 2 2
NOM1 WILD-TYPE 73 298 196 202
'NOM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S418.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
NOM1 MUTATED 2 0 1 1
NOM1 WILD-TYPE 153 66 55 95
'NOM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S419.  Gene #42: 'NOM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
NOM1 MUTATED 2 0 0 0 1 1 0
NOM1 WILD-TYPE 88 73 50 19 36 57 46
'CDK12 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.99

Table S420.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
CDK12 MUTATED 2 3 3
CDK12 WILD-TYPE 311 165 295
'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S421.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
CDK12 MUTATED 2 2 2 0 1
CDK12 WILD-TYPE 93 109 140 63 184
'CDK12 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S422.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
CDK12 MUTATED 2 1 1 4
CDK12 WILD-TYPE 161 160 169 171
'CDK12 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.61

Table S423.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
CDK12 MUTATED 2 1 1 0 2 2 0
CDK12 WILD-TYPE 176 61 104 129 50 59 82
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S424.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
CDK12 MUTATED 1 3 2 2
CDK12 WILD-TYPE 106 176 231 260
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.726 (Fisher's exact test), Q value = 1

Table S425.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
CDK12 MUTATED 1 1 1 0 3 0 1 0 1
CDK12 WILD-TYPE 83 49 121 77 104 32 89 52 166
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S426.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
CDK12 MUTATED 3 1 4
CDK12 WILD-TYPE 326 163 278
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.11 (Fisher's exact test), Q value = 0.54

Table S427.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
CDK12 MUTATED 1 6 1 0
CDK12 WILD-TYPE 72 294 197 204
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.645 (Fisher's exact test), Q value = 1

Table S428.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
CDK12 MUTATED 1 1 1 2
CDK12 WILD-TYPE 154 65 55 94
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.546 (Fisher's exact test), Q value = 1

Table S429.  Gene #43: 'CDK12 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
CDK12 MUTATED 0 1 1 0 0 2 1
CDK12 WILD-TYPE 90 72 49 19 37 56 45
'ARHGAP35 MUTATION STATUS' versus 'CN_CNMF'

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

Table S430.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
ARHGAP35 MUTATED 2 1 4
ARHGAP35 WILD-TYPE 311 167 294
'ARHGAP35 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.21

Table S431.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
ARHGAP35 MUTATED 1 1 1 3 0
ARHGAP35 WILD-TYPE 94 110 141 60 185

Figure S107.  Get High-res Image Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ARHGAP35 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.76 (Fisher's exact test), Q value = 1

Table S432.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
ARHGAP35 MUTATED 1 2 1 3
ARHGAP35 WILD-TYPE 162 159 169 172
'ARHGAP35 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S433.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
ARHGAP35 MUTATED 2 0 2 1 0 0 2
ARHGAP35 WILD-TYPE 176 62 103 128 52 61 80
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S434.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
ARHGAP35 MUTATED 1 2 3 1
ARHGAP35 WILD-TYPE 106 177 230 261
'ARHGAP35 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.99

Table S435.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
ARHGAP35 MUTATED 0 1 2 1 1 0 1 1 0
ARHGAP35 WILD-TYPE 84 49 120 76 106 32 89 51 167
'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0268 (Fisher's exact test), Q value = 0.22

Table S436.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
ARHGAP35 MUTATED 0 3 4
ARHGAP35 WILD-TYPE 329 161 278

Figure S108.  Get High-res Image Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ARHGAP35 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 0.78

Table S437.  Gene #44: 'ARHGAP35 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
ARHGAP35 MUTATED 0 5 2 0
ARHGAP35 WILD-TYPE 73 295 196 204
'RIMBP3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S438.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
RIMBP3 MUTATED 2 1 2
RIMBP3 WILD-TYPE 311 167 296
'RIMBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.522 (Fisher's exact test), Q value = 1

Table S439.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
RIMBP3 MUTATED 1 1 1 0 0
RIMBP3 WILD-TYPE 94 110 141 63 185
'RIMBP3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S440.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
RIMBP3 MUTATED 0 2 2 1
RIMBP3 WILD-TYPE 163 159 168 174
'RIMBP3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S441.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
RIMBP3 MUTATED 2 0 1 0 0 1 1
RIMBP3 WILD-TYPE 176 62 104 129 52 60 81
'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 0.77

Table S442.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
RIMBP3 MUTATED 1 1 3 0
RIMBP3 WILD-TYPE 106 178 230 262
'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0371 (Fisher's exact test), Q value = 0.27

Table S443.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
RIMBP3 MUTATED 1 1 0 0 0 0 3 0 0
RIMBP3 WILD-TYPE 83 49 122 77 107 32 87 52 167

Figure S109.  Get High-res Image Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.97

Table S444.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
RIMBP3 MUTATED 1 2 1
RIMBP3 WILD-TYPE 328 162 281
'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.85

Table S445.  Gene #45: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
RIMBP3 MUTATED 1 1 2 0
RIMBP3 WILD-TYPE 72 299 196 204
'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.127 (Fisher's exact test), Q value = 0.58

Table S446.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
FAT1 MUTATED 11 1 8
FAT1 WILD-TYPE 302 167 290
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S447.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
FAT1 MUTATED 2 4 2 3 7
FAT1 WILD-TYPE 93 107 140 60 178
'FAT1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S448.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
FAT1 MUTATED 4 5 5 4
FAT1 WILD-TYPE 159 156 165 171
'FAT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.471 (Fisher's exact test), Q value = 0.99

Table S449.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
FAT1 MUTATED 5 3 2 1 1 2 4
FAT1 WILD-TYPE 173 59 103 128 51 59 78
'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.027 (Fisher's exact test), Q value = 0.22

Table S450.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
FAT1 MUTATED 1 4 2 13
FAT1 WILD-TYPE 106 175 231 249

Figure S110.  Get High-res Image Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0509 (Fisher's exact test), Q value = 0.33

Table S451.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
FAT1 MUTATED 1 3 1 5 1 2 1 0 6
FAT1 WILD-TYPE 83 47 121 72 106 30 89 52 161
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.111 (Fisher's exact test), Q value = 0.54

Table S452.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
FAT1 MUTATED 12 5 3
FAT1 WILD-TYPE 317 159 279
'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 0.86

Table S453.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
FAT1 MUTATED 1 10 2 7
FAT1 WILD-TYPE 72 290 196 197
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S454.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
FAT1 MUTATED 6 3 1 1
FAT1 WILD-TYPE 149 63 55 95
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.86

Table S455.  Gene #46: 'FAT1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
FAT1 MUTATED 2 3 2 2 1 0 1
FAT1 WILD-TYPE 88 70 48 17 36 58 45
'FAM178A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0837 (Fisher's exact test), Q value = 0.45

Table S456.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
FAM178A MUTATED 2 0 6
FAM178A WILD-TYPE 311 168 292
'FAM178A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S457.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
FAM178A MUTATED 1 1 2 1 2
FAM178A WILD-TYPE 94 110 140 62 183
'FAM178A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.57 (Fisher's exact test), Q value = 1

Table S458.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
FAM178A MUTATED 2 2 0 2
FAM178A WILD-TYPE 161 159 170 173
'FAM178A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S459.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
FAM178A MUTATED 1 0 1 2 0 0 2
FAM178A WILD-TYPE 177 62 104 127 52 61 80
'FAM178A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.95

Table S460.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
FAM178A MUTATED 0 3 1 4
FAM178A WILD-TYPE 107 176 232 258
'FAM178A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S461.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
FAM178A MUTATED 0 1 1 1 1 1 1 0 2
FAM178A WILD-TYPE 84 49 121 76 106 31 89 52 165
'FAM178A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.814 (Fisher's exact test), Q value = 1

Table S462.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
FAM178A MUTATED 4 2 2
FAM178A WILD-TYPE 325 162 280
'FAM178A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S463.  Gene #47: 'FAM178A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
FAM178A MUTATED 0 4 2 2
FAM178A WILD-TYPE 73 296 196 202
'TCEB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.84

Table S464.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
TCEB1 MUTATED 3 1 0
TCEB1 WILD-TYPE 310 167 298
'TCEB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.64

Table S465.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
TCEB1 MUTATED 2 1 0 0
TCEB1 WILD-TYPE 161 160 170 175
'TCEB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.86

Table S466.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
TCEB1 MUTATED 1 0 0 0 0 0 2
TCEB1 WILD-TYPE 177 62 105 129 52 61 80
'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.84

Table S467.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
TCEB1 MUTATED 0 2 2 0
TCEB1 WILD-TYPE 107 177 231 262
'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00237 (Fisher's exact test), Q value = 0.037

Table S468.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
TCEB1 MUTATED 0 0 0 0 0 0 1 3 0
TCEB1 WILD-TYPE 84 50 122 77 107 32 89 49 167

Figure S111.  Get High-res Image Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0152 (Fisher's exact test), Q value = 0.15

Table S469.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
TCEB1 MUTATED 0 3 1
TCEB1 WILD-TYPE 329 161 281

Figure S112.  Get High-res Image Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.188 (Fisher's exact test), Q value = 0.73

Table S470.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
TCEB1 MUTATED 0 4 0 0
TCEB1 WILD-TYPE 73 296 198 204
'TCEB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.64

Table S471.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
TCEB1 MUTATED 0 0 1 2
TCEB1 WILD-TYPE 155 66 55 94
'TCEB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00202 (Fisher's exact test), Q value = 0.033

Table S472.  Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
TCEB1 MUTATED 0 0 0 0 3 0 0
TCEB1 WILD-TYPE 90 73 50 19 34 58 46

Figure S113.  Get High-res Image Gene #48: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PODXL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.225 (Fisher's exact test), Q value = 0.78

Table S473.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
PODXL MUTATED 2 3 1
PODXL WILD-TYPE 311 165 297
'PODXL MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.86

Table S474.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
PODXL MUTATED 1 2 2 0 0
PODXL WILD-TYPE 94 109 140 63 185
'PODXL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.76

Table S475.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
PODXL MUTATED 2 3 0 1
PODXL WILD-TYPE 161 158 170 174
'PODXL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.863 (Fisher's exact test), Q value = 1

Table S476.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
PODXL MUTATED 2 0 1 1 1 1 0
PODXL WILD-TYPE 176 62 104 128 51 60 82
'PODXL MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S477.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
PODXL MUTATED 1 1 2 2
PODXL WILD-TYPE 106 178 231 260
'PODXL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.237 (Fisher's exact test), Q value = 0.8

Table S478.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
PODXL MUTATED 1 1 1 1 0 1 1 0 0
PODXL WILD-TYPE 83 49 121 76 107 31 89 52 167
'PODXL MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S479.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
PODXL MUTATED 3 1 2
PODXL WILD-TYPE 326 163 280
'PODXL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S480.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
PODXL MUTATED 1 2 2 1
PODXL WILD-TYPE 72 298 196 203
'PODXL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.84

Table S481.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
PODXL MUTATED 0 1 1 1
PODXL WILD-TYPE 155 65 55 95
'PODXL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.364 (Fisher's exact test), Q value = 0.93

Table S482.  Gene #49: 'PODXL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
PODXL MUTATED 0 2 0 0 0 0 1
PODXL WILD-TYPE 90 71 50 19 37 58 45
'DNAJA3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S483.  Gene #50: 'DNAJA3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
DNAJA3 MUTATED 1 1 1
DNAJA3 WILD-TYPE 312 167 297
'DNAJA3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.512 (Fisher's exact test), Q value = 1

Table S484.  Gene #50: 'DNAJA3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
DNAJA3 MUTATED 1 1 0 1
DNAJA3 WILD-TYPE 106 178 233 261
'DNAJA3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 0.84

Table S485.  Gene #50: 'DNAJA3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
DNAJA3 MUTATED 1 0 0 0 0 1 0 0 1
DNAJA3 WILD-TYPE 83 50 122 77 107 31 90 52 166
'DNAJA3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.97

Table S486.  Gene #50: 'DNAJA3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
DNAJA3 MUTATED 2 1 0
DNAJA3 WILD-TYPE 327 163 282
'DNAJA3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S487.  Gene #50: 'DNAJA3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
DNAJA3 MUTATED 0 2 0 1
DNAJA3 WILD-TYPE 73 298 198 203
'DNAJA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S488.  Gene #50: 'DNAJA3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
DNAJA3 MUTATED 1 1 0 1
DNAJA3 WILD-TYPE 154 65 56 95
'DNAJA3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.66

Table S489.  Gene #50: 'DNAJA3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
DNAJA3 MUTATED 0 1 1 1 0 0 0
DNAJA3 WILD-TYPE 90 72 49 18 37 58 46
'NASP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S490.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
NASP MUTATED 3 0 2
NASP WILD-TYPE 310 168 296
'NASP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.85

Table S491.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
NASP MUTATED 2 1 0 1 1
NASP WILD-TYPE 93 110 142 62 184
'NASP MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.65

Table S492.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
NASP MUTATED 2 0 0 3
NASP WILD-TYPE 161 161 170 172
'NASP MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S493.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
NASP MUTATED 1 0 2 1 1 0 0
NASP WILD-TYPE 177 62 103 128 51 61 82
'NASP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.53

Table S494.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
NASP MUTATED 2 2 0 1
NASP WILD-TYPE 105 177 233 261
'NASP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.415 (Fisher's exact test), Q value = 0.97

Table S495.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
NASP MUTATED 2 1 0 0 1 0 0 0 1
NASP WILD-TYPE 82 49 122 77 106 32 90 52 166
'NASP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.85

Table S496.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
NASP MUTATED 4 0 1
NASP WILD-TYPE 325 164 281
'NASP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.121 (Fisher's exact test), Q value = 0.57

Table S497.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
NASP MUTATED 2 2 0 1
NASP WILD-TYPE 71 298 198 203
'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0339 (Fisher's exact test), Q value = 0.25

Table S498.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
NASP MUTATED 0 2 1 0
NASP WILD-TYPE 155 64 55 96

Figure S114.  Get High-res Image Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.176 (Fisher's exact test), Q value = 0.7

Table S499.  Gene #51: 'NASP MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
NASP MUTATED 0 1 0 0 0 0 2
NASP WILD-TYPE 90 72 50 19 37 58 44
'SLC23A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.877 (Fisher's exact test), Q value = 1

Table S500.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
SLC23A1 MUTATED 2 1 3
SLC23A1 WILD-TYPE 311 167 295
'SLC23A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S501.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
SLC23A1 MUTATED 0 0 1 1 2
SLC23A1 WILD-TYPE 95 111 141 62 183
'SLC23A1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 0.85

Table S502.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
SLC23A1 MUTATED 2 1 3 0
SLC23A1 WILD-TYPE 161 160 167 175
'SLC23A1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.417 (Fisher's exact test), Q value = 0.97

Table S503.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
SLC23A1 MUTATED 1 0 0 2 1 0 2
SLC23A1 WILD-TYPE 177 62 105 127 51 61 80
'SLC23A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.84

Table S504.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
SLC23A1 MUTATED 0 0 4 2
SLC23A1 WILD-TYPE 107 179 229 260
'SLC23A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.41 (Fisher's exact test), Q value = 0.96

Table S505.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
SLC23A1 MUTATED 0 0 1 0 0 0 3 0 2
SLC23A1 WILD-TYPE 84 50 121 77 107 32 87 52 165
'SLC23A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S506.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
SLC23A1 MUTATED 2 1 3
SLC23A1 WILD-TYPE 327 163 279
'SLC23A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0571 (Fisher's exact test), Q value = 0.35

Table S507.  Gene #52: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
SLC23A1 MUTATED 0 0 4 2
SLC23A1 WILD-TYPE 73 300 194 202
'RILPL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.846 (Fisher's exact test), Q value = 1

Table S508.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
RILPL1 MUTATED 3 1 1
RILPL1 WILD-TYPE 310 167 297
'RILPL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 0.96

Table S509.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
RILPL1 MUTATED 2 0 1 1 1
RILPL1 WILD-TYPE 93 111 141 62 184
'RILPL1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 0.99

Table S510.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
RILPL1 MUTATED 1 2 2 0
RILPL1 WILD-TYPE 162 159 168 175
'RILPL1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.248 (Fisher's exact test), Q value = 0.82

Table S511.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
RILPL1 MUTATED 0 1 0 2 0 1 1
RILPL1 WILD-TYPE 178 61 105 127 52 60 81
'RILPL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.84

Table S512.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
RILPL1 MUTATED 2 0 1 2
RILPL1 WILD-TYPE 105 179 232 260
'RILPL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.306 (Fisher's exact test), Q value = 0.86

Table S513.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
RILPL1 MUTATED 2 0 0 1 0 0 0 1 1
RILPL1 WILD-TYPE 82 50 122 76 107 32 90 51 166
'RILPL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S514.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
RILPL1 MUTATED 3 1 1
RILPL1 WILD-TYPE 326 163 281
'RILPL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.206 (Fisher's exact test), Q value = 0.75

Table S515.  Gene #53: 'RILPL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
RILPL1 MUTATED 2 1 1 1
RILPL1 WILD-TYPE 71 299 197 203
'NIPBL MUTATION STATUS' versus 'CN_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.6

Table S516.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
NIPBL MUTATED 10 2 3
NIPBL WILD-TYPE 303 166 295
'NIPBL MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S517.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
NIPBL MUTATED 2 1 2 2 7
NIPBL WILD-TYPE 93 110 140 61 178
'NIPBL MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S518.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
NIPBL MUTATED 3 3 1 4
NIPBL WILD-TYPE 160 158 169 171
'NIPBL MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.489 (Fisher's exact test), Q value = 0.99

Table S519.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
NIPBL MUTATED 3 0 2 1 1 3 1
NIPBL WILD-TYPE 175 62 103 128 51 58 81
'NIPBL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.51 (Fisher's exact test), Q value = 1

Table S520.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
NIPBL MUTATED 2 4 2 7
NIPBL WILD-TYPE 105 175 231 255
'NIPBL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.505 (Fisher's exact test), Q value = 1

Table S521.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
NIPBL MUTATED 2 1 1 2 1 1 0 2 5
NIPBL WILD-TYPE 82 49 121 75 106 31 90 50 162
'NIPBL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.66

Table S522.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
NIPBL MUTATED 10 1 4
NIPBL WILD-TYPE 319 163 278
'NIPBL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 0.97

Table S523.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
NIPBL MUTATED 2 5 2 6
NIPBL WILD-TYPE 71 295 196 198
'NIPBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S524.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
NIPBL MUTATED 5 1 1 1
NIPBL WILD-TYPE 150 65 55 95
'NIPBL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S525.  Gene #54: 'NIPBL MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
NIPBL MUTATED 2 2 2 0 0 1 1
NIPBL WILD-TYPE 88 71 48 19 37 57 45
'FAM47A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.88

Table S526.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
FAM47A MUTATED 1 1 4
FAM47A WILD-TYPE 312 167 294
'FAM47A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S527.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
FAM47A MUTATED 1 1 0 1 1
FAM47A WILD-TYPE 94 110 142 62 184
'FAM47A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.86

Table S528.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
FAM47A MUTATED 0 3 2 1
FAM47A WILD-TYPE 163 158 168 174
'FAM47A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S529.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
FAM47A MUTATED 2 1 1 2 0 0 0
FAM47A WILD-TYPE 176 61 104 127 52 61 82
'FAM47A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S530.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
FAM47A MUTATED 1 1 2 2
FAM47A WILD-TYPE 106 178 231 260
'FAM47A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0718 (Fisher's exact test), Q value = 0.4

Table S531.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
FAM47A MUTATED 1 0 0 1 0 1 2 1 0
FAM47A WILD-TYPE 83 50 122 76 107 31 88 51 167
'FAM47A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.321 (Fisher's exact test), Q value = 0.86

Table S532.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
FAM47A MUTATED 2 0 4
FAM47A WILD-TYPE 327 164 278
'FAM47A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S533.  Gene #55: 'FAM47A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
FAM47A MUTATED 1 2 2 1
FAM47A WILD-TYPE 72 298 196 203
'RHEB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.334 (Fisher's exact test), Q value = 0.88

Table S534.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
RHEB MUTATED 0 1 2
RHEB WILD-TYPE 313 167 296
'RHEB MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.237 (Fisher's exact test), Q value = 0.8

Table S535.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
RHEB MUTATED 2 0 1 0
RHEB WILD-TYPE 161 161 169 175
'RHEB MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.75

Table S536.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
RHEB MUTATED 0 0 1 0 1 0 1
RHEB WILD-TYPE 178 62 104 129 51 61 81
'RHEB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S537.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
RHEB MUTATED 0 1 1 1
RHEB WILD-TYPE 107 178 232 261
'RHEB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S538.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
RHEB MUTATED 0 0 0 1 1 0 1 0 0
RHEB WILD-TYPE 84 50 122 76 106 32 89 52 167
'RHEB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.106 (Fisher's exact test), Q value = 0.53

Table S539.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
RHEB MUTATED 0 2 1
RHEB WILD-TYPE 329 162 281
'RHEB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S540.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
RHEB MUTATED 0 2 1 0
RHEB WILD-TYPE 73 298 197 204
'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.149 (Fisher's exact test), Q value = 0.64

Table S541.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
RHEB MUTATED 0 0 1 2
RHEB WILD-TYPE 155 66 55 94
'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S542.  Gene #56: 'RHEB MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
RHEB MUTATED 0 1 0 0 1 1 0
RHEB WILD-TYPE 90 72 50 19 36 57 46
'BRAF MUTATION STATUS' versus 'CN_CNMF'

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

Table S543.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
BRAF MUTATED 2 1 2
BRAF WILD-TYPE 311 167 296
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 0.97

Table S544.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
BRAF MUTATED 0 2 0 0 1
BRAF WILD-TYPE 95 109 142 63 184
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S545.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
BRAF MUTATED 1 1 1 1
BRAF WILD-TYPE 162 160 169 174
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S546.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
BRAF MUTATED 1 1 0 1 0 0 1
BRAF WILD-TYPE 177 61 105 128 52 61 81
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.19 (Fisher's exact test), Q value = 0.73

Table S547.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
BRAF MUTATED 0 1 0 4
BRAF WILD-TYPE 107 178 233 258
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.478 (Fisher's exact test), Q value = 0.99

Table S548.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
BRAF MUTATED 0 0 0 1 1 1 0 0 2
BRAF WILD-TYPE 84 50 122 76 106 31 90 52 165
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S549.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
BRAF MUTATED 3 1 1
BRAF WILD-TYPE 326 163 281
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 0.83

Table S550.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
BRAF MUTATED 0 2 0 3
BRAF WILD-TYPE 73 298 198 201
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.96

Table S551.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
BRAF MUTATED 3 0 0 0
BRAF WILD-TYPE 152 66 56 96
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S552.  Gene #57: 'BRAF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
BRAF MUTATED 2 1 0 0 0 0 0
BRAF WILD-TYPE 88 72 50 19 37 58 46
'MLL3 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S553.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 15
MLL3 MUTATED 1 0 1 1
MLL3 WILD-TYPE 16 16 9 14
'MLL3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.658 (Fisher's exact test), Q value = 1

Table S554.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 16 10 9
MLL3 MUTATED 0 0 1 1 1
MLL3 WILD-TYPE 7 16 15 9 8
'MLL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.161 (Fisher's exact test), Q value = 0.66

Table S555.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
MLL3 MUTATED 23 7 12
MLL3 WILD-TYPE 290 161 286
'MLL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 0.97

Table S556.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
MLL3 MUTATED 10 5 7 3 11
MLL3 WILD-TYPE 85 106 135 60 174
'MLL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.291 (Fisher's exact test), Q value = 0.85

Table S557.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
MLL3 MUTATED 10 14 8 7
MLL3 WILD-TYPE 153 147 162 168
'MLL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.913 (Fisher's exact test), Q value = 1

Table S558.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
MLL3 MUTATED 11 3 7 7 1 4 6
MLL3 WILD-TYPE 167 59 98 122 51 57 76
'MLL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.014 (Fisher's exact test), Q value = 0.15

Table S559.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
MLL3 MUTATED 11 4 9 18
MLL3 WILD-TYPE 96 175 224 244

Figure S115.  Get High-res Image Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.221 (Fisher's exact test), Q value = 0.77

Table S560.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
MLL3 MUTATED 9 4 5 6 3 0 4 1 10
MLL3 WILD-TYPE 75 46 117 71 104 32 86 51 157
'MLL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.27

Table S561.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
MLL3 MUTATED 26 6 10
MLL3 WILD-TYPE 303 158 272

Figure S116.  Get High-res Image Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.16

Table S562.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
MLL3 MUTATED 9 9 11 13
MLL3 WILD-TYPE 64 291 187 191

Figure S117.  Get High-res Image Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 0.97

Table S563.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
MLL3 MUTATED 10 7 2 5
MLL3 WILD-TYPE 145 59 54 91
'MLL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.336 (Fisher's exact test), Q value = 0.88

Table S564.  Gene #58: 'MLL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
MLL3 MUTATED 6 5 3 0 0 4 6
MLL3 WILD-TYPE 84 68 47 19 37 54 40
'ANK3 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.302 (Fisher's exact test), Q value = 0.85

Table S565.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 15
ANK3 MUTATED 0 1 0 2
ANK3 WILD-TYPE 17 15 10 13
'ANK3 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.842 (Fisher's exact test), Q value = 1

Table S566.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 16 10 9
ANK3 MUTATED 0 1 2 0 0
ANK3 WILD-TYPE 7 15 14 10 9
'ANK3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.84

Table S567.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
ANK3 MUTATED 11 6 5
ANK3 WILD-TYPE 302 162 293
'ANK3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S568.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
ANK3 MUTATED 4 3 5 0 5
ANK3 WILD-TYPE 91 108 137 63 180
'ANK3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S569.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
ANK3 MUTATED 4 4 7 4
ANK3 WILD-TYPE 159 157 163 171
'ANK3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 0.99

Table S570.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
ANK3 MUTATED 2 2 2 5 2 2 4
ANK3 WILD-TYPE 176 60 103 124 50 59 78
'ANK3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.94

Table S571.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
ANK3 MUTATED 3 2 7 10
ANK3 WILD-TYPE 104 177 226 252
'ANK3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S572.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
ANK3 MUTATED 2 3 5 2 1 1 2 0 6
ANK3 WILD-TYPE 82 47 117 75 106 31 88 52 161
'ANK3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S573.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
ANK3 MUTATED 11 4 7
ANK3 WILD-TYPE 318 160 275
'ANK3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S574.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
ANK3 MUTATED 1 8 7 6
ANK3 WILD-TYPE 72 292 191 198
'ANK3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S575.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
ANK3 MUTATED 4 1 2 1
ANK3 WILD-TYPE 151 65 54 95
'ANK3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.297 (Fisher's exact test), Q value = 0.85

Table S576.  Gene #59: 'ANK3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
ANK3 MUTATED 1 3 2 1 1 0 0
ANK3 WILD-TYPE 89 70 48 18 36 58 46
'EMG1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.063

Table S577.  Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 17 16 10 15
EMG1 MUTATED 0 0 3 0
EMG1 WILD-TYPE 17 16 7 15

Figure S118.  Get High-res Image Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00428 (Fisher's exact test), Q value = 0.062

Table S578.  Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 7 16 16 10 9
EMG1 MUTATED 0 0 0 0 3
EMG1 WILD-TYPE 7 16 16 10 6

Figure S119.  Get High-res Image Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'EMG1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.84

Table S579.  Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
EMG1 MUTATED 3 1 0
EMG1 WILD-TYPE 310 167 298
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00856 (Fisher's exact test), Q value = 0.1

Table S580.  Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
EMG1 MUTATED 3 0 1 0
EMG1 WILD-TYPE 104 179 232 262

Figure S120.  Get High-res Image Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0326 (Fisher's exact test), Q value = 0.25

Table S581.  Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
EMG1 MUTATED 3 0 0 0 0 0 1 0 0
EMG1 WILD-TYPE 81 50 122 77 107 32 89 52 167

Figure S121.  Get High-res Image Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S582.  Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
EMG1 MUTATED 2 1 1
EMG1 WILD-TYPE 327 163 281
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-04 (Fisher's exact test), Q value = 0.017

Table S583.  Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
EMG1 MUTATED 3 0 1 0
EMG1 WILD-TYPE 70 300 197 204

Figure S122.  Get High-res Image Gene #60: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'LHX1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S584.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
LHX1 MUTATED 2 1 1
LHX1 WILD-TYPE 311 167 297
'LHX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.94

Table S585.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
LHX1 MUTATED 1 0 0 1 1
LHX1 WILD-TYPE 94 111 142 62 184
'LHX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.901 (Fisher's exact test), Q value = 1

Table S586.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
LHX1 MUTATED 0 1 1 1
LHX1 WILD-TYPE 163 160 169 174
'LHX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S587.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
LHX1 MUTATED 2 1 0 0 0 0 0
LHX1 WILD-TYPE 176 61 105 129 52 61 82
'LHX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S588.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
LHX1 MUTATED 1 0 2 1
LHX1 WILD-TYPE 106 179 231 261
'LHX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S589.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
LHX1 MUTATED 1 0 1 1 0 0 1 0 0
LHX1 WILD-TYPE 83 50 121 76 107 32 89 52 167
'LHX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S590.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
LHX1 MUTATED 2 0 2
LHX1 WILD-TYPE 327 164 280
'LHX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.123 (Fisher's exact test), Q value = 0.57

Table S591.  Gene #61: 'LHX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
LHX1 MUTATED 1 0 2 1
LHX1 WILD-TYPE 72 300 196 203
'SCARB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.216 (Fisher's exact test), Q value = 0.76

Table S592.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
SCARB2 MUTATED 0 1 3
SCARB2 WILD-TYPE 313 167 295
'SCARB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.122 (Fisher's exact test), Q value = 0.57

Table S593.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
SCARB2 MUTATED 0 0 2 1 0
SCARB2 WILD-TYPE 95 111 140 62 185
'SCARB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.15

Table S594.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
SCARB2 MUTATED 0 0 0 4
SCARB2 WILD-TYPE 163 161 170 171

Figure S123.  Get High-res Image Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'SCARB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S595.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
SCARB2 MUTATED 1 0 1 1 1 0 0
SCARB2 WILD-TYPE 177 62 104 128 51 61 82
'SCARB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 0.84

Table S596.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
SCARB2 MUTATED 0 2 2 0
SCARB2 WILD-TYPE 107 177 231 262
'SCARB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S597.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
SCARB2 MUTATED 0 0 2 0 1 0 1 0 0
SCARB2 WILD-TYPE 84 50 120 77 106 32 89 52 167
'SCARB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0488 (Fisher's exact test), Q value = 0.33

Table S598.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
SCARB2 MUTATED 0 0 4
SCARB2 WILD-TYPE 329 164 278

Figure S124.  Get High-res Image Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SCARB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.477 (Fisher's exact test), Q value = 0.99

Table S599.  Gene #62: 'SCARB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
SCARB2 MUTATED 0 2 2 0
SCARB2 WILD-TYPE 73 298 196 204
'C1ORF25 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S600.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
C1ORF25 MUTATED 3 2 1
C1ORF25 WILD-TYPE 310 166 297
'C1ORF25 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.487 (Fisher's exact test), Q value = 0.99

Table S601.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
C1ORF25 MUTATED 0 1 3 1 1
C1ORF25 WILD-TYPE 95 110 139 62 184
'C1ORF25 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.43 (Fisher's exact test), Q value = 0.97

Table S602.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
C1ORF25 MUTATED 2 1 0 3
C1ORF25 WILD-TYPE 161 160 170 172
'C1ORF25 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S603.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
C1ORF25 MUTATED 2 0 1 2 0 1 0
C1ORF25 WILD-TYPE 176 62 104 127 52 60 82
'C1ORF25 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S604.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
C1ORF25 MUTATED 0 1 3 2
C1ORF25 WILD-TYPE 107 178 230 260
'C1ORF25 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.138 (Fisher's exact test), Q value = 0.61

Table S605.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
C1ORF25 MUTATED 0 1 1 2 0 0 2 0 0
C1ORF25 WILD-TYPE 84 49 121 75 107 32 88 52 167
'C1ORF25 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.87 (Fisher's exact test), Q value = 1

Table S606.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
C1ORF25 MUTATED 2 1 3
C1ORF25 WILD-TYPE 327 163 279
'C1ORF25 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S607.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
C1ORF25 MUTATED 0 2 3 1
C1ORF25 WILD-TYPE 73 298 195 203
'C1ORF25 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 0.97

Table S608.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
C1ORF25 MUTATED 1 0 1 2
C1ORF25 WILD-TYPE 154 66 55 94
'C1ORF25 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.327 (Fisher's exact test), Q value = 0.87

Table S609.  Gene #63: 'C1ORF25 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
C1ORF25 MUTATED 0 1 0 0 1 2 0
C1ORF25 WILD-TYPE 90 72 50 19 36 56 46
'KDELR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.78

Table S610.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
KDELR3 MUTATED 5 0 2
KDELR3 WILD-TYPE 308 168 296
'KDELR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.76

Table S611.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
KDELR3 MUTATED 2 3 0 0 2
KDELR3 WILD-TYPE 93 108 142 63 183
'KDELR3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S612.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
KDELR3 MUTATED 2 1 0 4
KDELR3 WILD-TYPE 161 160 170 171
'KDELR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.458 (Fisher's exact test), Q value = 0.98

Table S613.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
KDELR3 MUTATED 3 0 2 0 0 0 2
KDELR3 WILD-TYPE 175 62 103 129 52 61 80
'KDELR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.54

Table S614.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
KDELR3 MUTATED 2 3 0 2
KDELR3 WILD-TYPE 105 176 233 260
'KDELR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.296 (Fisher's exact test), Q value = 0.85

Table S615.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
KDELR3 MUTATED 1 2 0 0 2 0 0 0 2
KDELR3 WILD-TYPE 83 48 122 77 105 32 90 52 165
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.258 (Fisher's exact test), Q value = 0.83

Table S616.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
KDELR3 MUTATED 3 3 1
KDELR3 WILD-TYPE 326 161 281
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S617.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
KDELR3 MUTATED 1 4 0 2
KDELR3 WILD-TYPE 72 296 198 202
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.74

Table S618.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
KDELR3 MUTATED 2 1 2 0
KDELR3 WILD-TYPE 153 65 54 96
'KDELR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S619.  Gene #64: 'KDELR3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
KDELR3 MUTATED 2 1 0 0 1 0 1
KDELR3 WILD-TYPE 88 72 50 19 36 58 45
'TTLL6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.165 (Fisher's exact test), Q value = 0.66

Table S620.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
TTLL6 MUTATED 2 2 0
TTLL6 WILD-TYPE 311 166 298
'TTLL6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.136 (Fisher's exact test), Q value = 0.6

Table S621.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
TTLL6 MUTATED 2 0 2 0 0
TTLL6 WILD-TYPE 93 111 140 63 185
'TTLL6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S622.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
TTLL6 MUTATED 0 2 1 1
TTLL6 WILD-TYPE 163 159 169 174
'TTLL6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.95

Table S623.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
TTLL6 MUTATED 3 0 0 0 0 1 0
TTLL6 WILD-TYPE 175 62 105 129 52 60 82
'TTLL6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.042 (Fisher's exact test), Q value = 0.29

Table S624.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
TTLL6 MUTATED 2 0 2 0
TTLL6 WILD-TYPE 105 179 231 262

Figure S125.  Get High-res Image Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TTLL6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.88

Table S625.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
TTLL6 MUTATED 2 0 1 0 0 0 1 0 0
TTLL6 WILD-TYPE 82 50 121 77 107 32 89 52 167
'TTLL6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.832 (Fisher's exact test), Q value = 1

Table S626.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
TTLL6 MUTATED 2 0 2
TTLL6 WILD-TYPE 327 164 280
'TTLL6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0574 (Fisher's exact test), Q value = 0.35

Table S627.  Gene #65: 'TTLL6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
TTLL6 MUTATED 2 1 1 0
TTLL6 WILD-TYPE 71 299 197 204
'STXBP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S628.  Gene #66: 'STXBP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
STXBP3 MUTATED 3 0 2
STXBP3 WILD-TYPE 310 168 296
'STXBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.543 (Fisher's exact test), Q value = 1

Table S629.  Gene #66: 'STXBP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
STXBP3 MUTATED 0 0 2 0 3
STXBP3 WILD-TYPE 95 111 140 63 182
'STXBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S630.  Gene #66: 'STXBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
STXBP3 MUTATED 1 0 1 3
STXBP3 WILD-TYPE 106 179 232 259
'STXBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.667 (Fisher's exact test), Q value = 1

Table S631.  Gene #66: 'STXBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
STXBP3 MUTATED 0 0 2 0 0 0 0 0 3
STXBP3 WILD-TYPE 84 50 120 77 107 32 90 52 164
'STXBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S632.  Gene #66: 'STXBP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
STXBP3 MUTATED 3 1 1
STXBP3 WILD-TYPE 326 163 281
'STXBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S633.  Gene #66: 'STXBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
STXBP3 MUTATED 0 1 1 3
STXBP3 WILD-TYPE 73 299 197 201
'FAM20C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0265 (Fisher's exact test), Q value = 0.22

Table S634.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
FAM20C MUTATED 5 0 0
FAM20C WILD-TYPE 308 168 298

Figure S126.  Get High-res Image Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'FAM20C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.203 (Fisher's exact test), Q value = 0.75

Table S635.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
FAM20C MUTATED 1 0 0 0 4
FAM20C WILD-TYPE 94 111 142 63 181
'FAM20C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S636.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
FAM20C MUTATED 2 1 1 1
FAM20C WILD-TYPE 161 160 169 174
'FAM20C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S637.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
FAM20C MUTATED 2 0 1 0 0 1 1
FAM20C WILD-TYPE 176 62 104 129 52 60 81
'FAM20C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0651 (Fisher's exact test), Q value = 0.37

Table S638.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
FAM20C MUTATED 1 0 0 4
FAM20C WILD-TYPE 106 179 233 258
'FAM20C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.88

Table S639.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
FAM20C MUTATED 1 0 0 0 0 0 0 0 4
FAM20C WILD-TYPE 83 50 122 77 107 32 90 52 163
'FAM20C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.29

Table S640.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
FAM20C MUTATED 5 0 0
FAM20C WILD-TYPE 324 164 282

Figure S127.  Get High-res Image Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'FAM20C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.16

Table S641.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
FAM20C MUTATED 1 0 0 4
FAM20C WILD-TYPE 72 300 198 200

Figure S128.  Get High-res Image Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'FAM20C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.96

Table S642.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
FAM20C MUTATED 3 0 0 0
FAM20C WILD-TYPE 152 66 56 96
'FAM20C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.323 (Fisher's exact test), Q value = 0.86

Table S643.  Gene #67: 'FAM20C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
FAM20C MUTATED 1 0 2 0 0 0 0
FAM20C WILD-TYPE 89 73 48 19 37 58 46
'CCBL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 0.97

Table S644.  Gene #68: 'CCBL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
CCBL2 MUTATED 2 1 0
CCBL2 WILD-TYPE 311 167 298
'CCBL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S645.  Gene #68: 'CCBL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
CCBL2 MUTATED 0 0 1 0 2
CCBL2 WILD-TYPE 95 111 141 63 183
'CCBL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S646.  Gene #68: 'CCBL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
CCBL2 MUTATED 0 0 1 2
CCBL2 WILD-TYPE 107 179 232 260
'CCBL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S647.  Gene #68: 'CCBL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
CCBL2 MUTATED 0 0 0 0 0 0 1 0 2
CCBL2 WILD-TYPE 84 50 122 77 107 32 89 52 165
'CCBL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S648.  Gene #68: 'CCBL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
CCBL2 MUTATED 2 0 1
CCBL2 WILD-TYPE 327 164 281
'CCBL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.84

Table S649.  Gene #68: 'CCBL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
CCBL2 MUTATED 0 0 1 2
CCBL2 WILD-TYPE 73 300 197 202
'B3GNT6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.177 (Fisher's exact test), Q value = 0.7

Table S650.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
B3GNT6 MUTATED 1 2 0
B3GNT6 WILD-TYPE 312 166 298
'B3GNT6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S651.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
B3GNT6 MUTATED 1 0 1 0 1
B3GNT6 WILD-TYPE 94 111 141 63 184
'B3GNT6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.714 (Fisher's exact test), Q value = 1

Table S652.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
B3GNT6 MUTATED 1 1 1 0
B3GNT6 WILD-TYPE 162 160 169 175
'B3GNT6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S653.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
B3GNT6 MUTATED 1 0 1 1 0 0 0
B3GNT6 WILD-TYPE 177 62 104 128 52 61 82
'B3GNT6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S654.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
B3GNT6 MUTATED 0 0 1 2
B3GNT6 WILD-TYPE 107 179 232 260
'B3GNT6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S655.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
B3GNT6 MUTATED 0 1 1 0 0 0 0 0 1
B3GNT6 WILD-TYPE 84 49 121 77 107 32 90 52 166
'B3GNT6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S656.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
B3GNT6 MUTATED 2 0 1
B3GNT6 WILD-TYPE 327 164 281
'B3GNT6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S657.  Gene #69: 'B3GNT6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
B3GNT6 MUTATED 0 1 1 1
B3GNT6 WILD-TYPE 73 299 197 203
'HNF1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S658.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 313 168 298
HNF1B MUTATED 2 0 2
HNF1B WILD-TYPE 311 168 296
'HNF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S659.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 95 111 142 63 185
HNF1B MUTATED 1 0 2 0 1
HNF1B WILD-TYPE 94 111 140 63 184
'HNF1B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0577 (Fisher's exact test), Q value = 0.35

Table S660.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 163 161 170 175
HNF1B MUTATED 0 3 1 0
HNF1B WILD-TYPE 163 158 169 175
'HNF1B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.73

Table S661.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 178 62 105 129 52 61 82
HNF1B MUTATED 2 2 0 0 0 0 0
HNF1B WILD-TYPE 176 60 105 129 52 61 82
'HNF1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S662.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 107 179 233 262
HNF1B MUTATED 1 0 2 1
HNF1B WILD-TYPE 106 179 231 261
'HNF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.6

Table S663.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7 CLUS_8 CLUS_9
ALL 84 50 122 77 107 32 90 52 167
HNF1B MUTATED 1 0 0 0 0 0 0 2 1
HNF1B WILD-TYPE 83 50 122 77 107 32 90 50 166
'HNF1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.834 (Fisher's exact test), Q value = 1

Table S664.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 329 164 282
HNF1B MUTATED 2 0 2
HNF1B WILD-TYPE 327 164 280
'HNF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S665.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 73 300 198 204
HNF1B MUTATED 1 1 1 1
HNF1B WILD-TYPE 72 299 197 203
'HNF1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S666.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 155 66 56 96
HNF1B MUTATED 1 1 0 1
HNF1B WILD-TYPE 154 65 56 95
'HNF1B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.97

Table S667.  Gene #70: 'HNF1B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 90 73 50 19 37 58 46
HNF1B MUTATED 0 0 1 0 0 1 1
HNF1B WILD-TYPE 90 73 49 19 37 57 45
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/KIPAN-TP/22815575/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/22570984/KIPAN-TP.transferedmergedcluster.txt

  • Number of patients = 784

  • Number of significantly mutated genes = 70

  • Number of Molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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