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 73 genes and 10 molecular subtypes across 668 patients, 160 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'.

  • PBRM1 mutation correlated to 'MRNA_CNMF',  'MRNA_CHIERARCHICAL',  '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',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

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

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

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

  • NF2 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

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

  • MUC5B mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • TDG mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF', and 'MRNASEQ_CNMF'.

  • NFE2L2 mutation correlated to 'MRNASEQ_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • ZNF814 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • DNMT3A mutation correlated to 'MRNASEQ_CNMF'.

  • CSGALNACT2 mutation correlated to 'CN_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

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

  • RIMBP3 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • ZNF598 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • STAG2 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

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

  • ARID1A mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • MED16 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • AHNAK2 mutation correlated to 'MRNA_CHIERARCHICAL',  'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • STAM mutation correlated to 'METHLYATION_CNMF' and 'MIRSEQ_MATURE_CNMF'.

  • RUFY3 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • FAM200A mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • NASP mutation correlated to 'MRNASEQ_CNMF'.

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

  • CCDC82 mutation correlated to 'CN_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • OR2L8 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • IDUA mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

  • GAPDHS mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • GFM1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_CHIERARCHICAL'.

  • FAT1 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 73 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 160 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
PBRM1 146 (22%) 522 0.015
(0.0925) 		0.022
(0.122) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243)
BAP1 49 (7%) 619 0.00032
(0.00508) 		0.00042
(0.00626) 		5e-05
(0.000986) 		3e-05
(0.000626) 		1e-05
(0.000243) 		1e-05
(0.000243) 		6e-05
(0.00112) 		9e-05
(0.0016) 		0.00281
(0.0253) 		0.0101
(0.0698)
VHL 174 (26%) 494 0.00031
(0.00503) 		0.00073
(0.00969) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243)
TP53 38 (6%) 630 2e-05
(0.000442) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		2e-05
(0.000442) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243)
HNRNPM 12 (2%) 656 0.0257
(0.138) 		0.00158
(0.017) 		0.00079
(0.00985) 		0.00173
(0.018) 		0.00122
(0.0139) 		0.0127
(0.0854) 		0.0308
(0.162) 		0.0202
(0.116)
MET 19 (3%) 649 0.00923
(0.0668) 		3e-05
(0.000626) 		1e-05
(0.000243) 		1e-05
(0.000243) 		2e-05
(0.000442) 		1e-05
(0.000243) 		0.0008
(0.00985) 		0.00015
(0.00255)
MUC5B 30 (4%) 638 0.0061
(0.0489) 		0.0001
(0.00174) 		8e-05
(0.00146) 		1e-05
(0.000243) 		1e-05
(0.000243) 		1e-05
(0.000243) 		0.0231
(0.127) 		0.00239
(0.0227)
ZNF814 13 (2%) 655 0.00779
(0.0577) 		0.00683
(0.0525) 		0.00173
(0.018) 		0.0143
(0.09) 		0.00977
(0.0686) 		0.0159
(0.0959) 		0.45
(0.951) 		0.304
(0.773)
ZNF598 11 (2%) 657 0.0319
(0.163) 		0.00222
(0.0215) 		0.00224
(0.0215) 		0.00081
(0.00985) 		0.00127
(0.0143) 		0.197
(0.578) 		0.0874
(0.337) 		0.00107
(0.0124)
SKI 9 (1%) 659 0.00083
(0.00993) 		0.128
(0.434) 		0.0003
(0.00498) 		0.00217
(0.0214) 		0.00073
(0.00969) 		0.0408
(0.195) 		0.0227
(0.125) 		0.0614
(0.27)
AHNAK2 33 (5%) 635 0.278
(0.732) 		0.0203
(0.116) 		0.544
(1.00) 		0.0334
(0.168) 		0.00588
(0.0477) 		0.00052
(0.0073) 		0.017
(0.1) 		0.0068
(0.0525) 		0.683
(1.00) 		0.275
(0.732)
PAM 4 (1%) 664 0.0194
(0.112) 		0.00585
(0.0477) 		0.0027
(0.0249) 		0.0154
(0.0944) 		0.0135
(0.0895) 		0.00075
(0.00978)
SETD2 58 (9%) 610 0.617
(1.00) 		0.662
(1.00) 		0.0162
(0.0971) 		0.0117
(0.0788) 		0.123
(0.424) 		6e-05
(0.00112) 		0.144
(0.465) 		0.00081
(0.00985) 		0.0386
(0.187) 		0.0636
(0.276)
KDM5C 30 (4%) 638 0.0258
(0.138) 		0.018
(0.105) 		0.0166
(0.0988) 		0.0054
(0.0448) 		0.00047
(0.00686) 		0.132
(0.441) 		0.865
(1.00) 		0.74
(1.00)
NEFH 15 (2%) 653 0.0705
(0.294) 		0.0136
(0.0895) 		0.00211
(0.0211) 		0.00433
(0.0368) 		0.0234
(0.128) 		5e-05
(0.000986) 		0.358
(0.844) 		0.253
(0.698)
KDM6A 11 (2%) 657 0.154
(0.481) 		0.00481
(0.0404) 		0.00938
(0.0668) 		0.0358
(0.177) 		0.026
(0.138) 		0.0014
(0.0153) 		0.28
(0.732) 		0.127
(0.433)
CSGALNACT2 8 (1%) 660 0.0039
(0.0335) 		0.248
(0.687) 		0.00924
(0.0668) 		0.0476
(0.217) 		0.0459
(0.211) 		0.0429
(0.2) 		0.0873
(0.337) 		0.235
(0.66)
GFM1 3 (0%) 665 0.277
(0.732) 		0.00997
(0.0693) 		0.00315
(0.0274) 		0.00178
(0.0183) 		0.0456
(0.211) 		0.00099
(0.0117)
PTEN 28 (4%) 640 0.314
(0.784) 		0.787
(1.00) 		0.0642
(0.277) 		0.425
(0.932) 		0.00648
(0.0509) 		0.00279
(0.0253) 		0.488
(0.999) 		0.0311
(0.162) 		0.0584
(0.259) 		0.00942
(0.0668)
NF2 16 (2%) 652 0.0726
(0.301) 		0.109
(0.389) 		0.00297
(0.0262) 		0.00035
(0.00532) 		0.0704
(0.294) 		0.173
(0.524) 		0.00252
(0.0236) 		0.0106
(0.0727)
MTOR 32 (5%) 636 0.00053
(0.0073) 		0.00782
(0.0577) 		0.146
(0.465) 		0.0851
(0.332) 		0.00134
(0.0148) 		0.00035
(0.00532) 		0.445
(0.947) 		0.0944
(0.357)
FAT1 22 (3%) 646 0.151
(0.476) 		0.0314
(0.162) 		0.00049
(0.00701) 		0.00184
(0.0187) 		0.0254
(0.137) 		0.131
(0.441) 		0.228
(0.65) 		0.068
(0.289)
TDG 5 (1%) 663 0.0327
(0.166) 		0.0377
(0.183) 		0.0351
(0.174) 		0.108
(0.389) 		0.121
(0.42) 		0.0534
(0.241) 		0.101
(0.374) 		0.28
(0.732)
IDUA 5 (1%) 663 0.545
(1.00) 		0.128
(0.434) 		0.00693
(0.0527) 		0.0158
(0.0959) 		0.0374
(0.183) 		0.0531
(0.241) 		0.322
(0.795) 		0.142
(0.461)
NFE2L2 10 (1%) 658 0.526
(1.00) 		0.108
(0.389) 		0.0431
(0.2) 		0.136
(0.448) 		0.5
(1.00) 		0.0337
(0.169) 		0.294
(0.757) 		0.441
(0.946)
STAM 6 (1%) 662 1
(1.00) 		0.0141
(0.09) 		0.33
(0.807) 		0.106
(0.387) 		0.32
(0.793) 		0.508
(1.00) 		0.00298
(0.0262) 		0.0575
(0.256)
CCDC82 6 (1%) 662 0.0217
(0.122) 		0.303
(0.773) 		0.0897
(0.343) 		0.0141
(0.09) 		0.278
(0.732) 		0.509
(1.00)
DNMT3A 10 (1%) 658 1
(1.00) 		0.348
(0.832) 		0.0313
(0.162) 		0.0971
(0.364) 		0.762
(1.00) 		0.384
(0.88) 		0.828
(1.00) 		0.438
(0.946)
RIMBP3 5 (1%) 663 0.446
(0.947) 		0.173
(0.524) 		0.62
(1.00) 		0.0143
(0.09) 		0.446
(0.947) 		0.472
(0.972)
STAG2 14 (2%) 654 1
(1.00) 		0.861
(1.00) 		0.539
(1.00) 		0.00624
(0.0495) 		0.197
(0.578) 		0.326
(0.802) 		0.135
(0.445) 		0.191
(0.568)
ARID1A 19 (3%) 649 0.956
(1.00) 		0.702
(1.00) 		0.0828
(0.328) 		0.261
(0.712) 		0.793
(1.00) 		0.28
(0.732) 		0.0139
(0.09) 		0.161
(0.495)
MED16 4 (1%) 664 0.461
(0.959) 		0.422
(0.932) 		0.906
(1.00) 		0.0417
(0.198) 		0.82
(1.00) 		1
(1.00) 		0.385
(0.88) 		0.207
(0.6)
RUFY3 7 (1%) 661 0.217
(0.622) 		0.423
(0.932) 		0.245
(0.684) 		0.124
(0.426) 		0.0766
(0.314) 		0.0205
(0.116)
FAM200A 5 (1%) 663 0.452
(0.952) 		0.0574
(0.256) 		0.00703
(0.0529) 		0.199
(0.582) 		0.769
(1.00)
NASP 4 (1%) 664 0.32
(0.793) 		0.068
(0.289) 		0.0407
(0.195) 		0.134
(0.445) 		0.273
(0.732) 		0.103
(0.377) 		0.0877
(0.337) 		0.145
(0.465)
OR2L8 7 (1%) 661 0.708
(1.00) 		0.589
(1.00) 		0.602
(1.00) 		0.084
(0.332) 		0.438
(0.946) 		0.677
(1.00) 		0.0426
(0.2) 		0.144
(0.464)
GAPDHS 5 (1%) 663 0.642
(1.00) 		0.26
(0.71) 		0.155
(0.482) 		0.0144
(0.09) 		0.12
(0.42) 		0.424
(0.932)
ATM 16 (2%) 652 0.73
(1.00) 		0.458
(0.959) 		0.383
(0.88) 		0.343
(0.827) 		0.748
(1.00) 		0.354
(0.843) 		0.756
(1.00) 		0.488
(0.999)
CDK12 9 (1%) 659 1
(1.00) 		0.884
(1.00) 		0.964
(1.00) 		0.993
(1.00) 		0.833
(1.00) 		0.533
(1.00) 		1
(1.00) 		0.425
(0.932)
PIK3CA 14 (2%) 654 0.134
(0.445) 		0.636
(1.00) 		0.12
(0.42) 		0.292
(0.754) 		0.61
(1.00) 		0.0628
(0.274)
KIAA1751 8 (1%) 660 0.903
(1.00) 		0.517
(1.00) 		0.629
(1.00) 		0.652
(1.00) 		0.215
(0.618) 		0.713
(1.00)
GPR50 5 (1%) 663 1
(1.00) 		0.615
(1.00) 		0.419
(0.932) 		0.555
(1.00) 		0.855
(1.00) 		0.425
(0.932)
CCDC120 4 (1%) 664 0.461
(0.959) 		0.528
(1.00) 		0.616
(1.00) 		0.355
(0.843) 		1
(1.00)
SLC6A14 5 (1%) 663 0.855
(1.00) 		0.1
(0.371) 		0.757
(1.00) 		0.555
(1.00) 		0.525
(1.00) 		0.423
(0.932) 		0.11
(0.391) 		0.152
(0.479)
CYP4F11 5 (1%) 663 0.451
(0.951) 		0.785
(1.00) 		0.371
(0.862) 		0.821
(1.00) 		0.245
(0.684) 		0.77
(1.00)
EGFR 7 (1%) 661 0.306
(0.773) 		0.339
(0.82) 		0.309
(0.774) 		0.528
(1.00) 		0.139
(0.456) 		0.652
(1.00)
DPCR1 8 (1%) 660 1
(1.00) 		0.799
(1.00) 		0.829
(1.00) 		0.892
(1.00) 		1
(1.00) 		1
(1.00)
GUSB 4 (1%) 664 0.39
(0.887) 		0.637
(1.00) 		0.363
(0.85) 		0.356
(0.843) 		1
(1.00)
PTCH1 8 (1%) 660 0.611
(1.00) 		0.718
(1.00) 		0.533
(1.00) 		0.334
(0.817) 		0.305
(0.773) 		0.851
(1.00)
RLIM 9 (1%) 659 0.702
(1.00) 		0.566
(1.00) 		0.584
(1.00) 		0.743
(1.00) 		0.081
(0.324) 		1
(1.00) 		0.908
(1.00) 		0.887
(1.00)
SLC23A1 7 (1%) 661 0.802
(1.00) 		0.516
(1.00) 		0.148
(0.469) 		0.233
(0.659) 		0.894
(1.00) 		0.68
(1.00)
RHEB 4 (1%) 664 0.564
(1.00) 		1
(1.00) 		1
(1.00) 		0.178
(0.534) 		0.214
(0.618) 		1
(1.00) 		0.44
(0.946) 		1
(1.00)
SLC4A8 6 (1%) 662 0.159
(0.491) 		0.363
(0.85) 		0.155
(0.482) 		0.428
(0.933) 		1
(1.00) 		0.192
(0.571)
PCK1 6 (1%) 662 0.882
(1.00) 		0.427
(0.933) 		0.845
(1.00) 		0.585
(1.00) 		0.584
(1.00) 		1
(1.00)
TXNIP 8 (1%) 660 0.181
(0.542) 		0.319
(0.793) 		0.391
(0.887) 		0.61
(1.00) 		0.305
(0.773) 		0.409
(0.924) 		0.583
(1.00) 		0.755
(1.00)
RNF128 5 (1%) 663 0.545
(1.00) 		0.175
(0.529) 		0.705
(1.00) 		0.677
(1.00) 		0.384
(0.88) 		1
(1.00)
ZFYVE26 9 (1%) 659 0.92
(1.00) 		0.483
(0.993) 		0.781
(1.00) 		0.366
(0.854) 		0.91
(1.00) 		0.639
(1.00) 		0.596
(1.00) 		0.259
(0.71)
FAM160B2 4 (1%) 664 0.844
(1.00) 		1
(1.00) 		0.905
(1.00) 		0.852
(1.00) 		0.445
(0.947) 		0.727
(1.00)
FAM47A 6 (1%) 662 0.882
(1.00) 		1
(1.00) 		0.892
(1.00) 		0.683
(1.00) 		0.497
(1.00) 		0.802
(1.00)
ATP1A1 10 (1%) 658 0.253
(0.698) 		0.634
(1.00) 		0.14
(0.456) 		1
(1.00) 		0.124
(0.426) 		0.787
(1.00) 		0.168
(0.514) 		0.503
(1.00)
SH3BP2 4 (1%) 664 0.068
(0.289) 		0.275
(0.732) 		0.109
(0.389) 		0.0922
(0.351) 		0.274
(0.732) 		0.193
(0.571)
RTL1 7 (1%) 661 0.502
(1.00) 		0.885
(1.00) 		0.078
(0.317) 		0.338
(0.82) 		0.493
(0.999) 		0.0812
(0.324) 		1
(1.00) 		0.235
(0.66)
RPL7A 3 (0%) 665 1
(1.00) 		0.0987
(0.368) 		0.0851
(0.332) 		0.0756
(0.312) 		0.233
(0.659) 		0.107
(0.389)
UIMC1 5 (1%) 663 0.548
(1.00) 		0.336
(0.818) 		0.931
(1.00) 		0.463
(0.959) 		0.0956
(0.36) 		0.771
(1.00)
TCEB1 3 (0%) 665 0.0686
(0.289) 		0.868
(1.00) 		0.63
(1.00) 		0.164
(0.502) 		1
(1.00)
SFMBT1 3 (0%) 665 0.49
(0.999) 		0.766
(1.00) 		0.745
(1.00) 		0.801
(1.00) 		0.622
(1.00)
SLC16A1 3 (0%) 665 1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.801
(1.00) 		0.626
(1.00)
TMCO3 7 (1%) 661 0.0782
(0.317) 		0.273
(0.732) 		0.867
(1.00) 		0.0806
(0.324) 		0.388
(0.885) 		1
(1.00)
NFAT5 8 (1%) 660 0.685
(1.00) 		0.632
(1.00) 		0.548
(1.00) 		0.679
(1.00) 		0.728
(1.00) 		1
(1.00)
HNF1B 3 (0%) 665 0.494
(0.999) 		0.786
(1.00) 		0.44
(0.946) 		0.494
(0.999) 		0.802
(1.00) 		0.359
(0.844)
ZC3H18 6 (1%) 662 0.882
(1.00) 		0.425
(0.932) 		0.801
(1.00) 		1
(1.00) 		0.869
(1.00) 		0.377
(0.874)
GPR137 4 (1%) 664 0.204
(0.595) 		0.598
(1.00) 		0.288
(0.745) 		0.346
(0.831) 		0.113
(0.397) 		0.307
(0.773)
RRP12 9 (1%) 659 0.84
(1.00) 		0.419
(0.932) 		0.467
(0.967) 		0.455
(0.954) 		0.287
(0.745) 		0.281
(0.732) 		0.93
(1.00) 		0.56
(1.00)
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
TP53 MUTATED 22 3 13
TP53 WILD-TYPE 158 239 230

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 = 0.00024

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TP53 MUTATED 26 5 3
TP53 WILD-TYPE 77 250 116

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
TP53 MUTATED 24 8 2 4
TP53 WILD-TYPE 74 166 243 145

Figure S3.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
TP53 MUTATED 23 6 2 5 1 1
TP53 WILD-TYPE 57 84 175 133 89 90

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
TP53 MUTATED 27 5 6
TP53 WILD-TYPE 187 143 290

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
TP53 MUTATED 23 12 3
TP53 WILD-TYPE 49 464 107

Figure S6.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
TP53 MUTATED 2 18 3 3
TP53 WILD-TYPE 74 42 39 96

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
TP53 MUTATED 0 0 5 3 18
TP53 WILD-TYPE 26 43 57 97 28

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.015 (Fisher's exact test), Q value = 0.093

Table S9.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 9 14
PBRM1 MUTATED 9 3 1 0
PBRM1 WILD-TYPE 12 14 8 14

Figure S9.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.022 (Fisher's exact test), Q value = 0.12

Table S10.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 17 14 10 9
PBRM1 MUTATED 5 3 0 4 1
PBRM1 WILD-TYPE 6 14 14 6 8

Figure S10.  Get High-res Image Gene #2: '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 = 0.00024

Table S11.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
PBRM1 MUTATED 5 71 70
PBRM1 WILD-TYPE 175 171 173

Figure S11.  Get High-res Image Gene #2: '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 = 0.00024

Table S12.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PBRM1 MUTATED 1 96 5
PBRM1 WILD-TYPE 102 159 114

Figure S12.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S13.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
PBRM1 MUTATED 2 42 94 7
PBRM1 WILD-TYPE 96 132 151 142

Figure S13.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S14.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
PBRM1 MUTATED 2 6 73 31 32 1
PBRM1 WILD-TYPE 78 84 104 107 58 90

Figure S14.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S15.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
PBRM1 MUTATED 7 24 111
PBRM1 WILD-TYPE 207 124 185

Figure S15.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S16.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
PBRM1 MUTATED 1 139 2
PBRM1 WILD-TYPE 71 337 108

Figure S16.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S17.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
PBRM1 MUTATED 4 1 2 31
PBRM1 WILD-TYPE 72 59 40 68

Figure S17.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'PBRM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S18.  Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
PBRM1 MUTATED 0 1 5 31 1
PBRM1 WILD-TYPE 26 42 57 69 45

Figure S18.  Get High-res Image Gene #2: 'PBRM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.314 (Fisher's exact test), Q value = 0.78

Table S19.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 9 14
PTEN MUTATED 0 2 1 1
PTEN WILD-TYPE 21 15 8 13
'PTEN MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S20.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 17 14 10 9
PTEN MUTATED 0 2 1 0 1
PTEN WILD-TYPE 11 15 13 10 8
'PTEN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0642 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
PTEN MUTATED 12 5 10
PTEN WILD-TYPE 168 237 233
'PTEN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S22.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PTEN MUTATED 6 8 5
PTEN WILD-TYPE 97 247 114
'PTEN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00648 (Fisher's exact test), Q value = 0.051

Table S23.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
PTEN MUTATED 7 12 3 6
PTEN WILD-TYPE 91 162 242 143

Figure S19.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PTEN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00279 (Fisher's exact test), Q value = 0.025

Table S24.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
PTEN MUTATED 7 0 4 10 1 6
PTEN WILD-TYPE 73 90 173 128 89 85

Figure S20.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S25.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
PTEN MUTATED 12 6 10
PTEN WILD-TYPE 202 142 286
'PTEN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0311 (Fisher's exact test), Q value = 0.16

Table S26.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
PTEN MUTATED 7 15 6
PTEN WILD-TYPE 65 461 104

Figure S21.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0584 (Fisher's exact test), Q value = 0.26

Table S27.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
PTEN MUTATED 6 5 0 2
PTEN WILD-TYPE 70 55 42 97
'PTEN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00942 (Fisher's exact test), Q value = 0.067

Table S28.  Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
PTEN MUTATED 2 4 0 2 5
PTEN WILD-TYPE 24 39 62 98 41

Figure S22.  Get High-res Image Gene #3: 'PTEN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.0051

Table S29.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 9 14
BAP1 MUTATED 1 8 0 0
BAP1 WILD-TYPE 20 9 9 14

Figure S23.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00042 (Fisher's exact test), Q value = 0.0063

Table S30.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 17 14 10 9
BAP1 MUTATED 0 8 0 1 0
BAP1 WILD-TYPE 11 9 14 9 9

Figure S24.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 5e-05 (Fisher's exact test), Q value = 0.00099

Table S31.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
BAP1 MUTATED 2 20 27
BAP1 WILD-TYPE 178 222 216

Figure S25.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'BAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00063

Table S32.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
BAP1 MUTATED 0 27 3
BAP1 WILD-TYPE 103 228 116

Figure S26.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S33.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
BAP1 MUTATED 0 30 14 5
BAP1 WILD-TYPE 98 144 231 144

Figure S27.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S34.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
BAP1 MUTATED 0 4 6 36 3 0
BAP1 WILD-TYPE 80 86 171 102 87 91

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

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S35.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
BAP1 MUTATED 5 21 23
BAP1 WILD-TYPE 209 127 273

Figure S29.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 9e-05 (Fisher's exact test), Q value = 0.0016

Table S36.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
BAP1 MUTATED 0 47 2
BAP1 WILD-TYPE 72 429 108

Figure S30.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00281 (Fisher's exact test), Q value = 0.025

Table S37.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
BAP1 MUTATED 0 0 2 9
BAP1 WILD-TYPE 76 60 40 90

Figure S31.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'BAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0101 (Fisher's exact test), Q value = 0.07

Table S38.  Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
BAP1 MUTATED 0 0 1 10 0
BAP1 WILD-TYPE 26 43 61 90 46

Figure S32.  Get High-res Image Gene #4: 'BAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.617 (Fisher's exact test), Q value = 1

Table S39.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 9 14
SETD2 MUTATED 2 2 0 0
SETD2 WILD-TYPE 19 15 9 14
'SETD2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.662 (Fisher's exact test), Q value = 1

Table S40.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 17 14 10 9
SETD2 MUTATED 1 2 0 1 0
SETD2 WILD-TYPE 10 15 14 9 9
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0162 (Fisher's exact test), Q value = 0.097

Table S41.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SETD2 MUTATED 7 24 27
SETD2 WILD-TYPE 173 218 216

Figure S33.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0117 (Fisher's exact test), Q value = 0.079

Table S42.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SETD2 MUTATED 3 31 8
SETD2 WILD-TYPE 100 224 111

Figure S34.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.123 (Fisher's exact test), Q value = 0.42

Table S43.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SETD2 MUTATED 3 18 25 12
SETD2 WILD-TYPE 95 156 220 137
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0011

Table S44.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SETD2 MUTATED 2 13 24 14 5 0
SETD2 WILD-TYPE 78 77 153 124 85 91

Figure S35.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.144 (Fisher's exact test), Q value = 0.46

Table S45.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SETD2 MUTATED 12 13 31
SETD2 WILD-TYPE 202 135 265
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0099

Table S46.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SETD2 MUTATED 2 52 2
SETD2 WILD-TYPE 70 424 108

Figure S36.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0386 (Fisher's exact test), Q value = 0.19

Table S47.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
SETD2 MUTATED 5 1 3 14
SETD2 WILD-TYPE 71 59 39 85

Figure S37.  Get High-res Image Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0636 (Fisher's exact test), Q value = 0.28

Table S48.  Gene #5: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
SETD2 MUTATED 0 2 7 13 1
SETD2 WILD-TYPE 26 41 55 87 45
'KDM5C MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0258 (Fisher's exact test), Q value = 0.14

Table S49.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
KDM5C MUTATED 4 8 18
KDM5C WILD-TYPE 176 234 225

Figure S38.  Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KDM5C MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.018 (Fisher's exact test), Q value = 0.11

Table S50.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
KDM5C MUTATED 1 17 2
KDM5C WILD-TYPE 102 238 117

Figure S39.  Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.099

Table S51.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
KDM5C MUTATED 1 12 14 2
KDM5C WILD-TYPE 97 162 231 147

Figure S40.  Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0054 (Fisher's exact test), Q value = 0.045

Table S52.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
KDM5C MUTATED 1 0 16 7 3 2
KDM5C WILD-TYPE 79 90 161 131 87 89

Figure S41.  Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00047 (Fisher's exact test), Q value = 0.0069

Table S53.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
KDM5C MUTATED 3 3 24
KDM5C WILD-TYPE 211 145 272

Figure S42.  Get High-res Image Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KDM5C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.44

Table S54.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
KDM5C MUTATED 1 27 2
KDM5C WILD-TYPE 71 449 108
'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.865 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
KDM5C MUTATED 1 1 0 3
KDM5C WILD-TYPE 75 59 42 96
'KDM5C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.74 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: 'KDM5C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
KDM5C MUTATED 0 1 0 3 1
KDM5C WILD-TYPE 26 42 62 97 45
'NEFH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0705 (Fisher's exact test), Q value = 0.29

Table S57.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
NEFH MUTATED 8 4 3
NEFH WILD-TYPE 172 238 240
'NEFH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0136 (Fisher's exact test), Q value = 0.09

Table S58.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NEFH MUTATED 1 4 8
NEFH WILD-TYPE 102 251 111

Figure S43.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00211 (Fisher's exact test), Q value = 0.021

Table S59.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
NEFH MUTATED 1 1 3 10
NEFH WILD-TYPE 97 173 242 139

Figure S44.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00433 (Fisher's exact test), Q value = 0.037

Table S60.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
NEFH MUTATED 0 6 2 2 0 5
NEFH WILD-TYPE 80 84 175 136 90 86

Figure S45.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0234 (Fisher's exact test), Q value = 0.13

Table S61.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
NEFH MUTATED 10 2 3
NEFH WILD-TYPE 204 146 293

Figure S46.  Get High-res Image Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NEFH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00099

Table S62.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
NEFH MUTATED 0 5 10
NEFH WILD-TYPE 72 471 100

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

'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.358 (Fisher's exact test), Q value = 0.84

Table S63.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
NEFH MUTATED 3 0 0 3
NEFH WILD-TYPE 73 60 42 96
'NEFH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.7

Table S64.  Gene #7: 'NEFH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
NEFH MUTATED 0 3 1 2 0
NEFH WILD-TYPE 26 40 61 98 46
'VHL MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.00031 (Fisher's exact test), Q value = 0.005

Table S65.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 9 14
VHL MUTATED 13 5 1 0
VHL WILD-TYPE 8 12 8 14

Figure S48.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

'VHL MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.00073 (Fisher's exact test), Q value = 0.0097

Table S66.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 17 14 10 9
VHL MUTATED 7 5 0 6 1
VHL WILD-TYPE 4 12 14 4 8

Figure S49.  Get High-res Image Gene #8: '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 = 0.00024

Table S67.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
VHL MUTATED 4 93 77
VHL WILD-TYPE 176 149 166

Figure S50.  Get High-res Image Gene #8: '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 = 0.00024

Table S68.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
VHL MUTATED 1 114 1
VHL WILD-TYPE 102 141 118

Figure S51.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S69.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
VHL MUTATED 4 58 110 2
VHL WILD-TYPE 94 116 135 147

Figure S52.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'VHL MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S70.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
VHL MUTATED 2 2 78 52 40 0
VHL WILD-TYPE 78 88 99 86 50 91

Figure S53.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S71.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
VHL MUTATED 4 46 120
VHL WILD-TYPE 210 102 176

Figure S54.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'VHL MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S72.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
VHL MUTATED 1 169 0
VHL WILD-TYPE 71 307 110

Figure S55.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S73.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
VHL MUTATED 0 1 0 47
VHL WILD-TYPE 76 59 42 52

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

'VHL MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S74.  Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
VHL MUTATED 0 0 0 47 1
VHL WILD-TYPE 26 43 62 53 45

Figure S57.  Get High-res Image Gene #8: 'VHL MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0726 (Fisher's exact test), Q value = 0.3

Table S75.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
NF2 MUTATED 7 2 7
NF2 WILD-TYPE 173 240 236
'NF2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.39

Table S76.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NF2 MUTATED 4 3 5
NF2 WILD-TYPE 99 252 114
'NF2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00297 (Fisher's exact test), Q value = 0.026

Table S77.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
NF2 MUTATED 1 5 1 9
NF2 WILD-TYPE 97 169 244 140

Figure S58.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NF2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0053

Table S78.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
NF2 MUTATED 0 8 1 3 0 4
NF2 WILD-TYPE 80 82 176 135 90 87

Figure S59.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0704 (Fisher's exact test), Q value = 0.29

Table S79.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
NF2 MUTATED 9 4 3
NF2 WILD-TYPE 205 144 293
'NF2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.52

Table S80.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
NF2 MUTATED 0 11 5
NF2 WILD-TYPE 72 465 105
'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00252 (Fisher's exact test), Q value = 0.024

Table S81.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
NF2 MUTATED 3 0 4 0
NF2 WILD-TYPE 73 60 38 99

Figure S60.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0106 (Fisher's exact test), Q value = 0.073

Table S82.  Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
NF2 MUTATED 0 3 4 0 0
NF2 WILD-TYPE 26 40 58 100 46

Figure S61.  Get High-res Image Gene #9: 'NF2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0257 (Fisher's exact test), Q value = 0.14

Table S83.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
HNRNPM MUTATED 7 4 1
HNRNPM WILD-TYPE 173 238 242

Figure S62.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'HNRNPM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00158 (Fisher's exact test), Q value = 0.017

Table S84.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
HNRNPM MUTATED 4 1 7
HNRNPM WILD-TYPE 99 254 112

Figure S63.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00079 (Fisher's exact test), Q value = 0.0099

Table S85.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
HNRNPM MUTATED 2 2 0 8
HNRNPM WILD-TYPE 96 172 245 141

Figure S64.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HNRNPM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00173 (Fisher's exact test), Q value = 0.018

Table S86.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
HNRNPM MUTATED 2 5 0 1 0 4
HNRNPM WILD-TYPE 78 85 177 137 90 87

Figure S65.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00122 (Fisher's exact test), Q value = 0.014

Table S87.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
HNRNPM MUTATED 8 4 0
HNRNPM WILD-TYPE 206 144 296

Figure S66.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0127 (Fisher's exact test), Q value = 0.085

Table S88.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
HNRNPM MUTATED 1 5 6
HNRNPM WILD-TYPE 71 471 104

Figure S67.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.16

Table S89.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
HNRNPM MUTATED 5 3 2 0
HNRNPM WILD-TYPE 71 57 40 99

Figure S68.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HNRNPM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0202 (Fisher's exact test), Q value = 0.12

Table S90.  Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
HNRNPM MUTATED 2 3 4 0 1
HNRNPM WILD-TYPE 24 40 58 100 45

Figure S69.  Get High-res Image Gene #10: 'HNRNPM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00923 (Fisher's exact test), Q value = 0.067

Table S91.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
MET MUTATED 11 4 3
MET WILD-TYPE 169 238 240

Figure S70.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.00063

Table S92.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MET MUTATED 1 3 13
MET WILD-TYPE 102 252 106

Figure S71.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S93.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
MET MUTATED 0 1 1 17
MET WILD-TYPE 98 173 244 132

Figure S72.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S94.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
MET MUTATED 0 4 1 0 0 14
MET WILD-TYPE 80 86 176 138 90 77

Figure S73.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00044

Table S95.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
MET MUTATED 15 3 1
MET WILD-TYPE 199 145 295

Figure S74.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S96.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
MET MUTATED 0 5 14
MET WILD-TYPE 72 471 96

Figure S75.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 8e-04 (Fisher's exact test), Q value = 0.0099

Table S97.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
MET MUTATED 9 0 3 1
MET WILD-TYPE 67 60 39 98

Figure S76.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00015 (Fisher's exact test), Q value = 0.0025

Table S98.  Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
MET MUTATED 4 5 4 0 0
MET WILD-TYPE 22 38 58 100 46

Figure S77.  Get High-res Image Gene #11: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0061 (Fisher's exact test), Q value = 0.049

Table S99.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
MUC5B MUTATED 16 6 8
MUC5B WILD-TYPE 164 236 235

Figure S78.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MUC5B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-04 (Fisher's exact test), Q value = 0.0017

Table S100.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MUC5B MUTATED 13 5 11
MUC5B WILD-TYPE 90 250 108

Figure S79.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.0015

Table S101.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
MUC5B MUTATED 10 3 4 13
MUC5B WILD-TYPE 88 171 241 136

Figure S80.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'MUC5B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S102.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
MUC5B MUTATED 10 10 4 1 0 5
MUC5B WILD-TYPE 70 80 173 137 90 86

Figure S81.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S103.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
MUC5B MUTATED 23 2 5
MUC5B WILD-TYPE 191 146 291

Figure S82.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00024

Table S104.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
MUC5B MUTATED 10 10 10
MUC5B WILD-TYPE 62 466 100

Figure S83.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0231 (Fisher's exact test), Q value = 0.13

Table S105.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
MUC5B MUTATED 8 8 4 2
MUC5B WILD-TYPE 68 52 38 97

Figure S84.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'MUC5B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00239 (Fisher's exact test), Q value = 0.023

Table S106.  Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
MUC5B MUTATED 3 4 6 1 8
MUC5B WILD-TYPE 23 39 56 99 38

Figure S85.  Get High-res Image Gene #12: 'MUC5B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.48

Table S107.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
KDM6A MUTATED 6 3 2
KDM6A WILD-TYPE 174 239 241
'KDM6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00481 (Fisher's exact test), Q value = 0.04

Table S108.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
KDM6A MUTATED 1 1 6
KDM6A WILD-TYPE 102 254 113

Figure S86.  Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00938 (Fisher's exact test), Q value = 0.067

Table S109.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
KDM6A MUTATED 1 0 3 7
KDM6A WILD-TYPE 97 174 242 142

Figure S87.  Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0358 (Fisher's exact test), Q value = 0.18

Table S110.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
KDM6A MUTATED 0 4 1 1 1 4
KDM6A WILD-TYPE 80 86 176 137 89 87

Figure S88.  Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.026 (Fisher's exact test), Q value = 0.14

Table S111.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
KDM6A MUTATED 8 1 2
KDM6A WILD-TYPE 206 147 294

Figure S89.  Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0014 (Fisher's exact test), Q value = 0.015

Table S112.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
KDM6A MUTATED 0 4 7
KDM6A WILD-TYPE 72 472 103

Figure S90.  Get High-res Image Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.28 (Fisher's exact test), Q value = 0.73

Table S113.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
KDM6A MUTATED 2 1 0 0
KDM6A WILD-TYPE 74 59 42 99
'KDM6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.127 (Fisher's exact test), Q value = 0.43

Table S114.  Gene #13: 'KDM6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
KDM6A MUTATED 0 2 1 0 0
KDM6A WILD-TYPE 26 41 61 100 46
'TDG MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0327 (Fisher's exact test), Q value = 0.17

Table S115.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
TDG MUTATED 4 0 1
TDG WILD-TYPE 176 242 242

Figure S91.  Get High-res Image Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'TDG MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0377 (Fisher's exact test), Q value = 0.18

Table S116.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TDG MUTATED 0 1 4
TDG WILD-TYPE 103 254 115

Figure S92.  Get High-res Image Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'TDG MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0351 (Fisher's exact test), Q value = 0.17

Table S117.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
TDG MUTATED 0 0 1 4
TDG WILD-TYPE 98 174 244 145

Figure S93.  Get High-res Image Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'TDG MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.39

Table S118.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
TDG MUTATED 0 2 0 1 0 2
TDG WILD-TYPE 80 88 177 137 90 89
'TDG MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.42

Table S119.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
TDG MUTATED 4 0 1
TDG WILD-TYPE 210 148 295
'TDG MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0534 (Fisher's exact test), Q value = 0.24

Table S120.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
TDG MUTATED 0 2 3
TDG WILD-TYPE 72 474 107
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.101 (Fisher's exact test), Q value = 0.37

Table S121.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
TDG MUTATED 4 0 0 1
TDG WILD-TYPE 72 60 42 98
'TDG MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.73

Table S122.  Gene #14: 'TDG MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
TDG MUTATED 1 2 1 1 0
TDG WILD-TYPE 25 41 61 99 46
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.526 (Fisher's exact test), Q value = 1

Table S123.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
NFE2L2 MUTATED 4 2 4
NFE2L2 WILD-TYPE 176 240 239
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.39

Table S124.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NFE2L2 MUTATED 0 3 4
NFE2L2 WILD-TYPE 103 252 115
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0431 (Fisher's exact test), Q value = 0.2

Table S125.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
NFE2L2 MUTATED 0 4 1 5
NFE2L2 WILD-TYPE 98 170 244 144

Figure S94.  Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.136 (Fisher's exact test), Q value = 0.45

Table S126.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
NFE2L2 MUTATED 0 2 1 4 0 3
NFE2L2 WILD-TYPE 80 88 176 134 90 88
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.5 (Fisher's exact test), Q value = 1

Table S127.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
NFE2L2 MUTATED 5 2 3
NFE2L2 WILD-TYPE 209 146 293
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0337 (Fisher's exact test), Q value = 0.17

Table S128.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
NFE2L2 MUTATED 0 5 5
NFE2L2 WILD-TYPE 72 471 105

Figure S95.  Get High-res Image Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 0.76

Table S129.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
NFE2L2 MUTATED 3 0 0 1
NFE2L2 WILD-TYPE 73 60 42 98
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.441 (Fisher's exact test), Q value = 0.95

Table S130.  Gene #15: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
NFE2L2 MUTATED 0 2 1 1 0
NFE2L2 WILD-TYPE 26 41 61 99 46
'ATM MUTATION STATUS' versus 'CN_CNMF'

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

Table S131.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
ATM MUTATED 3 7 6
ATM WILD-TYPE 177 235 237
'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.96

Table S132.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ATM MUTATED 3 8 1
ATM WILD-TYPE 100 247 118
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.88

Table S133.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
ATM MUTATED 3 4 8 1
ATM WILD-TYPE 95 170 237 148
'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.343 (Fisher's exact test), Q value = 0.83

Table S134.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
ATM MUTATED 3 0 5 3 4 1
ATM WILD-TYPE 77 90 172 135 86 90
'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.748 (Fisher's exact test), Q value = 1

Table S135.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
ATM MUTATED 5 2 8
ATM WILD-TYPE 209 146 288
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.84

Table S136.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
ATM MUTATED 3 11 1
ATM WILD-TYPE 69 465 109
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.756 (Fisher's exact test), Q value = 1

Table S137.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
ATM MUTATED 1 2 0 2
ATM WILD-TYPE 75 58 42 97
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.488 (Fisher's exact test), Q value = 1

Table S138.  Gene #16: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
ATM MUTATED 0 1 0 2 2
ATM WILD-TYPE 26 42 62 98 44
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00779 (Fisher's exact test), Q value = 0.058

Table S139.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
ZNF814 MUTATED 6 0 7
ZNF814 WILD-TYPE 174 242 236

Figure S96.  Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00683 (Fisher's exact test), Q value = 0.052

Table S140.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ZNF814 MUTATED 4 2 7
ZNF814 WILD-TYPE 99 253 112

Figure S97.  Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00173 (Fisher's exact test), Q value = 0.018

Table S141.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
ZNF814 MUTATED 3 1 1 8
ZNF814 WILD-TYPE 95 173 244 141

Figure S98.  Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.09

Table S142.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
ZNF814 MUTATED 3 5 1 1 0 3
ZNF814 WILD-TYPE 77 85 176 137 90 88

Figure S99.  Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00977 (Fisher's exact test), Q value = 0.069

Table S143.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
ZNF814 MUTATED 7 5 1
ZNF814 WILD-TYPE 207 143 295

Figure S100.  Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.096

Table S144.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
ZNF814 MUTATED 3 5 5
ZNF814 WILD-TYPE 69 471 105

Figure S101.  Get High-res Image Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 0.95

Table S145.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
ZNF814 MUTATED 5 2 1 2
ZNF814 WILD-TYPE 71 58 41 97
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.77

Table S146.  Gene #17: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
ZNF814 MUTATED 1 2 4 1 2
ZNF814 WILD-TYPE 25 41 58 99 44
'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

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

Table S147.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
DNMT3A MUTATED 2 4 4
DNMT3A WILD-TYPE 178 238 239
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.348 (Fisher's exact test), Q value = 0.83

Table S148.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
DNMT3A MUTATED 0 5 3
DNMT3A WILD-TYPE 103 250 116
'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0313 (Fisher's exact test), Q value = 0.16

Table S149.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
DNMT3A MUTATED 0 0 5 5
DNMT3A WILD-TYPE 98 174 240 144

Figure S102.  Get High-res Image Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0971 (Fisher's exact test), Q value = 0.36

Table S150.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
DNMT3A MUTATED 0 2 2 0 3 3
DNMT3A WILD-TYPE 80 88 175 138 87 88
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.762 (Fisher's exact test), Q value = 1

Table S151.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
DNMT3A MUTATED 4 2 3
DNMT3A WILD-TYPE 210 146 293
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.88

Table S152.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
DNMT3A MUTATED 0 6 3
DNMT3A WILD-TYPE 72 470 107
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.828 (Fisher's exact test), Q value = 1

Table S153.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
DNMT3A MUTATED 2 1 0 1
DNMT3A WILD-TYPE 74 59 42 98
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.438 (Fisher's exact test), Q value = 0.95

Table S154.  Gene #18: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
DNMT3A MUTATED 0 2 1 1 0
DNMT3A WILD-TYPE 26 41 61 99 46
'CDK12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S155.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
CDK12 MUTATED 2 3 4
CDK12 WILD-TYPE 178 239 239
'CDK12 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S156.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
CDK12 MUTATED 2 4 1
CDK12 WILD-TYPE 101 251 118
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.964 (Fisher's exact test), Q value = 1

Table S157.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
CDK12 MUTATED 1 3 3 2
CDK12 WILD-TYPE 97 171 242 147
'CDK12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.993 (Fisher's exact test), Q value = 1

Table S158.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
CDK12 MUTATED 1 1 2 3 1 1
CDK12 WILD-TYPE 79 89 175 135 89 90
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S159.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
CDK12 MUTATED 3 1 5
CDK12 WILD-TYPE 211 147 291
'CDK12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S160.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
CDK12 MUTATED 1 8 0
CDK12 WILD-TYPE 71 468 110
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S161.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
CDK12 MUTATED 1 1 1 2
CDK12 WILD-TYPE 75 59 41 97
'CDK12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S162.  Gene #19: 'CDK12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
CDK12 MUTATED 1 0 0 3 1
CDK12 WILD-TYPE 25 43 62 97 45
'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0039 (Fisher's exact test), Q value = 0.033

Table S163.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
CSGALNACT2 MUTATED 6 0 2
CSGALNACT2 WILD-TYPE 174 242 241

Figure S103.  Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.69

Table S164.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
CSGALNACT2 MUTATED 3 2 3
CSGALNACT2 WILD-TYPE 100 253 116
'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00924 (Fisher's exact test), Q value = 0.067

Table S165.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
CSGALNACT2 MUTATED 3 1 0 4
CSGALNACT2 WILD-TYPE 95 173 245 145

Figure S104.  Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0476 (Fisher's exact test), Q value = 0.22

Table S166.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
CSGALNACT2 MUTATED 2 3 0 1 0 2
CSGALNACT2 WILD-TYPE 78 87 177 137 90 89

Figure S105.  Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0459 (Fisher's exact test), Q value = 0.21

Table S167.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
CSGALNACT2 MUTATED 6 1 1
CSGALNACT2 WILD-TYPE 208 147 295

Figure S106.  Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0429 (Fisher's exact test), Q value = 0.2

Table S168.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
CSGALNACT2 MUTATED 2 3 3
CSGALNACT2 WILD-TYPE 70 473 107

Figure S107.  Get High-res Image Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0873 (Fisher's exact test), Q value = 0.34

Table S169.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
CSGALNACT2 MUTATED 0 2 1 0
CSGALNACT2 WILD-TYPE 76 58 41 99
'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.66

Table S170.  Gene #20: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
CSGALNACT2 MUTATED 0 0 2 0 1
CSGALNACT2 WILD-TYPE 26 43 60 100 45
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.134 (Fisher's exact test), Q value = 0.44

Table S171.  Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
PIK3CA MUTATED 1 5 8
PIK3CA WILD-TYPE 179 237 235
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.636 (Fisher's exact test), Q value = 1

Table S172.  Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PIK3CA MUTATED 1 6 1
PIK3CA WILD-TYPE 102 249 118
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.42

Table S173.  Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
PIK3CA MUTATED 0 6 7 1
PIK3CA WILD-TYPE 98 168 238 148
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.292 (Fisher's exact test), Q value = 0.75

Table S174.  Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
PIK3CA MUTATED 0 1 3 5 4 1
PIK3CA WILD-TYPE 80 89 174 133 86 90
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S175.  Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
PIK3CA MUTATED 3 4 7
PIK3CA WILD-TYPE 211 144 289
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0628 (Fisher's exact test), Q value = 0.27

Table S176.  Gene #21: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
PIK3CA MUTATED 0 14 0
PIK3CA WILD-TYPE 72 462 110
'KIAA1751 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.903 (Fisher's exact test), Q value = 1

Table S177.  Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
KIAA1751 MUTATED 2 2 4
KIAA1751 WILD-TYPE 178 240 239
'KIAA1751 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S178.  Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
KIAA1751 MUTATED 0 5 2
KIAA1751 WILD-TYPE 103 250 117
'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S179.  Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
KIAA1751 MUTATED 0 1 4 2
KIAA1751 WILD-TYPE 98 173 241 147
'KIAA1751 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S180.  Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
KIAA1751 MUTATED 0 0 3 1 1 2
KIAA1751 WILD-TYPE 80 90 174 137 89 89
'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.215 (Fisher's exact test), Q value = 0.62

Table S181.  Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
KIAA1751 MUTATED 2 0 6
KIAA1751 WILD-TYPE 212 148 290
'KIAA1751 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.713 (Fisher's exact test), Q value = 1

Table S182.  Gene #22: 'KIAA1751 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
KIAA1751 MUTATED 0 6 2
KIAA1751 WILD-TYPE 72 470 108
'MTOR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00053 (Fisher's exact test), Q value = 0.0073

Table S183.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
MTOR MUTATED 1 11 20
MTOR WILD-TYPE 179 231 223

Figure S108.  Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MTOR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00782 (Fisher's exact test), Q value = 0.058

Table S184.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MTOR MUTATED 5 21 1
MTOR WILD-TYPE 98 234 118

Figure S109.  Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'MTOR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.46

Table S185.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
MTOR MUTATED 3 12 14 3
MTOR WILD-TYPE 95 162 231 146
'MTOR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0851 (Fisher's exact test), Q value = 0.33

Table S186.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
MTOR MUTATED 2 4 7 9 9 1
MTOR WILD-TYPE 78 86 170 129 81 90
'MTOR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00134 (Fisher's exact test), Q value = 0.015

Table S187.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
MTOR MUTATED 2 9 21
MTOR WILD-TYPE 212 139 275

Figure S110.  Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'MTOR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00035 (Fisher's exact test), Q value = 0.0053

Table S188.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
MTOR MUTATED 0 32 0
MTOR WILD-TYPE 72 444 110

Figure S111.  Get High-res Image Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.95

Table S189.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
MTOR MUTATED 1 2 2 6
MTOR WILD-TYPE 75 58 40 93
'MTOR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0944 (Fisher's exact test), Q value = 0.36

Table S190.  Gene #23: 'MTOR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
MTOR MUTATED 0 0 4 7 0
MTOR WILD-TYPE 26 43 58 93 46
'RIMBP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.95

Table S191.  Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RIMBP3 MUTATED 0 2 3
RIMBP3 WILD-TYPE 180 240 240
'RIMBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.52

Table S192.  Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RIMBP3 MUTATED 2 1 0
RIMBP3 WILD-TYPE 101 254 119
'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.62 (Fisher's exact test), Q value = 1

Table S193.  Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RIMBP3 MUTATED 1 1 3 0
RIMBP3 WILD-TYPE 97 173 242 149
'RIMBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.09

Table S194.  Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RIMBP3 MUTATED 1 1 0 0 3 0
RIMBP3 WILD-TYPE 79 89 177 138 87 91

Figure S112.  Get High-res Image Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 0.95

Table S195.  Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RIMBP3 MUTATED 1 2 1
RIMBP3 WILD-TYPE 213 146 295
'RIMBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S196.  Gene #24: 'RIMBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RIMBP3 MUTATED 1 3 0
RIMBP3 WILD-TYPE 71 473 110
'ZNF598 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0319 (Fisher's exact test), Q value = 0.16

Table S197.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
ZNF598 MUTATED 7 2 2
ZNF598 WILD-TYPE 173 240 241

Figure S113.  Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ZNF598 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00222 (Fisher's exact test), Q value = 0.022

Table S198.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ZNF598 MUTATED 2 1 7
ZNF598 WILD-TYPE 101 254 112

Figure S114.  Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00224 (Fisher's exact test), Q value = 0.022

Table S199.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
ZNF598 MUTATED 1 1 1 8
ZNF598 WILD-TYPE 97 173 244 141

Figure S115.  Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ZNF598 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00081 (Fisher's exact test), Q value = 0.0099

Table S200.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
ZNF598 MUTATED 1 3 0 1 0 6
ZNF598 WILD-TYPE 79 87 177 137 90 85

Figure S116.  Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00127 (Fisher's exact test), Q value = 0.014

Table S201.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
ZNF598 MUTATED 8 3 0
ZNF598 WILD-TYPE 206 145 296

Figure S117.  Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'ZNF598 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.58

Table S202.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
ZNF598 MUTATED 1 6 4
ZNF598 WILD-TYPE 71 470 106
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0874 (Fisher's exact test), Q value = 0.34

Table S203.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
ZNF598 MUTATED 3 3 4 1
ZNF598 WILD-TYPE 73 57 38 98
'ZNF598 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00107 (Fisher's exact test), Q value = 0.012

Table S204.  Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
ZNF598 MUTATED 5 0 4 1 1
ZNF598 WILD-TYPE 21 43 58 99 45

Figure S118.  Get High-res Image Gene #25: 'ZNF598 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'GPR50 MUTATION STATUS' versus 'CN_CNMF'

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

Table S205.  Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
GPR50 MUTATED 1 2 2
GPR50 WILD-TYPE 179 240 241
'GPR50 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.615 (Fisher's exact test), Q value = 1

Table S206.  Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
GPR50 MUTATED 2 2 1
GPR50 WILD-TYPE 101 253 118
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 0.93

Table S207.  Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
GPR50 MUTATED 2 1 1 1
GPR50 WILD-TYPE 96 173 244 148
'GPR50 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.555 (Fisher's exact test), Q value = 1

Table S208.  Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
GPR50 MUTATED 1 1 0 1 1 1
GPR50 WILD-TYPE 79 89 177 137 89 90
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S209.  Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
GPR50 MUTATED 1 1 3
GPR50 WILD-TYPE 213 147 293
'GPR50 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S210.  Gene #26: 'GPR50 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
GPR50 MUTATED 1 3 1
GPR50 WILD-TYPE 71 473 109
'CCDC120 MUTATION STATUS' versus 'CN_CNMF'

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

Table S211.  Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
CCDC120 MUTATED 0 1 3
CCDC120 WILD-TYPE 180 241 240
'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S212.  Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
CCDC120 MUTATED 0 1 3 0
CCDC120 WILD-TYPE 98 173 242 149
'CCDC120 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S213.  Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
CCDC120 MUTATED 0 0 3 1 0 0
CCDC120 WILD-TYPE 80 90 174 137 90 91
'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.355 (Fisher's exact test), Q value = 0.84

Table S214.  Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
CCDC120 MUTATED 0 1 3
CCDC120 WILD-TYPE 214 147 293
'CCDC120 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S215.  Gene #27: 'CCDC120 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
CCDC120 MUTATED 0 4 0
CCDC120 WILD-TYPE 72 472 110
'SLC6A14 MUTATION STATUS' versus 'CN_CNMF'

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

Table S216.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SLC6A14 MUTATED 2 1 2
SLC6A14 WILD-TYPE 178 241 241
'SLC6A14 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.1 (Fisher's exact test), Q value = 0.37

Table S217.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SLC6A14 MUTATED 1 0 2
SLC6A14 WILD-TYPE 102 255 117
'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.757 (Fisher's exact test), Q value = 1

Table S218.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SLC6A14 MUTATED 1 2 1 1
SLC6A14 WILD-TYPE 97 172 244 148
'SLC6A14 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.555 (Fisher's exact test), Q value = 1

Table S219.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SLC6A14 MUTATED 1 1 0 1 1 1
SLC6A14 WILD-TYPE 79 89 177 137 89 90
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.525 (Fisher's exact test), Q value = 1

Table S220.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SLC6A14 MUTATED 2 2 1
SLC6A14 WILD-TYPE 212 146 295
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.423 (Fisher's exact test), Q value = 0.93

Table S221.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SLC6A14 MUTATED 1 3 1
SLC6A14 WILD-TYPE 71 473 109
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.11 (Fisher's exact test), Q value = 0.39

Table S222.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
SLC6A14 MUTATED 1 1 2 0
SLC6A14 WILD-TYPE 75 59 40 99
'SLC6A14 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.152 (Fisher's exact test), Q value = 0.48

Table S223.  Gene #28: 'SLC6A14 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
SLC6A14 MUTATED 1 0 2 0 1
SLC6A14 WILD-TYPE 25 43 60 100 45
'CYP4F11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 0.95

Table S224.  Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
CYP4F11 MUTATED 0 2 3
CYP4F11 WILD-TYPE 180 240 240
'CYP4F11 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S225.  Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
CYP4F11 MUTATED 1 2 0
CYP4F11 WILD-TYPE 102 253 119
'CYP4F11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.371 (Fisher's exact test), Q value = 0.86

Table S226.  Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
CYP4F11 MUTATED 0 3 2 0
CYP4F11 WILD-TYPE 98 171 243 149
'CYP4F11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S227.  Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
CYP4F11 MUTATED 0 1 1 2 1 0
CYP4F11 WILD-TYPE 80 89 176 136 89 91
'CYP4F11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.68

Table S228.  Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
CYP4F11 MUTATED 0 2 3
CYP4F11 WILD-TYPE 214 146 293
'CYP4F11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S229.  Gene #29: 'CYP4F11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
CYP4F11 MUTATED 0 5 0
CYP4F11 WILD-TYPE 72 471 110
'STAG2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S230.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
STAG2 MUTATED 4 5 5
STAG2 WILD-TYPE 176 237 238
'STAG2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S231.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
STAG2 MUTATED 3 7 2
STAG2 WILD-TYPE 100 248 117
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S232.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
STAG2 MUTATED 3 5 3 3
STAG2 WILD-TYPE 95 169 242 146
'STAG2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00624 (Fisher's exact test), Q value = 0.05

Table S233.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
STAG2 MUTATED 0 6 1 4 3 0
STAG2 WILD-TYPE 80 84 176 134 87 91

Figure S119.  Get High-res Image Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'STAG2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.58

Table S234.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
STAG2 MUTATED 4 6 4
STAG2 WILD-TYPE 210 142 292
'STAG2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.326 (Fisher's exact test), Q value = 0.8

Table S235.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
STAG2 MUTATED 0 13 1
STAG2 WILD-TYPE 72 463 109
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.44

Table S236.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
STAG2 MUTATED 1 1 4 3
STAG2 WILD-TYPE 75 59 38 96
'STAG2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.57

Table S237.  Gene #30: 'STAG2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
STAG2 MUTATED 0 1 5 3 0
STAG2 WILD-TYPE 26 42 57 97 46
'SKI MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00083 (Fisher's exact test), Q value = 0.0099

Table S238.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SKI MUTATED 7 2 0
SKI WILD-TYPE 173 240 243

Figure S120.  Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SKI MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.43

Table S239.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SKI MUTATED 2 2 4
SKI WILD-TYPE 101 253 115
'SKI MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 3e-04 (Fisher's exact test), Q value = 0.005

Table S240.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SKI MUTATED 3 0 0 6
SKI WILD-TYPE 95 174 245 143

Figure S121.  Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SKI MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00217 (Fisher's exact test), Q value = 0.021

Table S241.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SKI MUTATED 3 3 0 0 0 3
SKI WILD-TYPE 77 87 177 138 90 88

Figure S122.  Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00073 (Fisher's exact test), Q value = 0.0097

Table S242.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SKI MUTATED 8 1 0
SKI WILD-TYPE 206 147 296

Figure S123.  Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SKI MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0408 (Fisher's exact test), Q value = 0.19

Table S243.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SKI MUTATED 3 4 2
SKI WILD-TYPE 69 472 108

Figure S124.  Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0227 (Fisher's exact test), Q value = 0.13

Table S244.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
SKI MUTATED 1 2 3 0
SKI WILD-TYPE 75 58 39 99

Figure S125.  Get High-res Image Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SKI MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0614 (Fisher's exact test), Q value = 0.27

Table S245.  Gene #31: 'SKI MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
SKI MUTATED 0 1 4 0 1
SKI WILD-TYPE 26 42 58 100 45
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S246.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
ARID1A MUTATED 5 6 8
ARID1A WILD-TYPE 175 236 235
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S247.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ARID1A MUTATED 2 9 5
ARID1A WILD-TYPE 101 246 114
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0828 (Fisher's exact test), Q value = 0.33

Table S248.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
ARID1A MUTATED 0 5 6 8
ARID1A WILD-TYPE 98 169 239 141
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.71

Table S249.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
ARID1A MUTATED 0 4 3 4 4 4
ARID1A WILD-TYPE 80 86 174 134 86 87
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S250.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
ARID1A MUTATED 7 3 9
ARID1A WILD-TYPE 207 145 287
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.73

Table S251.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
ARID1A MUTATED 0 15 4
ARID1A WILD-TYPE 72 461 106
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0139 (Fisher's exact test), Q value = 0.09

Table S252.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
ARID1A MUTATED 4 0 5 2
ARID1A WILD-TYPE 72 60 37 97

Figure S126.  Get High-res Image Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.161 (Fisher's exact test), Q value = 0.49

Table S253.  Gene #32: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
ARID1A MUTATED 3 2 3 3 0
ARID1A WILD-TYPE 23 41 59 97 46
'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.77

Table S254.  Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
EGFR MUTATED 0 3 4
EGFR WILD-TYPE 180 239 239
'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.339 (Fisher's exact test), Q value = 0.82

Table S255.  Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
EGFR MUTATED 0 4 0
EGFR WILD-TYPE 103 251 119
'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.309 (Fisher's exact test), Q value = 0.77

Table S256.  Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
EGFR MUTATED 0 3 4 0
EGFR WILD-TYPE 98 171 241 149
'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.528 (Fisher's exact test), Q value = 1

Table S257.  Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
EGFR MUTATED 0 0 3 3 1 0
EGFR WILD-TYPE 80 90 174 135 89 91
'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.46

Table S258.  Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
EGFR MUTATED 0 2 4
EGFR WILD-TYPE 214 146 292
'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.652 (Fisher's exact test), Q value = 1

Table S259.  Gene #33: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
EGFR MUTATED 0 6 0
EGFR WILD-TYPE 72 470 110
'DPCR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S260.  Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
DPCR1 MUTATED 2 3 3
DPCR1 WILD-TYPE 178 239 240
'DPCR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S261.  Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
DPCR1 MUTATED 2 5 1
DPCR1 WILD-TYPE 101 250 118
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S262.  Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
DPCR1 MUTATED 2 2 3 1
DPCR1 WILD-TYPE 96 172 242 148
'DPCR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S263.  Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
DPCR1 MUTATED 1 1 2 3 0 1
DPCR1 WILD-TYPE 79 89 175 135 90 90
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S264.  Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
DPCR1 MUTATED 2 2 4
DPCR1 WILD-TYPE 212 146 292
'DPCR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S265.  Gene #34: 'DPCR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
DPCR1 MUTATED 1 6 1
DPCR1 WILD-TYPE 71 470 109
'GUSB MUTATION STATUS' versus 'CN_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.89

Table S266.  Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
GUSB MUTATED 0 3 1
GUSB WILD-TYPE 180 239 242
'GUSB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S267.  Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
GUSB MUTATED 0 2 2 0
GUSB WILD-TYPE 98 172 243 149
'GUSB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 0.85

Table S268.  Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
GUSB MUTATED 0 0 1 3 0 0
GUSB WILD-TYPE 80 90 176 135 90 91
'GUSB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.356 (Fisher's exact test), Q value = 0.84

Table S269.  Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
GUSB MUTATED 0 1 3
GUSB WILD-TYPE 214 147 293
'GUSB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S270.  Gene #35: 'GUSB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
GUSB MUTATED 0 4 0
GUSB WILD-TYPE 72 472 110
'MED16 MUTATION STATUS' versus 'CN_CNMF'

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

Table S271.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
MED16 MUTATED 0 1 3
MED16 WILD-TYPE 180 241 240
'MED16 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.422 (Fisher's exact test), Q value = 0.93

Table S272.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
MED16 MUTATED 1 1 2
MED16 WILD-TYPE 102 254 117
'MED16 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.906 (Fisher's exact test), Q value = 1

Table S273.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
MED16 MUTATED 1 1 1 1
MED16 WILD-TYPE 97 173 244 148
'MED16 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0417 (Fisher's exact test), Q value = 0.2

Table S274.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
MED16 MUTATED 0 3 1 0 0 0
MED16 WILD-TYPE 80 87 176 138 90 91

Figure S127.  Get High-res Image Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'MED16 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S275.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
MED16 MUTATED 2 1 1
MED16 WILD-TYPE 212 147 295
'MED16 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S276.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
MED16 MUTATED 0 4 0
MED16 WILD-TYPE 72 472 110
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.88

Table S277.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
MED16 MUTATED 1 1 1 0
MED16 WILD-TYPE 75 59 41 99
'MED16 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.6

Table S278.  Gene #36: 'MED16 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
MED16 MUTATED 0 1 2 0 0
MED16 WILD-TYPE 26 42 60 100 46
'PTCH1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S279.  Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
PTCH1 MUTATED 1 3 4
PTCH1 WILD-TYPE 179 239 239
'PTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S280.  Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PTCH1 MUTATED 0 4 1
PTCH1 WILD-TYPE 103 251 118
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.533 (Fisher's exact test), Q value = 1

Table S281.  Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
PTCH1 MUTATED 0 2 5 1
PTCH1 WILD-TYPE 98 172 240 148
'PTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.82

Table S282.  Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
PTCH1 MUTATED 0 0 5 2 0 1
PTCH1 WILD-TYPE 80 90 172 136 90 90
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.77

Table S283.  Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
PTCH1 MUTATED 1 1 6
PTCH1 WILD-TYPE 213 147 290
'PTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S284.  Gene #37: 'PTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
PTCH1 MUTATED 0 7 1
PTCH1 WILD-TYPE 72 469 109
'AHNAK2 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.73

Table S285.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 9 14
AHNAK2 MUTATED 3 0 0 2
AHNAK2 WILD-TYPE 18 17 9 12
'AHNAK2 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.0203 (Fisher's exact test), Q value = 0.12

Table S286.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 17 14 10 9
AHNAK2 MUTATED 0 0 2 3 0
AHNAK2 WILD-TYPE 11 17 12 7 9

Figure S128.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S287.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
AHNAK2 MUTATED 10 9 14
AHNAK2 WILD-TYPE 170 233 229
'AHNAK2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0334 (Fisher's exact test), Q value = 0.17

Table S288.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
AHNAK2 MUTATED 11 10 4
AHNAK2 WILD-TYPE 92 245 115

Figure S129.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00588 (Fisher's exact test), Q value = 0.048

Table S289.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
AHNAK2 MUTATED 10 2 12 9
AHNAK2 WILD-TYPE 88 172 233 140

Figure S130.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00052 (Fisher's exact test), Q value = 0.0073

Table S290.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
AHNAK2 MUTATED 10 6 4 1 8 4
AHNAK2 WILD-TYPE 70 84 173 137 82 87

Figure S131.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.017 (Fisher's exact test), Q value = 0.1

Table S291.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
AHNAK2 MUTATED 18 3 12
AHNAK2 WILD-TYPE 196 145 284

Figure S132.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0068 (Fisher's exact test), Q value = 0.052

Table S292.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
AHNAK2 MUTATED 9 17 7
AHNAK2 WILD-TYPE 63 459 103

Figure S133.  Get High-res Image Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S293.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
AHNAK2 MUTATED 5 5 2 4
AHNAK2 WILD-TYPE 71 55 40 95
'AHNAK2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 0.73

Table S294.  Gene #38: 'AHNAK2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
AHNAK2 MUTATED 1 4 3 3 5
AHNAK2 WILD-TYPE 25 39 59 97 41
'RLIM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S295.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RLIM MUTATED 3 4 2
RLIM WILD-TYPE 177 238 241
'RLIM MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S296.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RLIM MUTATED 2 3 3
RLIM WILD-TYPE 101 252 116
'RLIM MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S297.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RLIM MUTATED 2 2 2 3
RLIM WILD-TYPE 96 172 243 146
'RLIM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S298.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RLIM MUTATED 2 2 2 2 0 1
RLIM WILD-TYPE 78 88 175 136 90 90
'RLIM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.081 (Fisher's exact test), Q value = 0.32

Table S299.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RLIM MUTATED 6 0 3
RLIM WILD-TYPE 208 148 293
'RLIM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S300.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RLIM MUTATED 1 7 1
RLIM WILD-TYPE 71 469 109
'RLIM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S301.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
RLIM MUTATED 1 1 1 1
RLIM WILD-TYPE 75 59 41 98
'RLIM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S302.  Gene #39: 'RLIM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
RLIM MUTATED 0 1 1 1 1
RLIM WILD-TYPE 26 42 61 99 45
'SLC23A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S303.  Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SLC23A1 MUTATED 1 3 3
SLC23A1 WILD-TYPE 179 239 240
'SLC23A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S304.  Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SLC23A1 MUTATED 0 3 2
SLC23A1 WILD-TYPE 103 252 117
'SLC23A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.148 (Fisher's exact test), Q value = 0.47

Table S305.  Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SLC23A1 MUTATED 0 0 5 2
SLC23A1 WILD-TYPE 98 174 240 147
'SLC23A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.66

Table S306.  Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SLC23A1 MUTATED 0 1 2 0 3 1
SLC23A1 WILD-TYPE 80 89 175 138 87 90
'SLC23A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.894 (Fisher's exact test), Q value = 1

Table S307.  Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SLC23A1 MUTATED 2 1 4
SLC23A1 WILD-TYPE 212 147 292
'SLC23A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S308.  Gene #40: 'SLC23A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SLC23A1 MUTATED 0 5 2
SLC23A1 WILD-TYPE 72 471 108
'STAM MUTATION STATUS' versus 'CN_CNMF'

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

Table S309.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
STAM MUTATED 2 2 2
STAM WILD-TYPE 178 240 241
'STAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0141 (Fisher's exact test), Q value = 0.09

Table S310.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
STAM MUTATED 4 1 0
STAM WILD-TYPE 99 254 119

Figure S134.  Get High-res Image Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'STAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 0.81

Table S311.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
STAM MUTATED 2 2 2 0
STAM WILD-TYPE 96 172 243 149
'STAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.106 (Fisher's exact test), Q value = 0.39

Table S312.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
STAM MUTATED 1 3 1 0 1 0
STAM WILD-TYPE 79 87 176 138 89 91
'STAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.79

Table S313.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
STAM MUTATED 1 3 2
STAM WILD-TYPE 213 145 294
'STAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S314.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
STAM MUTATED 1 5 0
STAM WILD-TYPE 71 471 110
'STAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.026

Table S315.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
STAM MUTATED 0 0 3 0
STAM WILD-TYPE 76 60 39 99

Figure S135.  Get High-res Image Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'STAM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0575 (Fisher's exact test), Q value = 0.26

Table S316.  Gene #41: 'STAM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
STAM MUTATED 0 0 3 0 0
STAM WILD-TYPE 26 43 59 100 46
'RHEB MUTATION STATUS' versus 'CN_CNMF'

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

Table S317.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RHEB MUTATED 0 2 2
RHEB WILD-TYPE 180 240 241
'RHEB MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S318.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RHEB MUTATED 0 2 1
RHEB WILD-TYPE 103 253 118
'RHEB MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S319.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RHEB MUTATED 0 1 2 1
RHEB WILD-TYPE 98 173 243 148
'RHEB MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.178 (Fisher's exact test), Q value = 0.53

Table S320.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RHEB MUTATED 0 1 0 1 2 0
RHEB WILD-TYPE 80 89 177 137 88 91
'RHEB MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.214 (Fisher's exact test), Q value = 0.62

Table S321.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RHEB MUTATED 0 2 2
RHEB WILD-TYPE 214 146 294
'RHEB MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S322.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RHEB MUTATED 0 4 0
RHEB WILD-TYPE 72 472 110
'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.95

Table S323.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
RHEB MUTATED 0 0 1 2
RHEB WILD-TYPE 76 60 41 97
'RHEB MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S324.  Gene #42: 'RHEB MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
RHEB MUTATED 0 0 1 2 0
RHEB WILD-TYPE 26 43 61 98 46
'SLC4A8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.49

Table S325.  Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SLC4A8 MUTATED 2 0 4
SLC4A8 WILD-TYPE 178 242 239
'SLC4A8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.85

Table S326.  Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SLC4A8 MUTATED 2 4 0
SLC4A8 WILD-TYPE 101 251 119
'SLC4A8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.48

Table S327.  Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SLC4A8 MUTATED 2 3 1 0
SLC4A8 WILD-TYPE 96 171 244 149
'SLC4A8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.428 (Fisher's exact test), Q value = 0.93

Table S328.  Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SLC4A8 MUTATED 2 0 2 2 0 0
SLC4A8 WILD-TYPE 78 90 175 136 90 91
'SLC4A8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S329.  Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SLC4A8 MUTATED 2 1 3
SLC4A8 WILD-TYPE 212 147 293
'SLC4A8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.192 (Fisher's exact test), Q value = 0.57

Table S330.  Gene #43: 'SLC4A8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SLC4A8 MUTATED 2 4 0
SLC4A8 WILD-TYPE 70 472 110
'RUFY3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.62

Table S331.  Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RUFY3 MUTATED 4 2 1
RUFY3 WILD-TYPE 176 240 242
'RUFY3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.423 (Fisher's exact test), Q value = 0.93

Table S332.  Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RUFY3 MUTATED 1 1 2
RUFY3 WILD-TYPE 102 254 117
'RUFY3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.245 (Fisher's exact test), Q value = 0.68

Table S333.  Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RUFY3 MUTATED 2 1 1 3
RUFY3 WILD-TYPE 96 173 244 146
'RUFY3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.43

Table S334.  Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RUFY3 MUTATED 2 0 1 1 0 3
RUFY3 WILD-TYPE 78 90 176 137 90 88
'RUFY3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 0.31

Table S335.  Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RUFY3 MUTATED 5 0 2
RUFY3 WILD-TYPE 209 148 294
'RUFY3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0205 (Fisher's exact test), Q value = 0.12

Table S336.  Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RUFY3 MUTATED 2 2 3
RUFY3 WILD-TYPE 70 474 107

Figure S136.  Get High-res Image Gene #44: 'RUFY3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'PCK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S337.  Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
PCK1 MUTATED 1 2 3
PCK1 WILD-TYPE 179 240 240
'PCK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.427 (Fisher's exact test), Q value = 0.93

Table S338.  Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PCK1 MUTATED 0 3 0
PCK1 WILD-TYPE 103 252 119
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S339.  Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
PCK1 MUTATED 0 2 3 1
PCK1 WILD-TYPE 98 172 242 148
'PCK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S340.  Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
PCK1 MUTATED 0 0 1 2 2 1
PCK1 WILD-TYPE 80 90 176 136 88 90
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S341.  Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
PCK1 MUTATED 1 1 4
PCK1 WILD-TYPE 213 147 292
'PCK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S342.  Gene #45: 'PCK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
PCK1 MUTATED 0 5 1
PCK1 WILD-TYPE 72 471 109
'TXNIP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.54

Table S343.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
TXNIP MUTATED 0 4 4
TXNIP WILD-TYPE 180 238 239
'TXNIP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.319 (Fisher's exact test), Q value = 0.79

Table S344.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TXNIP MUTATED 2 5 0
TXNIP WILD-TYPE 101 250 119
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.391 (Fisher's exact test), Q value = 0.89

Table S345.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
TXNIP MUTATED 2 2 4 0
TXNIP WILD-TYPE 96 172 241 149
'TXNIP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S346.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
TXNIP MUTATED 0 2 2 3 1 0
TXNIP WILD-TYPE 80 88 175 135 89 91
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.77

Table S347.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
TXNIP MUTATED 1 1 6
TXNIP WILD-TYPE 213 147 290
'TXNIP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.92

Table S348.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
TXNIP MUTATED 0 8 0
TXNIP WILD-TYPE 72 468 110
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S349.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
TXNIP MUTATED 0 1 1 2
TXNIP WILD-TYPE 76 59 41 97
'TXNIP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.755 (Fisher's exact test), Q value = 1

Table S350.  Gene #46: 'TXNIP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
TXNIP MUTATED 0 0 2 2 0
TXNIP WILD-TYPE 26 43 60 98 46
'RNF128 MUTATION STATUS' versus 'CN_CNMF'

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

Table S351.  Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RNF128 MUTATED 1 3 1
RNF128 WILD-TYPE 179 239 242
'RNF128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.175 (Fisher's exact test), Q value = 0.53

Table S352.  Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RNF128 MUTATED 2 1 0
RNF128 WILD-TYPE 101 254 119
'RNF128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S353.  Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RNF128 MUTATED 1 1 1 2
RNF128 WILD-TYPE 97 173 244 147
'RNF128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S354.  Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RNF128 MUTATED 1 1 2 0 0 1
RNF128 WILD-TYPE 79 89 175 138 90 90
'RNF128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.88

Table S355.  Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RNF128 MUTATED 3 0 2
RNF128 WILD-TYPE 211 148 294
'RNF128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S356.  Gene #47: 'RNF128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RNF128 MUTATED 0 4 1
RNF128 WILD-TYPE 72 472 109
'ZFYVE26 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S357.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
ZFYVE26 MUTATED 2 4 3
ZFYVE26 WILD-TYPE 178 238 240
'ZFYVE26 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 0.99

Table S358.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ZFYVE26 MUTATED 0 5 1
ZFYVE26 WILD-TYPE 103 250 118
'ZFYVE26 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S359.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
ZFYVE26 MUTATED 0 3 4 2
ZFYVE26 WILD-TYPE 98 171 241 147
'ZFYVE26 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.366 (Fisher's exact test), Q value = 0.85

Table S360.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
ZFYVE26 MUTATED 0 0 4 3 0 2
ZFYVE26 WILD-TYPE 80 90 173 135 90 89
'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.91 (Fisher's exact test), Q value = 1

Table S361.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
ZFYVE26 MUTATED 2 2 5
ZFYVE26 WILD-TYPE 212 146 291
'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S362.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
ZFYVE26 MUTATED 0 7 2
ZFYVE26 WILD-TYPE 72 469 108
'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S363.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
ZFYVE26 MUTATED 2 0 0 1
ZFYVE26 WILD-TYPE 74 60 42 98
'ZFYVE26 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.71

Table S364.  Gene #48: 'ZFYVE26 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
ZFYVE26 MUTATED 0 2 0 1 0
ZFYVE26 WILD-TYPE 26 41 62 99 46
'FAM160B2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S365.  Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
FAM160B2 MUTATED 1 2 1
FAM160B2 WILD-TYPE 179 240 242
'FAM160B2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S366.  Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
FAM160B2 MUTATED 1 2 1
FAM160B2 WILD-TYPE 102 253 118
'FAM160B2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.905 (Fisher's exact test), Q value = 1

Table S367.  Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
FAM160B2 MUTATED 1 1 1 1
FAM160B2 WILD-TYPE 97 173 244 148
'FAM160B2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S368.  Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
FAM160B2 MUTATED 1 0 1 1 0 1
FAM160B2 WILD-TYPE 79 90 176 137 90 90
'FAM160B2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 0.95

Table S369.  Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
FAM160B2 MUTATED 1 2 1
FAM160B2 WILD-TYPE 213 146 295
'FAM160B2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S370.  Gene #49: 'FAM160B2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
FAM160B2 MUTATED 0 3 1
FAM160B2 WILD-TYPE 72 473 109
'FAM47A MUTATION STATUS' versus 'CN_CNMF'

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

Table S371.  Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
FAM47A MUTATED 1 2 3
FAM47A WILD-TYPE 179 240 240
'FAM47A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S372.  Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
FAM47A MUTATED 1 2 1
FAM47A WILD-TYPE 102 253 118
'FAM47A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.892 (Fisher's exact test), Q value = 1

Table S373.  Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
FAM47A MUTATED 1 1 2 2
FAM47A WILD-TYPE 97 173 243 147
'FAM47A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S374.  Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
FAM47A MUTATED 1 1 1 1 2 0
FAM47A WILD-TYPE 79 89 176 137 88 91
'FAM47A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S375.  Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
FAM47A MUTATED 2 0 4
FAM47A WILD-TYPE 212 148 292
'FAM47A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S376.  Gene #50: 'FAM47A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
FAM47A MUTATED 1 4 1
FAM47A WILD-TYPE 71 472 109
'ATP1A1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.253 (Fisher's exact test), Q value = 0.7

Table S377.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 21 17 9 14
ATP1A1 MUTATED 0 1 1 2
ATP1A1 WILD-TYPE 21 16 8 12
'ATP1A1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S378.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 11 17 14 10 9
ATP1A1 MUTATED 0 1 2 0 1
ATP1A1 WILD-TYPE 11 16 12 10 8
'ATP1A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.14 (Fisher's exact test), Q value = 0.46

Table S379.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
ATP1A1 MUTATED 5 4 1
ATP1A1 WILD-TYPE 175 238 242
'ATP1A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S380.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ATP1A1 MUTATED 0 2 1
ATP1A1 WILD-TYPE 103 253 118
'ATP1A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.43

Table S381.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
ATP1A1 MUTATED 2 0 4 4
ATP1A1 WILD-TYPE 96 174 241 145
'ATP1A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S382.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
ATP1A1 MUTATED 1 1 3 1 1 3
ATP1A1 WILD-TYPE 79 89 174 137 89 88
'ATP1A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.51

Table S383.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
ATP1A1 MUTATED 5 0 5
ATP1A1 WILD-TYPE 209 148 291
'ATP1A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.503 (Fisher's exact test), Q value = 1

Table S384.  Gene #51: 'ATP1A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
ATP1A1 MUTATED 1 6 3
ATP1A1 WILD-TYPE 71 470 107
'SH3BP2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.29

Table S385.  Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SH3BP2 MUTATED 3 1 0
SH3BP2 WILD-TYPE 177 241 243
'SH3BP2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.275 (Fisher's exact test), Q value = 0.73

Table S386.  Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SH3BP2 MUTATED 0 1 2
SH3BP2 WILD-TYPE 103 254 117
'SH3BP2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.39

Table S387.  Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SH3BP2 MUTATED 0 0 1 3
SH3BP2 WILD-TYPE 98 174 244 146
'SH3BP2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0922 (Fisher's exact test), Q value = 0.35

Table S388.  Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SH3BP2 MUTATED 0 1 0 0 1 2
SH3BP2 WILD-TYPE 80 89 177 138 89 89
'SH3BP2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.73

Table S389.  Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SH3BP2 MUTATED 3 0 1
SH3BP2 WILD-TYPE 211 148 295
'SH3BP2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.193 (Fisher's exact test), Q value = 0.57

Table S390.  Gene #52: 'SH3BP2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SH3BP2 MUTATED 0 2 2
SH3BP2 WILD-TYPE 72 474 108
'FAM200A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.452 (Fisher's exact test), Q value = 0.95

Table S391.  Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
FAM200A MUTATED 0 2 3
FAM200A WILD-TYPE 180 240 240
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0574 (Fisher's exact test), Q value = 0.26

Table S392.  Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
FAM200A MUTATED 0 0 5 0
FAM200A WILD-TYPE 98 174 240 149
'FAM200A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00703 (Fisher's exact test), Q value = 0.053

Table S393.  Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
FAM200A MUTATED 0 0 1 0 4 0
FAM200A WILD-TYPE 80 90 176 138 86 91

Figure S137.  Get High-res Image Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FAM200A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.58

Table S394.  Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
FAM200A MUTATED 0 1 4
FAM200A WILD-TYPE 214 147 292
'FAM200A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S395.  Gene #53: 'FAM200A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
FAM200A MUTATED 0 5 0
FAM200A WILD-TYPE 72 471 110
'RTL1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S396.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RTL1 MUTATED 2 1 4
RTL1 WILD-TYPE 178 241 239
'RTL1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S397.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RTL1 MUTATED 2 4 1
RTL1 WILD-TYPE 101 251 118
'RTL1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.078 (Fisher's exact test), Q value = 0.32

Table S398.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RTL1 MUTATED 2 3 0 2
RTL1 WILD-TYPE 96 171 245 147
'RTL1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.338 (Fisher's exact test), Q value = 0.82

Table S399.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RTL1 MUTATED 2 2 1 2 0 0
RTL1 WILD-TYPE 78 88 176 136 90 91
'RTL1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.493 (Fisher's exact test), Q value = 1

Table S400.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RTL1 MUTATED 4 1 2
RTL1 WILD-TYPE 210 147 294
'RTL1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0812 (Fisher's exact test), Q value = 0.32

Table S401.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RTL1 MUTATED 2 3 2
RTL1 WILD-TYPE 70 473 108
'RTL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S402.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
RTL1 MUTATED 1 1 0 1
RTL1 WILD-TYPE 75 59 42 98
'RTL1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.235 (Fisher's exact test), Q value = 0.66

Table S403.  Gene #54: 'RTL1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
RTL1 MUTATED 0 0 2 0 1
RTL1 WILD-TYPE 26 43 60 100 45
'NASP MUTATION STATUS' versus 'CN_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.79

Table S404.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
NASP MUTATED 2 0 2
NASP WILD-TYPE 178 242 241
'NASP MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.29

Table S405.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NASP MUTATED 3 1 0
NASP WILD-TYPE 100 254 119
'NASP MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0407 (Fisher's exact test), Q value = 0.19

Table S406.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
NASP MUTATED 2 2 0 0
NASP WILD-TYPE 96 172 245 149

Figure S138.  Get High-res Image Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NASP MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.134 (Fisher's exact test), Q value = 0.44

Table S407.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
NASP MUTATED 2 1 0 1 0 0
NASP WILD-TYPE 78 89 177 137 90 91
'NASP MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.73

Table S408.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
NASP MUTATED 3 0 1
NASP WILD-TYPE 211 148 295
'NASP MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.38

Table S409.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
NASP MUTATED 2 2 0
NASP WILD-TYPE 70 474 110
'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0877 (Fisher's exact test), Q value = 0.34

Table S410.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
NASP MUTATED 0 2 1 0
NASP WILD-TYPE 76 58 41 99
'NASP MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.46

Table S411.  Gene #55: 'NASP MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
NASP MUTATED 0 0 1 0 2
NASP WILD-TYPE 26 43 61 100 44
'RPL7A MUTATION STATUS' versus 'CN_CNMF'

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

Table S412.  Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RPL7A MUTATED 1 1 1
RPL7A WILD-TYPE 179 241 242
'RPL7A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0987 (Fisher's exact test), Q value = 0.37

Table S413.  Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RPL7A MUTATED 1 0 2
RPL7A WILD-TYPE 102 255 117
'RPL7A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0851 (Fisher's exact test), Q value = 0.33

Table S414.  Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RPL7A MUTATED 1 0 0 2
RPL7A WILD-TYPE 97 174 245 147
'RPL7A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0756 (Fisher's exact test), Q value = 0.31

Table S415.  Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RPL7A MUTATED 0 2 0 0 0 1
RPL7A WILD-TYPE 80 88 177 138 90 90
'RPL7A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.66

Table S416.  Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RPL7A MUTATED 2 1 0
RPL7A WILD-TYPE 212 147 296
'RPL7A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.107 (Fisher's exact test), Q value = 0.39

Table S417.  Gene #56: 'RPL7A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RPL7A MUTATED 0 1 2
RPL7A WILD-TYPE 72 475 108
'UIMC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S418.  Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
UIMC1 MUTATED 1 3 1
UIMC1 WILD-TYPE 179 239 242
'UIMC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 0.82

Table S419.  Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
UIMC1 MUTATED 0 4 0
UIMC1 WILD-TYPE 103 251 119
'UIMC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S420.  Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
UIMC1 MUTATED 0 2 2 1
UIMC1 WILD-TYPE 98 172 243 148
'UIMC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.463 (Fisher's exact test), Q value = 0.96

Table S421.  Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
UIMC1 MUTATED 0 1 1 3 0 0
UIMC1 WILD-TYPE 80 89 176 135 90 91
'UIMC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0956 (Fisher's exact test), Q value = 0.36

Table S422.  Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
UIMC1 MUTATED 0 3 2
UIMC1 WILD-TYPE 214 145 294
'UIMC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S423.  Gene #57: 'UIMC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
UIMC1 MUTATED 0 5 0
UIMC1 WILD-TYPE 72 471 110
'TCEB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0686 (Fisher's exact test), Q value = 0.29

Table S424.  Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
TCEB1 MUTATED 0 3 0
TCEB1 WILD-TYPE 180 239 243
'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.868 (Fisher's exact test), Q value = 1

Table S425.  Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
TCEB1 MUTATED 0 1 2 0
TCEB1 WILD-TYPE 98 173 243 149
'TCEB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S426.  Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
TCEB1 MUTATED 0 0 2 0 1 0
TCEB1 WILD-TYPE 80 90 175 138 89 91
'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.164 (Fisher's exact test), Q value = 0.5

Table S427.  Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
TCEB1 MUTATED 0 2 1
TCEB1 WILD-TYPE 214 146 295
'TCEB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S428.  Gene #58: 'TCEB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
TCEB1 MUTATED 0 3 0
TCEB1 WILD-TYPE 72 473 110
'SFMBT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.49 (Fisher's exact test), Q value = 1

Table S429.  Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SFMBT1 MUTATED 1 0 2
SFMBT1 WILD-TYPE 179 242 241
'SFMBT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S430.  Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SFMBT1 MUTATED 0 0 2 1
SFMBT1 WILD-TYPE 98 174 243 148
'SFMBT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.745 (Fisher's exact test), Q value = 1

Table S431.  Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SFMBT1 MUTATED 0 0 1 0 1 1
SFMBT1 WILD-TYPE 80 90 176 138 89 90
'SFMBT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S432.  Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SFMBT1 MUTATED 1 0 2
SFMBT1 WILD-TYPE 213 148 294
'SFMBT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S433.  Gene #59: 'SFMBT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SFMBT1 MUTATED 0 2 1
SFMBT1 WILD-TYPE 72 474 109
'SLC16A1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S434.  Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
SLC16A1 MUTATED 1 1 1
SLC16A1 WILD-TYPE 179 241 242
'SLC16A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S435.  Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
SLC16A1 MUTATED 0 2 1
SLC16A1 WILD-TYPE 103 253 118
'SLC16A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S436.  Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
SLC16A1 MUTATED 0 1 1 1
SLC16A1 WILD-TYPE 98 173 244 148
'SLC16A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S437.  Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
SLC16A1 MUTATED 0 0 1 1 0 1
SLC16A1 WILD-TYPE 80 90 176 137 90 90
'SLC16A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S438.  Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
SLC16A1 MUTATED 1 0 2
SLC16A1 WILD-TYPE 213 148 294
'SLC16A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S439.  Gene #60: 'SLC16A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
SLC16A1 MUTATED 0 2 1
SLC16A1 WILD-TYPE 72 474 109
'PAM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0194 (Fisher's exact test), Q value = 0.11

Table S440.  Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
PAM MUTATED 3 0 0
PAM WILD-TYPE 177 242 243

Figure S139.  Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PAM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00585 (Fisher's exact test), Q value = 0.048

Table S441.  Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
PAM MUTATED 0 0 4
PAM WILD-TYPE 103 255 115

Figure S140.  Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'PAM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0027 (Fisher's exact test), Q value = 0.025

Table S442.  Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
PAM MUTATED 0 0 0 4
PAM WILD-TYPE 98 174 245 145

Figure S141.  Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'PAM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.094

Table S443.  Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
PAM MUTATED 0 1 0 0 0 3
PAM WILD-TYPE 80 89 177 138 90 88

Figure S142.  Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'PAM MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0135 (Fisher's exact test), Q value = 0.09

Table S444.  Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
PAM MUTATED 4 0 0
PAM WILD-TYPE 210 148 296

Figure S143.  Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'PAM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00075 (Fisher's exact test), Q value = 0.0098

Table S445.  Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
PAM MUTATED 0 0 4
PAM WILD-TYPE 72 476 106

Figure S144.  Get High-res Image Gene #61: 'PAM MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'TMCO3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0782 (Fisher's exact test), Q value = 0.32

Table S446.  Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
TMCO3 MUTATED 2 0 5
TMCO3 WILD-TYPE 178 242 238
'TMCO3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.73

Table S447.  Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
TMCO3 MUTATED 0 1 2
TMCO3 WILD-TYPE 103 254 117
'TMCO3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S448.  Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
TMCO3 MUTATED 0 2 3 2
TMCO3 WILD-TYPE 98 172 242 147
'TMCO3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0806 (Fisher's exact test), Q value = 0.32

Table S449.  Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
TMCO3 MUTATED 0 1 0 1 3 2
TMCO3 WILD-TYPE 80 89 177 137 87 89
'TMCO3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.88

Table S450.  Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
TMCO3 MUTATED 3 0 4
TMCO3 WILD-TYPE 211 148 292
'TMCO3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S451.  Gene #62: 'TMCO3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
TMCO3 MUTATED 0 6 1
TMCO3 WILD-TYPE 72 470 109
'CCDC82 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.12

Table S452.  Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
CCDC82 MUTATED 1 5 0
CCDC82 WILD-TYPE 179 237 243

Figure S145.  Get High-res Image Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'CCDC82 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.77

Table S453.  Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
CCDC82 MUTATED 1 5 0
CCDC82 WILD-TYPE 102 250 119
'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 0.34

Table S454.  Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
CCDC82 MUTATED 1 0 5 0
CCDC82 WILD-TYPE 97 174 240 149
'CCDC82 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0141 (Fisher's exact test), Q value = 0.09

Table S455.  Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
CCDC82 MUTATED 1 0 1 0 4 0
CCDC82 WILD-TYPE 79 90 176 138 86 91

Figure S146.  Get High-res Image Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.73

Table S456.  Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
CCDC82 MUTATED 1 0 5
CCDC82 WILD-TYPE 213 148 291
'CCDC82 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S457.  Gene #63: 'CCDC82 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
CCDC82 MUTATED 1 5 0
CCDC82 WILD-TYPE 71 471 110
'NFAT5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S458.  Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
NFAT5 MUTATED 3 3 2
NFAT5 WILD-TYPE 177 239 241
'NFAT5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S459.  Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
NFAT5 MUTATED 1 6 1
NFAT5 WILD-TYPE 102 249 118
'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S460.  Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
NFAT5 MUTATED 1 4 2 1
NFAT5 WILD-TYPE 97 170 243 148
'NFAT5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S461.  Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
NFAT5 MUTATED 1 1 4 2 0 0
NFAT5 WILD-TYPE 79 89 173 136 90 91
'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.728 (Fisher's exact test), Q value = 1

Table S462.  Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
NFAT5 MUTATED 2 1 5
NFAT5 WILD-TYPE 212 147 291
'NFAT5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S463.  Gene #64: 'NFAT5 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
NFAT5 MUTATED 1 6 1
NFAT5 WILD-TYPE 71 470 109
'HNF1B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S464.  Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
HNF1B MUTATED 1 0 2
HNF1B WILD-TYPE 179 242 241
'HNF1B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.786 (Fisher's exact test), Q value = 1

Table S465.  Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
HNF1B MUTATED 1 2 0
HNF1B WILD-TYPE 102 253 119
'HNF1B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.95

Table S466.  Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
HNF1B MUTATED 1 0 2 0
HNF1B WILD-TYPE 97 174 243 149
'HNF1B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.494 (Fisher's exact test), Q value = 1

Table S467.  Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
HNF1B MUTATED 1 0 2 0 0 0
HNF1B WILD-TYPE 79 90 175 138 90 91
'HNF1B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S468.  Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
HNF1B MUTATED 1 0 2
HNF1B WILD-TYPE 213 148 294
'HNF1B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.359 (Fisher's exact test), Q value = 0.84

Table S469.  Gene #65: 'HNF1B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
HNF1B MUTATED 1 2 0
HNF1B WILD-TYPE 71 474 110
'OR2L8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S470.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
OR2L8 MUTATED 3 2 2
OR2L8 WILD-TYPE 177 240 241
'OR2L8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S471.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
OR2L8 MUTATED 1 3 3
OR2L8 WILD-TYPE 102 252 116
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S472.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
OR2L8 MUTATED 1 1 2 3
OR2L8 WILD-TYPE 97 173 243 146
'OR2L8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.084 (Fisher's exact test), Q value = 0.33

Table S473.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
OR2L8 MUTATED 0 1 0 1 2 3
OR2L8 WILD-TYPE 80 89 177 137 88 88
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.438 (Fisher's exact test), Q value = 0.95

Table S474.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
OR2L8 MUTATED 2 3 2
OR2L8 WILD-TYPE 212 145 294
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S475.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
OR2L8 MUTATED 0 5 2
OR2L8 WILD-TYPE 72 471 108
'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0426 (Fisher's exact test), Q value = 0.2

Table S476.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
OR2L8 MUTATED 2 0 2 0
OR2L8 WILD-TYPE 74 60 40 99

Figure S147.  Get High-res Image Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'OR2L8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.46

Table S477.  Gene #66: 'OR2L8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
OR2L8 MUTATED 1 1 2 0 0
OR2L8 WILD-TYPE 25 42 60 100 46
'IDUA MUTATION STATUS' versus 'CN_CNMF'

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

Table S478.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
IDUA MUTATED 1 3 1
IDUA WILD-TYPE 179 239 242
'IDUA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.43

Table S479.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
IDUA MUTATED 1 1 3
IDUA WILD-TYPE 102 254 116
'IDUA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00693 (Fisher's exact test), Q value = 0.053

Table S480.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
IDUA MUTATED 1 0 0 4
IDUA WILD-TYPE 97 174 245 145

Figure S148.  Get High-res Image Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'IDUA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0158 (Fisher's exact test), Q value = 0.096

Table S481.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
IDUA MUTATED 1 3 0 0 0 1
IDUA WILD-TYPE 79 87 177 138 90 90

Figure S149.  Get High-res Image Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'IDUA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.18

Table S482.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
IDUA MUTATED 4 1 0
IDUA WILD-TYPE 210 147 296

Figure S150.  Get High-res Image Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'IDUA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0531 (Fisher's exact test), Q value = 0.24

Table S483.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
IDUA MUTATED 0 2 3
IDUA WILD-TYPE 72 474 107
'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.322 (Fisher's exact test), Q value = 0.79

Table S484.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
IDUA MUTATED 2 1 1 0
IDUA WILD-TYPE 74 59 41 99
'IDUA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.46

Table S485.  Gene #67: 'IDUA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
IDUA MUTATED 1 1 2 0 0
IDUA WILD-TYPE 25 42 60 100 46
'ZC3H18 MUTATION STATUS' versus 'CN_CNMF'

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

Table S486.  Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
ZC3H18 MUTATED 1 2 3
ZC3H18 WILD-TYPE 179 240 240
'ZC3H18 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 0.93

Table S487.  Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
ZC3H18 MUTATED 0 3 0
ZC3H18 WILD-TYPE 103 252 119
'ZC3H18 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.801 (Fisher's exact test), Q value = 1

Table S488.  Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
ZC3H18 MUTATED 0 2 2 2
ZC3H18 WILD-TYPE 98 172 243 147
'ZC3H18 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S489.  Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
ZC3H18 MUTATED 0 1 2 1 1 1
ZC3H18 WILD-TYPE 80 89 175 137 89 90
'ZC3H18 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S490.  Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
ZC3H18 MUTATED 2 2 2
ZC3H18 WILD-TYPE 212 146 294
'ZC3H18 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.377 (Fisher's exact test), Q value = 0.87

Table S491.  Gene #68: 'ZC3H18 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
ZC3H18 MUTATED 0 4 2
ZC3H18 WILD-TYPE 72 472 108
'GAPDHS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S492.  Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
GAPDHS MUTATED 1 1 3
GAPDHS WILD-TYPE 179 241 240
'GAPDHS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.71

Table S493.  Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
GAPDHS MUTATED 2 1 2
GAPDHS WILD-TYPE 101 254 117
'GAPDHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.48

Table S494.  Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
GAPDHS MUTATED 1 0 1 3
GAPDHS WILD-TYPE 97 174 244 146
'GAPDHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0144 (Fisher's exact test), Q value = 0.09

Table S495.  Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
GAPDHS MUTATED 1 3 0 0 1 0
GAPDHS WILD-TYPE 79 87 177 138 89 91

Figure S151.  Get High-res Image Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'GAPDHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.12 (Fisher's exact test), Q value = 0.42

Table S496.  Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
GAPDHS MUTATED 4 0 1
GAPDHS WILD-TYPE 210 148 295
'GAPDHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.424 (Fisher's exact test), Q value = 0.93

Table S497.  Gene #69: 'GAPDHS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
GAPDHS MUTATED 1 3 1
GAPDHS WILD-TYPE 71 473 109
'GPR137 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.59

Table S498.  Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
GPR137 MUTATED 1 0 3
GPR137 WILD-TYPE 179 242 240
'GPR137 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S499.  Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
GPR137 MUTATED 1 1 1
GPR137 WILD-TYPE 102 254 118
'GPR137 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.75

Table S500.  Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
GPR137 MUTATED 1 2 0 1
GPR137 WILD-TYPE 97 172 245 148
'GPR137 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.346 (Fisher's exact test), Q value = 0.83

Table S501.  Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
GPR137 MUTATED 1 0 0 2 0 1
GPR137 WILD-TYPE 79 90 177 136 90 90
'GPR137 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.113 (Fisher's exact test), Q value = 0.4

Table S502.  Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
GPR137 MUTATED 2 2 0
GPR137 WILD-TYPE 212 146 296
'GPR137 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.77

Table S503.  Gene #70: 'GPR137 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
GPR137 MUTATED 1 2 1
GPR137 WILD-TYPE 71 474 109
'GFM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.73

Table S504.  Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
GFM1 MUTATED 2 0 1
GFM1 WILD-TYPE 178 242 242
'GFM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00997 (Fisher's exact test), Q value = 0.069

Table S505.  Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
GFM1 MUTATED 3 0 0
GFM1 WILD-TYPE 100 255 119

Figure S152.  Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'GFM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00315 (Fisher's exact test), Q value = 0.027

Table S506.  Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
GFM1 MUTATED 3 0 0 0
GFM1 WILD-TYPE 95 174 245 149

Figure S153.  Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'GFM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00178 (Fisher's exact test), Q value = 0.018

Table S507.  Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
GFM1 MUTATED 3 0 0 0 0 0
GFM1 WILD-TYPE 77 90 177 138 90 91

Figure S154.  Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'GFM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0456 (Fisher's exact test), Q value = 0.21

Table S508.  Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
GFM1 MUTATED 3 0 0
GFM1 WILD-TYPE 211 148 296

Figure S155.  Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'GFM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00099 (Fisher's exact test), Q value = 0.012

Table S509.  Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
GFM1 MUTATED 3 0 0
GFM1 WILD-TYPE 69 476 110

Figure S156.  Get High-res Image Gene #71: 'GFM1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.48

Table S510.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
FAT1 MUTATED 10 5 7
FAT1 WILD-TYPE 170 237 236
'FAT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0314 (Fisher's exact test), Q value = 0.16

Table S511.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
FAT1 MUTATED 4 5 9
FAT1 WILD-TYPE 99 250 110

Figure S157.  Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00049 (Fisher's exact test), Q value = 0.007

Table S512.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
FAT1 MUTATED 2 5 2 13
FAT1 WILD-TYPE 96 169 243 136

Figure S158.  Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00184 (Fisher's exact test), Q value = 0.019

Table S513.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
FAT1 MUTATED 1 9 2 3 1 6
FAT1 WILD-TYPE 79 81 175 135 89 85

Figure S159.  Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0254 (Fisher's exact test), Q value = 0.14

Table S514.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
FAT1 MUTATED 13 4 5
FAT1 WILD-TYPE 201 144 291

Figure S160.  Get High-res Image Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'FAT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.131 (Fisher's exact test), Q value = 0.44

Table S515.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
FAT1 MUTATED 1 14 7
FAT1 WILD-TYPE 71 462 103
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.65

Table S516.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
FAT1 MUTATED 5 1 3 2
FAT1 WILD-TYPE 71 59 39 97
'FAT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.068 (Fisher's exact test), Q value = 0.29

Table S517.  Gene #72: 'FAT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
FAT1 MUTATED 1 2 6 1 1
FAT1 WILD-TYPE 25 41 56 99 45
'RRP12 MUTATION STATUS' versus 'CN_CNMF'

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

Table S518.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 180 242 243
RRP12 MUTATED 3 3 3
RRP12 WILD-TYPE 177 239 240
'RRP12 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.419 (Fisher's exact test), Q value = 0.93

Table S519.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 103 255 119
RRP12 MUTATED 1 2 3
RRP12 WILD-TYPE 102 253 116
'RRP12 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.97

Table S520.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 98 174 245 149
RRP12 MUTATED 1 1 3 4
RRP12 WILD-TYPE 97 173 242 145
'RRP12 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.455 (Fisher's exact test), Q value = 0.95

Table S521.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 80 90 177 138 90 91
RRP12 MUTATED 1 1 1 1 2 3
RRP12 WILD-TYPE 79 89 176 137 88 88
'RRP12 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 0.75

Table S522.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 214 148 296
RRP12 MUTATED 5 2 2
RRP12 WILD-TYPE 209 146 294
'RRP12 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.73

Table S523.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 72 476 110
RRP12 MUTATED 1 5 3
RRP12 WILD-TYPE 71 471 107
'RRP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S524.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 76 60 42 99
RRP12 MUTATED 2 1 0 2
RRP12 WILD-TYPE 74 59 42 97
'RRP12 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S525.  Gene #73: 'RRP12 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 26 43 62 100 46
RRP12 MUTATED 1 1 0 2 1
RRP12 WILD-TYPE 25 42 62 98 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/15639742/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIPAN-TP/15165233/KIPAN-TP.transferedmergedcluster.txt

  • Number of patients = 668

  • Number of significantly mutated genes = 73

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

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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