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 90 genes and 12 molecular subtypes across 481 patients, 78 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • KEAP1 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • EGFR mutation correlated to 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • STK11 mutation correlated to 'CN_CNMF',  'METHLYATION_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • RB1 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • SMARCA4 mutation correlated to 'METHLYATION_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • MGA mutation correlated to 'MRNASEQ_CNMF'.

  • SETD2 mutation correlated to 'MIRSEQ_MATURE_CNMF'.

  • U2AF1 mutation correlated to 'MIRSEQ_CNMF'.

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

  • PPP3CA mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • SLC4A3 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • SLAMF9 mutation correlated to 'CN_CNMF' and 'MIRSEQ_CHIERARCHICAL'.

  • DNMT3A mutation correlated to 'MIRSEQ_MATURE_CNMF' and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

  • ZNF608 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • STIM1 mutation correlated to 'CN_CNMF'.

  • PHKA1 mutation correlated to 'CN_CNMF'.

  • TRERF1 mutation correlated to 'MRNASEQ_CNMF'.

  • CACNA1F mutation correlated to 'MIRSEQ_CNMF'.

  • STRA8 mutation correlated to 'CN_CNMF',  'RPPA_CNMF', and 'MIRSEQ_CNMF'.

  • WDR66 mutation correlated to 'RPPA_CNMF'.

  • HSPA8 mutation correlated to 'MIRSEQ_CNMF'.

  • CD244 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • DSC2 mutation correlated to 'RPPA_CNMF' and 'RPPA_CHIERARCHICAL'.

  • DOT1L mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • MIA2 mutation correlated to 'CN_CNMF'.

  • DLX5 mutation correlated to 'MIRSEQ_CNMF'.

  • ATAD2 mutation correlated to 'MIRSEQ_CHIERARCHICAL'.

  • A2M mutation correlated to 'MIRSEQ_CNMF'.

  • SND1 mutation correlated to 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • ADAMTS2 mutation correlated to 'METHLYATION_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 90 genes and 12 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 78 significant findings detected.

Clinical
Features 		MRNA
CNMF 		MRNA
CHIERARCHICAL 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
TP53 256 (53%) 225 0.0253
(0.297) 		0.149
(0.61) 		1e-05
(0.000568) 		0.00054
(0.0188) 		0.00015
(0.00648) 		1e-05
(0.000568) 		1e-05
(0.000568) 		1e-05
(0.000568) 		1e-05
(0.000568) 		1e-05
(0.000568) 		0.885
(1.00) 		1e-05
(0.000568)
KEAP1 84 (17%) 397 2e-05
(0.00103) 		1e-05
(0.000568) 		0.00081
(0.026) 		0.37
(0.901) 		1e-05
(0.000568) 		1e-05
(0.000568) 		0.121
(0.558) 		0.00018
(0.00748) 		0.0547
(0.427) 		0.00082
(0.026)
KRAS 150 (31%) 331 0.899
(1.00) 		1
(1.00) 		0.00184
(0.0523) 		0.00227
(0.0597) 		0.31
(0.822) 		0.119
(0.552) 		0.0103
(0.17) 		1e-05
(0.000568) 		0.00155
(0.0452) 		6e-05
(0.00282) 		0.44
(0.949) 		0.156
(0.62)
EGFR 67 (14%) 414 0.00039
(0.0145) 		0.434
(0.947) 		0.00189
(0.0523) 		0.0212
(0.276) 		2e-05
(0.00103) 		1e-05
(0.000568) 		0.00505
(0.105) 		0.0312
(0.331) 		0.0714
(0.467) 		0.00282
(0.0708)
STK11 77 (16%) 404 1e-05
(0.000568) 		0.00058
(0.0196) 		1e-05
(0.000568) 		0.0957
(0.513) 		1e-05
(0.000568) 		1e-05
(0.000568) 		0.445
(0.952) 		0.0104
(0.17) 		0.208
(0.703) 		0.117
(0.552)
SMARCA4 38 (8%) 443 0.492
(0.989) 		1e-05
(0.000568) 		0.509
(1.00) 		0.108
(0.54) 		1e-05
(0.000568) 		1e-05
(0.000568) 		0.00539
(0.106) 		0.00036
(0.0139) 		0.0494
(0.427) 		5e-05
(0.00245)
ATM 42 (9%) 439 0.00019
(0.0076) 		0.001
(0.0309) 		0.332
(0.859) 		0.933
(1.00) 		0.00206
(0.0556) 		0.00047
(0.0169) 		0.89
(1.00) 		0.0533
(0.427) 		0.509
(1.00) 		0.915
(1.00)
PTPRU 18 (4%) 463 0.0138
(0.204) 		0.108
(0.54) 		0.103
(0.532) 		0.0261
(0.302) 		0.0112
(0.177) 		0.061
(0.434) 		0.00296
(0.0727) 		0.00739
(0.14) 		1
(1.00) 		0.189
(0.691)
STRA8 8 (2%) 473 0.0047
(0.0995) 		0.0766
(0.476) 		0.00851
(0.153) 		0.0229
(0.284) 		0.105
(0.535) 		0.0338
(0.348) 		0.0128
(0.195) 		0.118
(0.552) 		0.528
(1.00) 		0.24
(0.748)
SLAMF9 12 (2%) 469 0.00899
(0.154) 		0.0404
(0.386) 		0.934
(1.00) 		1
(1.00) 		0.2
(0.697) 		0.601
(1.00) 		0.0824
(0.482) 		0.0122
(0.189) 		0.606
(1.00) 		0.625
(1.00)
DNMT3A 19 (4%) 462 0.603
(1.00) 		0.486
(0.984) 		0.576
(1.00) 		0.295
(0.808) 		0.587
(1.00) 		0.563
(1.00) 		0.338
(0.866) 		0.111
(0.545) 		0.00913
(0.154) 		0.00831
(0.152)
DSC2 20 (4%) 461 0.578
(1.00) 		0.0755
(0.474) 		0.00317
(0.0761) 		0.00444
(0.0959) 		0.627
(1.00) 		0.878
(1.00) 		0.191
(0.691) 		0.344
(0.873) 		0.0624
(0.434) 		0.173
(0.655)
RB1 26 (5%) 455 0.437
(0.947) 		0.0829
(0.482) 		0.183
(0.676) 		0.432
(0.947) 		0.073
(0.474) 		7e-05
(0.00315) 		0.151
(0.611) 		0.0276
(0.304) 		0.0577
(0.429) 		0.96
(1.00)
MGA 40 (8%) 441 0.266
(0.781) 		0.0557
(0.427) 		0.723
(1.00) 		0.103
(0.532) 		0.00232
(0.0597) 		0.153
(0.618) 		0.0311
(0.331) 		0.0658
(0.447) 		0.328
(0.855) 		0.0806
(0.481)
SETD2 30 (6%) 451 0.208
(0.703) 		0.377
(0.901) 		0.611
(1.00) 		0.681
(1.00) 		0.102
(0.529) 		0.228
(0.73) 		0.555
(1.00) 		0.97
(1.00) 		0.013
(0.195) 		0.054
(0.427)
U2AF1 11 (2%) 470 0.717
(1.00) 		0.841
(1.00) 		0.058
(0.429) 		0.686
(1.00) 		0.0482
(0.427) 		0.126
(0.571) 		0.00866
(0.153) 		0.648
(1.00) 		0.0986
(0.522) 		0.529
(1.00)
PPP3CA 12 (2%) 469 0.926
(1.00) 		0.3
(0.816) 		0.64
(1.00) 		0.806
(1.00) 		0.47
(0.97) 		0.0154
(0.218) 		0.142
(0.596) 		0.242
(0.75) 		0.458
(0.962) 		0.253
(0.768)
SLC4A3 18 (4%) 463 1
(1.00) 		0.374
(0.901) 		0.176
(0.66) 		0.0583
(0.429) 		0.13
(0.576) 		0.454
(0.959) 		0.146
(0.604) 		0.752
(1.00) 		0.344
(0.873) 		0.00348
(0.0783)
ZNF608 9 (2%) 472 0.183
(0.676) 		0.641
(1.00) 		0.233
(0.73) 		1
(1.00) 		0.199
(0.697) 		0.00889
(0.154) 		0.504
(1.00) 		0.533
(1.00) 		0.564
(1.00) 		0.374
(0.901)
STIM1 9 (2%) 472 0.0154
(0.218) 		1
(1.00) 		0.876
(1.00) 		0.862
(1.00) 		0.699
(1.00) 		0.265
(0.781) 		0.119
(0.552) 		0.191
(0.691) 		0.435
(0.947) 		0.882
(1.00)
PHKA1 12 (2%) 469 0.00124
(0.0372) 		0.345
(0.873) 		0.693
(1.00) 		0.781
(1.00) 		0.135
(0.583) 		0.355
(0.886) 		0.398
(0.92) 		0.279
(0.791) 		0.418
(0.93) 		0.0505
(0.427)
TRERF1 18 (4%) 463 0.157
(0.62) 		0.0598
(0.431) 		0.292
(0.808) 		0.654
(1.00) 		0.0111
(0.177) 		0.307
(0.816) 		0.0692
(0.456) 		0.298
(0.816) 		0.554
(1.00) 		0.195
(0.697)
CACNA1F 27 (6%) 454 1
(1.00) 		0.937
(1.00) 		0.202
(0.7) 		0.819
(1.00) 		0.561
(1.00) 		0.1
(0.525) 		0.00784
(0.146) 		0.992
(1.00) 		0.589
(1.00) 		0.677
(1.00)
WDR66 14 (3%) 467 0.0547
(0.427) 		0.0454
(0.416) 		0.00342
(0.0783) 		0.104
(0.532) 		0.551
(1.00) 		0.491
(0.989) 		0.155
(0.619) 		0.511
(1.00) 		0.128
(0.575) 		0.159
(0.622)
HSPA8 9 (2%) 472 0.156
(0.62) 		0.206
(0.703) 		0.426
(0.94) 		1
(1.00) 		0.699
(1.00) 		0.223
(0.728) 		0.00535
(0.106) 		0.157
(0.62) 		0.294
(0.808) 		0.886
(1.00)
CD244 12 (2%) 469 0.26
(0.778) 		0.661
(1.00) 		0.63
(1.00) 		0.772
(1.00) 		0.378
(0.901) 		0.261
(0.778) 		0.0747
(0.474) 		0.0142
(0.207) 		1
(1.00) 		0.594
(1.00)
DOT1L 14 (3%) 467 0.655
(1.00) 		0.563
(1.00) 		0.0622
(0.434) 		0.228
(0.73) 		0.787
(1.00) 		0.00706
(0.136) 		0.774
(1.00) 		0.0825
(0.482) 		0.585
(1.00) 		0.291
(0.808)
MIA2 13 (3%) 468 0.0119
(0.186) 		0.315
(0.835) 		0.951
(1.00) 		0.141
(0.596) 		0.304
(0.816) 		0.266
(0.781) 		0.875
(1.00) 		0.679
(1.00) 		1
(1.00) 		0.769
(1.00)
DLX5 13 (3%) 468 0.754
(1.00) 		1
(1.00) 		0.0901
(0.495) 		0.322
(0.846) 		0.359
(0.891) 		0.718
(1.00) 		0.00412
(0.0908) 		0.135
(0.583) 		0.151
(0.611) 		0.26
(0.778)
ATAD2 14 (3%) 467 0.0247
(0.296) 		0.0271
(0.302) 		0.0969
(0.516) 		0.49
(0.989) 		0.0552
(0.427) 		0.277
(0.79) 		0.374
(0.901) 		0.0162
(0.224) 		0.761
(1.00) 		0.404
(0.92)
A2M 20 (4%) 461 0.0991
(0.522) 		0.624
(1.00) 		0.204
(0.7) 		0.387
(0.91) 		0.0504
(0.427) 		0.0511
(0.427) 		0.00525
(0.106) 		0.135
(0.583) 		0.202
(0.7) 		0.132
(0.579)
SND1 16 (3%) 465 0.0521
(0.427) 		0.0594
(0.431) 		0.852
(1.00) 		0.0197
(0.263) 		0.0564
(0.429) 		0.0229
(0.284) 		0.0343
(0.349) 		0.0886
(0.493) 		0.274
(0.789) 		0.0159
(0.224)
ADAMTS2 39 (8%) 442 0.197
(0.697) 		0.00339
(0.0783) 		0.898
(1.00) 		0.189
(0.691) 		0.468
(0.97) 		0.819
(1.00) 		0.0818
(0.482) 		0.0502
(0.427) 		0.109
(0.54) 		0.793
(1.00)
RBM10 33 (7%) 448 0.64
(1.00) 		0.057
(0.429) 		0.284
(0.802) 		0.45
(0.959) 		0.923
(1.00) 		0.774
(1.00) 		0.893
(1.00) 		0.0535
(0.427) 		0.429
(0.943) 		0.65
(1.00)
ARID1A 30 (6%) 451 0.72
(1.00) 		0.78
(1.00) 		0.467
(0.97) 		0.7
(1.00) 		0.44
(0.949) 		0.877
(1.00) 		0.242
(0.75) 		0.0779
(0.476) 		0.0531
(0.427) 		0.112
(0.547)
NF1 55 (11%) 426 0.639
(1.00) 		0.792
(1.00) 		0.538
(1.00) 		0.931
(1.00) 		0.0616
(0.434) 		0.481
(0.98) 		0.0629
(0.434) 		0.261
(0.778) 		0.109
(0.54) 		0.352
(0.884) 		0.107
(0.54) 		0.0884
(0.493)
BRAF 39 (8%) 442 0.147
(0.604) 		1
(1.00) 		0.63
(1.00) 		0.0783
(0.476) 		0.574
(1.00) 		0.893
(1.00) 		0.273
(0.787) 		0.385
(0.91) 		0.591
(1.00) 		0.0329
(0.342) 		0.919
(1.00) 		0.514
(1.00)
FTSJD1 24 (5%) 457 0.268
(0.783) 		0.341
(0.873) 		0.93
(1.00) 		0.384
(0.91) 		0.223
(0.728) 		0.289
(0.807) 		0.626
(1.00) 		0.668
(1.00) 		0.0895
(0.495) 		0.199
(0.697)
MET 21 (4%) 460 0.0849
(0.483) 		0.73
(1.00) 		0.457
(0.962) 		0.266
(0.781) 		0.521
(1.00) 		0.626
(1.00) 		0.0849
(0.483) 		0.21
(0.704) 		0.47
(0.97) 		0.169
(0.652)
GAGE2A 8 (2%) 473 0.436
(0.947) 		0.598
(1.00) 		0.721
(1.00) 		0.482
(0.98) 		0.361
(0.891) 		0.574
(1.00) 		0.0689
(0.456) 		0.738
(1.00) 		0.525
(1.00) 		0.317
(0.836)
ERBB2 11 (2%) 470 0.683
(1.00) 		0.096
(0.513) 		0.172
(0.655) 		1
(1.00) 		0.515
(1.00) 		0.139
(0.59) 		0.734
(1.00) 		0.241
(0.749) 		0.501
(1.00) 		0.222
(0.728)
CDKN2A 16 (3%) 465 0.769
(1.00) 		0.936
(1.00) 		0.821
(1.00) 		0.689
(1.00) 		0.0603
(0.431) 		0.207
(0.703) 		1
(1.00) 		0.858
(1.00) 		0.531
(1.00) 		0.917
(1.00)
SRPX 14 (3%) 467 0.886
(1.00) 		0.798
(1.00) 		0.638
(1.00) 		0.0388
(0.375) 		0.586
(1.00) 		0.911
(1.00) 		0.456
(0.962) 		0.589
(1.00) 		0.775
(1.00) 		0.304
(0.816)
TCEAL5 13 (3%) 468 0.564
(1.00) 		0.663
(1.00) 		0.331
(0.859) 		0.926
(1.00) 		0.936
(1.00) 		0.866
(1.00) 		0.933
(1.00) 		0.625
(1.00) 		0.746
(1.00) 		0.576
(1.00)
FCRLA 15 (3%) 466 0.174
(0.656) 		0.799
(1.00) 		0.845
(1.00) 		0.332
(0.859) 		0.848
(1.00) 		0.375
(0.901) 		1
(1.00) 		0.844
(1.00) 		0.643
(1.00) 		0.199
(0.697)
ARID2 24 (5%) 457 0.792
(1.00) 		0.641
(1.00) 		0.826
(1.00) 		1
(1.00) 		0.138
(0.59) 		0.0918
(0.498) 		0.0791
(0.477) 		0.286
(0.803) 		0.126
(0.571) 		0.385
(0.91)
APC 20 (4%) 461 0.882
(1.00) 		0.642
(1.00) 		0.889
(1.00) 		0.884
(1.00) 		0.0861
(0.485) 		0.222
(0.728) 		0.063
(0.434) 		0.0516
(0.427) 		0.83
(1.00) 		0.276
(0.79)
ZEB1 32 (7%) 449 0.639
(1.00) 		1
(1.00) 		0.657
(1.00) 		0.689
(1.00) 		0.768
(1.00) 		0.877
(1.00) 		0.462
(0.968) 		0.476
(0.976) 		0.506
(1.00) 		0.044
(0.413) 		0.964
(1.00) 		0.664
(1.00)
SIP1 4 (1%) 477 0.114
(0.552) 		0.119
(0.552) 		0.0662
(0.447) 		0.471
(0.97) 		1
(1.00) 		1
(1.00) 		0.978
(1.00) 		0.408
(0.921) 		0.144
(0.599)
STK19 5 (1%) 476 0.67
(1.00) 		1
(1.00) 		0.823
(1.00) 		0.588
(1.00) 		0.39
(0.913) 		0.976
(1.00) 		0.848
(1.00) 		0.653
(1.00) 		0.0555
(0.427) 		0.828
(1.00)
NUDT11 5 (1%) 476 0.8
(1.00) 		1
(1.00) 		0.623
(1.00) 		0.832
(1.00) 		0.83
(1.00) 		0.307
(0.816) 		0.067
(0.447) 		0.23
(0.73) 		1
(1.00) 		0.146
(0.604)
CTNNB1 19 (4%) 462 0.435
(0.947) 		0.278
(0.79) 		0.0347
(0.35) 		0.252
(0.768) 		0.27
(0.784) 		0.408
(0.921) 		0.0269
(0.302) 		0.791
(1.00) 		0.264
(0.781) 		0.769
(1.00)
PIK3CA 28 (6%) 453 0.368
(0.899) 		0.306
(0.816) 		0.15
(0.61) 		0.135
(0.583) 		0.0504
(0.427) 		0.0249
(0.296) 		0.874
(1.00) 		0.562
(1.00) 		0.159
(0.622) 		0.164
(0.636)
EMG1 5 (1%) 476 1
(1.00) 		0.558
(1.00) 		0.61
(1.00) 		0.401
(0.92) 		0.75
(1.00) 		0.295
(0.808) 		0.0747
(0.474) 		0.262
(0.779) 		0.212
(0.705) 		0.373
(0.901)
PAK1 9 (2%) 472 0.353
(0.884) 		0.641
(1.00) 		0.292
(0.808) 		0.884
(1.00) 		0.3
(0.816) 		0.255
(0.771) 		0.912
(1.00) 		0.84
(1.00) 		1
(1.00) 		1
(1.00)
NRAS 3 (1%) 478 0.0765
(0.476) 		0.115
(0.552) 		0.895
(1.00) 		0.305
(0.816) 		0.35
(0.883)
G3BP1 8 (2%) 473 0.176
(0.66) 		0.694
(1.00) 		0.931
(1.00) 		0.334
(0.861) 		0.499
(0.999) 		0.833
(1.00) 		0.898
(1.00) 		0.82
(1.00) 		0.687
(1.00) 		0.653
(1.00)
NFE2L2 13 (3%) 468 0.606
(1.00) 		0.581
(1.00) 		0.271
(0.785) 		0.25
(0.768) 		0.0746
(0.474) 		0.0383
(0.375) 		1
(1.00) 		0.196
(0.697) 		0.657
(1.00) 		0.758
(1.00)
RPL5 8 (2%) 473 1
(1.00) 		0.743
(1.00) 		0.902
(1.00) 		0.129
(0.576) 		0.738
(1.00) 		0.719
(1.00) 		0.42
(0.93) 		0.367
(0.899) 		0.469
(0.97) 		1
(1.00)
NLRP6 10 (2%) 471 0.131
(0.579) 		0.443
(0.952) 		0.0263
(0.302) 		0.165
(0.639) 		0.734
(1.00) 		0.0187
(0.253) 		0.137
(0.586) 		0.0778
(0.476) 		0.561
(1.00) 		0.0907
(0.495)
FAM65C 14 (3%) 467 0.567
(1.00) 		0.832
(1.00) 		0.0573
(0.429) 		0.0542
(0.427) 		0.945
(1.00) 		0.688
(1.00) 		0.107
(0.54) 		0.48
(0.98) 		0.796
(1.00) 		0.132
(0.579)
RIT1 8 (2%) 473 0.0315
(0.331) 		0.877
(1.00) 		0.363
(0.892) 		1
(1.00) 		0.907
(1.00) 		0.173
(0.655) 		0.269
(0.784) 		1
(1.00) 		0.5
(0.999) 		0.27
(0.784)
TGFBR3 14 (3%) 467 0.601
(1.00) 		0.665
(1.00) 		0.799
(1.00) 		0.139
(0.59) 		0.388
(0.91) 		0.228
(0.73) 		0.0448
(0.414) 		0.203
(0.7) 		0.198
(0.697) 		0.0224
(0.284)
CXCR7 10 (2%) 471 0.751
(1.00) 		0.789
(1.00) 		0.655
(1.00) 		0.19
(0.691) 		0.669
(1.00) 		0.657
(1.00) 		0.337
(0.866) 		0.657
(1.00) 		1
(1.00) 		0.59
(1.00)
GAN 10 (2%) 471 0.479
(0.979) 		0.908
(1.00) 		0.888
(1.00) 		0.838
(1.00) 		0.732
(1.00) 		0.405
(0.92) 		0.537
(1.00) 		0.792
(1.00) 		1
(1.00) 		0.767
(1.00)
TMEM49 5 (1%) 476 0.517
(1.00) 		0.236
(0.739) 		0.934
(1.00) 		0.0907
(0.495) 		0.281
(0.795) 		0.22
(0.728) 		0.426
(0.94) 		0.467
(0.97) 		0.617
(1.00) 		0.409
(0.922)
KIF18B 4 (1%) 477 0.289
(0.807) 		0.391
(0.913) 		0.0461
(0.418) 		0.361
(0.891) 		0.126
(0.571) 		0.472
(0.972) 		0.753
(1.00) 		1
(1.00) 		0.454
(0.959)
PDE6A 16 (3%) 465 0.326
(0.852) 		0.405
(0.92) 		1
(1.00) 		0.119
(0.552) 		0.0246
(0.296) 		0.0268
(0.302) 		0.0185
(0.253) 		0.0297
(0.325) 		0.695
(1.00) 		0.574
(1.00)
CHRND 16 (3%) 465 0.159
(0.622) 		0.535
(1.00) 		0.133
(0.58) 		0.093
(0.502) 		0.405
(0.92) 		0.204
(0.701) 		0.398
(0.92) 		0.118
(0.552) 		0.606
(1.00) 		0.572
(1.00)
KLK1 8 (2%) 473 0.0375
(0.371) 		0.0794
(0.477) 		0.568
(1.00) 		0.0385
(0.375) 		0.554
(1.00) 		0.648
(1.00) 		0.196
(0.697) 		0.225
(0.73) 		0.206
(0.703) 		0.23
(0.73)
KLHL5 14 (3%) 467 0.418
(0.93) 		0.937
(1.00) 		0.758
(1.00) 		0.0862
(0.485) 		0.433
(0.947) 		0.797
(1.00) 		0.939
(1.00) 		0.652
(1.00) 		0.674
(1.00) 		0.768
(1.00)
RNF160 15 (3%) 466 0.155
(0.619) 		0.102
(0.529) 		0.0217
(0.279) 		0.128
(0.574) 		0.021
(0.276) 		0.414
(0.925) 		0.376
(0.901) 		0.209
(0.703) 		1
(1.00) 		0.404
(0.92)
AIFM1 12 (2%) 469 0.656
(1.00) 		0.329
(0.856) 		0.119
(0.552) 		0.0653
(0.446) 		0.762
(1.00) 		0.493
(0.989) 		0.317
(0.836) 		0.085
(0.483) 		0.0667
(0.447) 		0.857
(1.00)
MCM9 3 (1%) 478 1
(1.00) 		0.639
(1.00) 		0.765
(1.00) 		1
(1.00) 		0.484
(0.983)
NCKAP1L 19 (4%) 462 0.303
(0.816) 		0.249
(0.765) 		0.77
(1.00) 		0.625
(1.00) 		0.0441
(0.413) 		0.212
(0.705) 		0.0359
(0.359) 		0.0592
(0.431) 		0.463
(0.968) 		0.772
(1.00)
ESYT3 8 (2%) 473 0.843
(1.00) 		0.352
(0.884) 		0.232
(0.73) 		0.261
(0.778) 		0.403
(0.92) 		0.537
(1.00) 		0.466
(0.97) 		0.325
(0.852) 		0.251
(0.768) 		0.397
(0.92)
TUBB4 17 (4%) 464 0.571
(1.00) 		0.718
(1.00) 		0.664
(1.00) 		0.452
(0.959) 		0.747
(1.00) 		0.807
(1.00) 		0.808
(1.00) 		0.451
(0.959) 		0.599
(1.00) 		0.117
(0.552)
ABHD12B 7 (1%) 474 0.222
(0.728) 		0.229
(0.73) 		0.625
(1.00) 		1
(1.00) 		1
(1.00) 		0.836
(1.00) 		0.0821
(0.482) 		0.763
(1.00) 		0.766
(1.00) 		0.401
(0.92)
ANTXR1 19 (4%) 462 0.772
(1.00) 		0.641
(1.00) 		0.943
(1.00) 		0.92
(1.00) 		0.699
(1.00) 		0.719
(1.00) 		0.485
(0.984) 		0.734
(1.00) 		0.721
(1.00) 		0.445
(0.952)
FLCN 9 (2%) 472 0.362
(0.892) 		0.361
(0.891) 		0.232
(0.73) 		0.861
(1.00) 		0.838
(1.00) 		0.802
(1.00) 		0.609
(1.00) 		0.476
(0.976) 		0.307
(0.816) 		0.893
(1.00)
ZNF556 12 (2%) 469 0.278
(0.79) 		0.598
(1.00) 		0.731
(1.00) 		0.883
(1.00) 		0.17
(0.653) 		0.184
(0.677) 		0.232
(0.73) 		0.581
(1.00) 		0.924
(1.00) 		0.0519
(0.427)
ASCL3 7 (1%) 474 0.392
(0.913) 		0.383
(0.91) 		0.343
(0.873) 		0.392
(0.913) 		0.277
(0.79) 		0.907
(1.00) 		0.0496
(0.427) 		0.124
(0.567) 		0.852
(1.00) 		0.502
(1.00)
DSG3 33 (7%) 448 0.0845
(0.483) 		0.387
(0.91) 		0.197
(0.697) 		0.857
(1.00) 		0.173
(0.655) 		0.708
(1.00) 		0.42
(0.93) 		0.401
(0.92) 		0.765
(1.00) 		0.414
(0.925)
C5AR1 6 (1%) 475 0.647
(1.00) 		0.292
(0.808) 		0.304
(0.816) 		0.85
(1.00) 		0.229
(0.73) 		0.59
(1.00) 		0.115
(0.552) 		0.201
(0.7) 		1
(1.00) 		0.112
(0.547)
ASXL2 18 (4%) 463 0.549
(1.00) 		0.511
(1.00) 		0.533
(1.00) 		0.074
(0.474) 		0.41
(0.923) 		0.716
(1.00) 		0.377
(0.901) 		0.42
(0.93) 		0.145
(0.604) 		0.782
(1.00)
RAF1 6 (1%) 475 1
(1.00) 		1
(1.00) 		0.181
(0.674) 		0.075
(0.474) 		0.777
(1.00) 		0.552
(1.00) 		1
(1.00) 		0.211
(0.705) 		0.0444
(0.413) 		0.0246
(0.296)
C7ORF36 6 (1%) 475 0.451
(0.959) 		0.556
(1.00) 		0.443
(0.952) 		0.852
(1.00) 		0.229
(0.73) 		0.354
(0.884) 		1
(1.00) 		0.253
(0.769) 		1
(1.00) 		1
(1.00)
HTRA1 10 (2%) 471 0.248
(0.764) 		0.18
(0.674) 		0.505
(1.00) 		0.684
(1.00) 		1
(1.00) 		0.763
(1.00) 		0.841
(1.00) 		0.0785
(0.476) 		1
(1.00) 		0.76
(1.00)
TAF1L 50 (10%) 431 0.638
(1.00) 		0.794
(1.00) 		0.343
(0.873) 		0.372
(0.901) 		0.44
(0.949) 		0.507
(1.00) 		0.0474
(0.426) 		0.286
(0.803) 		0.0308
(0.331) 		0.924
(1.00) 		0.768
(1.00) 		0.627
(1.00)
PLEKHB2 6 (1%) 475 0.182
(0.676) 		0.877
(1.00) 		0.699
(1.00) 		0.411
(0.923) 		0.776
(1.00) 		0.357
(0.887) 		0.581
(1.00) 		0.112
(0.547) 		0.585
(1.00) 		0.143
(0.599)
'TP53 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.0253 (Fisher's exact test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
TP53 MUTATED 1 4 0 3
TP53 WILD-TYPE 4 3 5 0

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

'TP53 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.149 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
TP53 MUTATED 1 4 3
TP53 WILD-TYPE 6 5 1
'TP53 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
TP53 MUTATED 27 76 45 106
TP53 WILD-TYPE 38 134 27 25

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

'TP53 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00054 (Fisher's exact test), Q value = 0.019

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
TP53 MUTATED 53 86 95
TP53 WILD-TYPE 78 52 66

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

'TP53 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00015 (Fisher's exact test), Q value = 0.0065

Table S5.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
TP53 MUTATED 52 10 18 46 50
TP53 WILD-TYPE 37 12 41 19 51

Figure S4.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'TP53 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
TP53 MUTATED 62 86 28
TP53 WILD-TYPE 94 35 31

Figure S5.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
TP53 MUTATED 59 141 55
TP53 WILD-TYPE 91 44 88

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

'TP53 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
TP53 MUTATED 19 80 73 6 19 26 32
TP53 WILD-TYPE 53 29 17 38 30 20 36

Figure S7.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
TP53 MUTATED 63 141 49
TP53 WILD-TYPE 112 70 41

Figure S8.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TP53 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S10.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
TP53 MUTATED 24 101 59 69
TP53 WILD-TYPE 46 85 72 20

Figure S9.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.885 (Fisher's exact test), Q value = 1

Table S11.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
TP53 MUTATED 76 103 50
TP53 WILD-TYPE 65 79 39
'TP53 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S12.  Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
TP53 MUTATED 32 152 45
TP53 WILD-TYPE 62 81 40

Figure S10.  Get High-res Image Gene #1: 'TP53 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S13.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
KRAS MUTATED 2 2 1 0
KRAS WILD-TYPE 3 5 4 3
'KRAS MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S14.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
KRAS MUTATED 2 2 1
KRAS WILD-TYPE 5 7 3
'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00184 (Fisher's exact test), Q value = 0.052

Table S15.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
KRAS MUTATED 30 70 24 26
KRAS WILD-TYPE 35 140 48 105

Figure S11.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00227 (Fisher's exact test), Q value = 0.06

Table S16.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
KRAS MUTATED 33 35 67
KRAS WILD-TYPE 98 103 94

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

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 0.82

Table S17.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
KRAS MUTATED 20 6 22 16 32
KRAS WILD-TYPE 69 16 37 49 69
'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.55

Table S18.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
KRAS MUTATED 48 27 21
KRAS WILD-TYPE 108 94 38
'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.17

Table S19.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
KRAS MUTATED 49 44 56
KRAS WILD-TYPE 101 141 87

Figure S13.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S20.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
KRAS MUTATED 23 30 7 17 26 18 28
KRAS WILD-TYPE 49 79 83 27 23 28 40

Figure S14.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00155 (Fisher's exact test), Q value = 0.045

Table S21.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
KRAS MUTATED 71 57 19
KRAS WILD-TYPE 104 154 71

Figure S15.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.0028

Table S22.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
KRAS MUTATED 29 62 45 11
KRAS WILD-TYPE 41 124 86 78

Figure S16.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.95

Table S23.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
KRAS MUTATED 44 61 23
KRAS WILD-TYPE 97 121 66
'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.156 (Fisher's exact test), Q value = 0.62

Table S24.  Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
KRAS MUTATED 37 67 24
KRAS WILD-TYPE 57 166 61
'KEAP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.001

Table S25.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
KEAP1 MUTATED 17 32 24 11
KEAP1 WILD-TYPE 48 178 48 120

Figure S17.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KEAP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S26.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
KEAP1 MUTATED 12 47 15
KEAP1 WILD-TYPE 119 91 146

Figure S18.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'KEAP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00081 (Fisher's exact test), Q value = 0.026

Table S27.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
KEAP1 MUTATED 6 3 16 20 18
KEAP1 WILD-TYPE 83 19 43 45 83

Figure S19.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'KEAP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.9

Table S28.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
KEAP1 MUTATED 28 27 8
KEAP1 WILD-TYPE 128 94 51
'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S29.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
KEAP1 MUTATED 9 23 51
KEAP1 WILD-TYPE 141 162 92

Figure S20.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'KEAP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S30.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
KEAP1 MUTATED 2 7 18 24 7 24 1
KEAP1 WILD-TYPE 70 102 72 20 42 22 67

Figure S21.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.56

Table S31.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
KEAP1 MUTATED 31 41 9
KEAP1 WILD-TYPE 144 170 81
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00018 (Fisher's exact test), Q value = 0.0075

Table S32.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
KEAP1 MUTATED 20 26 11 24
KEAP1 WILD-TYPE 50 160 120 65

Figure S22.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0547 (Fisher's exact test), Q value = 0.43

Table S33.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
KEAP1 MUTATED 25 37 8
KEAP1 WILD-TYPE 116 145 81
'KEAP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00082 (Fisher's exact test), Q value = 0.026

Table S34.  Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
KEAP1 MUTATED 16 50 4
KEAP1 WILD-TYPE 78 183 81

Figure S23.  Get High-res Image Gene #3: 'KEAP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00039 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
EGFR MUTATED 2 26 7 31
EGFR WILD-TYPE 63 184 65 100

Figure S24.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'EGFR MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.95

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
EGFR MUTATED 22 17 19
EGFR WILD-TYPE 109 121 142
'EGFR MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00189 (Fisher's exact test), Q value = 0.052

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
EGFR MUTATED 18 7 11 3 9
EGFR WILD-TYPE 71 15 48 62 92

Figure S25.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'EGFR MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0212 (Fisher's exact test), Q value = 0.28

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
EGFR MUTATED 30 15 3
EGFR WILD-TYPE 126 106 56

Figure S26.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.001

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
EGFR MUTATED 30 33 4
EGFR WILD-TYPE 120 152 139

Figure S27.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
EGFR MUTATED 16 16 22 0 1 1 11
EGFR WILD-TYPE 56 93 68 44 48 45 57

Figure S28.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00505 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
EGFR MUTATED 15 31 21
EGFR WILD-TYPE 160 180 69

Figure S29.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'EGFR MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0312 (Fisher's exact test), Q value = 0.33

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
EGFR MUTATED 4 35 19 9
EGFR WILD-TYPE 66 151 112 80

Figure S30.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0714 (Fisher's exact test), Q value = 0.47

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
EGFR MUTATED 18 20 19
EGFR WILD-TYPE 123 162 70
'EGFR MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00282 (Fisher's exact test), Q value = 0.071

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
EGFR MUTATED 9 26 22
EGFR WILD-TYPE 85 207 63

Figure S31.  Get High-res Image Gene #4: 'EGFR MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'CN_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S45.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
STK11 MUTATED 26 29 15 7
STK11 WILD-TYPE 39 181 57 124

Figure S32.  Get High-res Image Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'STK11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00058 (Fisher's exact test), Q value = 0.02

Table S46.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
STK11 MUTATED 10 34 26
STK11 WILD-TYPE 121 104 135

Figure S33.  Get High-res Image Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'STK11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S47.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
STK11 MUTATED 2 1 19 15 20
STK11 WILD-TYPE 87 21 40 50 81

Figure S34.  Get High-res Image Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'STK11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0957 (Fisher's exact test), Q value = 0.51

Table S48.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
STK11 MUTATED 27 15 15
STK11 WILD-TYPE 129 106 44
'STK11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S49.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
STK11 MUTATED 10 9 56
STK11 WILD-TYPE 140 176 87

Figure S35.  Get High-res Image Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'STK11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S50.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
STK11 MUTATED 3 2 1 24 25 17 3
STK11 WILD-TYPE 69 107 89 20 24 29 65

Figure S36.  Get High-res Image Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S51.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
STK11 MUTATED 26 38 11
STK11 WILD-TYPE 149 173 79
'STK11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0104 (Fisher's exact test), Q value = 0.17

Table S52.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
STK11 MUTATED 18 30 11 16
STK11 WILD-TYPE 52 156 120 73

Figure S37.  Get High-res Image Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'STK11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.7

Table S53.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
STK11 MUTATED 23 36 10
STK11 WILD-TYPE 118 146 79
'STK11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.55

Table S54.  Gene #5: 'STK11 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
STK11 MUTATED 18 43 8
STK11 WILD-TYPE 76 190 77
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S55.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
RBM10 MUTATED 3 18 5 7
RBM10 WILD-TYPE 62 192 67 124
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.057 (Fisher's exact test), Q value = 0.43

Table S56.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
RBM10 MUTATED 4 8 16
RBM10 WILD-TYPE 127 130 145
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 0.8

Table S57.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
RBM10 MUTATED 3 0 6 2 7
RBM10 WILD-TYPE 86 22 53 63 94
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.45 (Fisher's exact test), Q value = 0.96

Table S58.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
RBM10 MUTATED 10 4 4
RBM10 WILD-TYPE 146 117 55
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.923 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
RBM10 MUTATED 10 14 9
RBM10 WILD-TYPE 140 171 134
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S60.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
RBM10 MUTATED 3 8 7 2 2 5 6
RBM10 WILD-TYPE 69 101 83 42 47 41 62
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S61.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
RBM10 MUTATED 13 15 5
RBM10 WILD-TYPE 162 196 85
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0535 (Fisher's exact test), Q value = 0.43

Table S62.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
RBM10 MUTATED 9 8 7 9
RBM10 WILD-TYPE 61 178 124 80
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.94

Table S63.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
RBM10 MUTATED 12 9 5
RBM10 WILD-TYPE 129 173 84
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.65 (Fisher's exact test), Q value = 1

Table S64.  Gene #6: 'RBM10 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
RBM10 MUTATED 6 13 7
RBM10 WILD-TYPE 88 220 78
'RB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.437 (Fisher's exact test), Q value = 0.95

Table S65.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
RB1 MUTATED 3 9 3 11
RB1 WILD-TYPE 62 201 69 120
'RB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0829 (Fisher's exact test), Q value = 0.48

Table S66.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
RB1 MUTATED 4 13 8
RB1 WILD-TYPE 127 125 153
'RB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.68

Table S67.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
RB1 MUTATED 4 2 4 6 2
RB1 WILD-TYPE 85 20 55 59 99
'RB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.432 (Fisher's exact test), Q value = 0.95

Table S68.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
RB1 MUTATED 6 9 3
RB1 WILD-TYPE 150 112 56
'RB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.073 (Fisher's exact test), Q value = 0.47

Table S69.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
RB1 MUTATED 9 14 3
RB1 WILD-TYPE 141 171 140
'RB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 7e-05 (Fisher's exact test), Q value = 0.0031

Table S70.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
RB1 MUTATED 2 2 16 0 1 1 4
RB1 WILD-TYPE 70 107 74 44 48 45 64

Figure S38.  Get High-res Image Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.61

Table S71.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
RB1 MUTATED 5 15 6
RB1 WILD-TYPE 170 196 84
'RB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0276 (Fisher's exact test), Q value = 0.3

Table S72.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
RB1 MUTATED 0 8 10 8
RB1 WILD-TYPE 70 178 121 81

Figure S39.  Get High-res Image Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0577 (Fisher's exact test), Q value = 0.43

Table S73.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
RB1 MUTATED 10 14 1
RB1 WILD-TYPE 131 168 88
'RB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S74.  Gene #7: 'RB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
RB1 MUTATED 5 15 5
RB1 WILD-TYPE 89 218 80
'ARID1A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.72 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ARID1A MUTATED 4 14 6 6
ARID1A WILD-TYPE 61 196 66 125
'ARID1A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S76.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ARID1A MUTATED 7 9 12
ARID1A WILD-TYPE 124 129 149
'ARID1A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 0.97

Table S77.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ARID1A MUTATED 3 0 3 4 9
ARID1A WILD-TYPE 86 22 56 61 92
'ARID1A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.7 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ARID1A MUTATED 7 8 4
ARID1A WILD-TYPE 149 113 55
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.95

Table S79.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ARID1A MUTATED 7 15 8
ARID1A WILD-TYPE 143 170 135
'ARID1A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S80.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ARID1A MUTATED 7 6 7 2 3 2 3
ARID1A WILD-TYPE 65 103 83 42 46 44 65
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.242 (Fisher's exact test), Q value = 0.75

Table S81.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ARID1A MUTATED 8 18 4
ARID1A WILD-TYPE 167 193 86
'ARID1A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0779 (Fisher's exact test), Q value = 0.48

Table S82.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ARID1A MUTATED 2 9 8 11
ARID1A WILD-TYPE 68 177 123 78
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0531 (Fisher's exact test), Q value = 0.43

Table S83.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ARID1A MUTATED 11 6 9
ARID1A WILD-TYPE 130 176 80
'ARID1A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.55

Table S84.  Gene #8: 'ARID1A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ARID1A MUTATED 2 19 5
ARID1A WILD-TYPE 92 214 80
'NF1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
NF1 MUTATED 0 2 1 1
NF1 WILD-TYPE 5 5 4 2
'NF1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
NF1 MUTATED 2 1 1
NF1 WILD-TYPE 5 8 3
'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.538 (Fisher's exact test), Q value = 1

Table S87.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
NF1 MUTATED 5 22 10 18
NF1 WILD-TYPE 60 188 62 113
'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
NF1 MUTATED 15 18 19
NF1 WILD-TYPE 116 120 142
'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0616 (Fisher's exact test), Q value = 0.43

Table S89.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
NF1 MUTATED 16 1 2 9 12
NF1 WILD-TYPE 73 21 57 56 89
'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 0.98

Table S90.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
NF1 MUTATED 15 17 8
NF1 WILD-TYPE 141 104 51
'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0629 (Fisher's exact test), Q value = 0.43

Table S91.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
NF1 MUTATED 12 29 13
NF1 WILD-TYPE 138 156 130
'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.78

Table S92.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
NF1 MUTATED 4 18 12 2 5 5 8
NF1 WILD-TYPE 68 91 78 42 44 41 60
'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.54

Table S93.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
NF1 MUTATED 13 29 12
NF1 WILD-TYPE 162 182 78
'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.352 (Fisher's exact test), Q value = 0.88

Table S94.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
NF1 MUTATED 4 22 15 13
NF1 WILD-TYPE 66 164 116 76
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.54

Table S95.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
NF1 MUTATED 17 15 15
NF1 WILD-TYPE 124 167 74
'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0884 (Fisher's exact test), Q value = 0.49

Table S96.  Gene #9: 'NF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
NF1 MUTATED 5 32 10
NF1 WILD-TYPE 89 201 75
'SMARCA4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.492 (Fisher's exact test), Q value = 0.99

Table S97.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
SMARCA4 MUTATED 4 15 9 10
SMARCA4 WILD-TYPE 61 195 63 121
'SMARCA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S98.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
SMARCA4 MUTATED 6 26 4
SMARCA4 WILD-TYPE 125 112 157

Figure S40.  Get High-res Image Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SMARCA4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
SMARCA4 MUTATED 4 2 3 7 9
SMARCA4 WILD-TYPE 85 20 56 58 92
'SMARCA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.54

Table S100.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
SMARCA4 MUTATED 8 14 3
SMARCA4 WILD-TYPE 148 107 56
'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S101.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
SMARCA4 MUTATED 1 18 19
SMARCA4 WILD-TYPE 149 167 124

Figure S41.  Get High-res Image Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'SMARCA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00057

Table S102.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
SMARCA4 MUTATED 0 5 13 2 4 14 0
SMARCA4 WILD-TYPE 72 104 77 42 45 32 68

Figure S42.  Get High-res Image Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00539 (Fisher's exact test), Q value = 0.11

Table S103.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
SMARCA4 MUTATED 7 26 4
SMARCA4 WILD-TYPE 168 185 86

Figure S43.  Get High-res Image Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00036 (Fisher's exact test), Q value = 0.014

Table S104.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
SMARCA4 MUTATED 6 14 2 15
SMARCA4 WILD-TYPE 64 172 129 74

Figure S44.  Get High-res Image Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0494 (Fisher's exact test), Q value = 0.43

Table S105.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
SMARCA4 MUTATED 7 22 5
SMARCA4 WILD-TYPE 134 160 84

Figure S45.  Get High-res Image Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'SMARCA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.0025

Table S106.  Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
SMARCA4 MUTATED 1 31 2
SMARCA4 WILD-TYPE 93 202 83

Figure S46.  Get High-res Image Gene #10: 'SMARCA4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.147 (Fisher's exact test), Q value = 0.6

Table S107.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
BRAF MUTATED 0 3 0 0
BRAF WILD-TYPE 5 4 5 3
'BRAF MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S108.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
BRAF MUTATED 1 2 0
BRAF WILD-TYPE 6 7 4
'BRAF MUTATION STATUS' versus 'CN_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S109.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
BRAF MUTATED 5 16 4 14
BRAF WILD-TYPE 60 194 68 117
'BRAF MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0783 (Fisher's exact test), Q value = 0.48

Table S110.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
BRAF MUTATED 8 8 20
BRAF WILD-TYPE 123 130 141
'BRAF MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S111.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
BRAF MUTATED 9 3 5 3 7
BRAF WILD-TYPE 80 19 54 62 94
'BRAF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S112.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
BRAF MUTATED 14 9 4
BRAF WILD-TYPE 142 112 55
'BRAF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.273 (Fisher's exact test), Q value = 0.79

Table S113.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
BRAF MUTATED 10 20 9
BRAF WILD-TYPE 140 165 134
'BRAF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.91

Table S114.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
BRAF MUTATED 5 14 8 4 2 1 5
BRAF WILD-TYPE 67 95 82 40 47 45 63
'BRAF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S115.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
BRAF MUTATED 16 18 5
BRAF WILD-TYPE 159 193 85
'BRAF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0329 (Fisher's exact test), Q value = 0.34

Table S116.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
BRAF MUTATED 10 19 5 5
BRAF WILD-TYPE 60 167 126 84

Figure S47.  Get High-res Image Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.919 (Fisher's exact test), Q value = 1

Table S117.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
BRAF MUTATED 12 15 6
BRAF WILD-TYPE 129 167 83
'BRAF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.514 (Fisher's exact test), Q value = 1

Table S118.  Gene #11: 'BRAF MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
BRAF MUTATED 8 16 9
BRAF WILD-TYPE 86 217 76
'MGA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.266 (Fisher's exact test), Q value = 0.78

Table S119.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
MGA MUTATED 5 12 8 14
MGA WILD-TYPE 60 198 64 117
'MGA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0557 (Fisher's exact test), Q value = 0.43

Table S120.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
MGA MUTATED 5 15 16
MGA WILD-TYPE 126 123 145
'MGA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.723 (Fisher's exact test), Q value = 1

Table S121.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
MGA MUTATED 9 1 4 8 7
MGA WILD-TYPE 80 21 55 57 94
'MGA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.53

Table S122.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
MGA MUTATED 10 16 3
MGA WILD-TYPE 146 105 56
'MGA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00232 (Fisher's exact test), Q value = 0.06

Table S123.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
MGA MUTATED 7 26 7
MGA WILD-TYPE 143 159 136

Figure S48.  Get High-res Image Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'MGA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.153 (Fisher's exact test), Q value = 0.62

Table S124.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
MGA MUTATED 3 15 11 3 2 2 4
MGA WILD-TYPE 69 94 79 41 47 44 64
'MGA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0311 (Fisher's exact test), Q value = 0.33

Table S125.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
MGA MUTATED 8 25 6
MGA WILD-TYPE 167 186 84

Figure S49.  Get High-res Image Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'MGA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0658 (Fisher's exact test), Q value = 0.45

Table S126.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
MGA MUTATED 5 17 5 12
MGA WILD-TYPE 65 169 126 77
'MGA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.328 (Fisher's exact test), Q value = 0.85

Table S127.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
MGA MUTATED 13 18 4
MGA WILD-TYPE 128 164 85
'MGA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0806 (Fisher's exact test), Q value = 0.48

Table S128.  Gene #12: 'MGA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
MGA MUTATED 3 23 9
MGA WILD-TYPE 91 210 76
'FTSJD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.268 (Fisher's exact test), Q value = 0.78

Table S129.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
FTSJD1 MUTATED 1 11 2 10
FTSJD1 WILD-TYPE 64 199 70 121
'FTSJD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.87

Table S130.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
FTSJD1 MUTATED 4 6 11
FTSJD1 WILD-TYPE 127 132 150
'FTSJD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.93 (Fisher's exact test), Q value = 1

Table S131.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
FTSJD1 MUTATED 3 1 3 4 6
FTSJD1 WILD-TYPE 86 21 56 61 95
'FTSJD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.384 (Fisher's exact test), Q value = 0.91

Table S132.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
FTSJD1 MUTATED 6 9 2
FTSJD1 WILD-TYPE 150 112 57
'FTSJD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.223 (Fisher's exact test), Q value = 0.73

Table S133.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
FTSJD1 MUTATED 7 13 4
FTSJD1 WILD-TYPE 143 172 139
'FTSJD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.289 (Fisher's exact test), Q value = 0.81

Table S134.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
FTSJD1 MUTATED 2 11 5 2 1 1 2
FTSJD1 WILD-TYPE 70 98 85 42 48 45 66
'FTSJD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S135.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
FTSJD1 MUTATED 7 13 4
FTSJD1 WILD-TYPE 168 198 86
'FTSJD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S136.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
FTSJD1 MUTATED 4 11 4 5
FTSJD1 WILD-TYPE 66 175 127 84
'FTSJD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0895 (Fisher's exact test), Q value = 0.49

Table S137.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
FTSJD1 MUTATED 3 13 3
FTSJD1 WILD-TYPE 138 169 86
'FTSJD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 0.7

Table S138.  Gene #13: 'FTSJD1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
FTSJD1 MUTATED 6 12 1
FTSJD1 WILD-TYPE 88 221 84
'MET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0849 (Fisher's exact test), Q value = 0.48

Table S139.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
MET MUTATED 0 12 1 8
MET WILD-TYPE 65 198 71 123
'MET MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S140.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
MET MUTATED 5 5 9
MET WILD-TYPE 126 133 152
'MET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 0.96

Table S141.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
MET MUTATED 8 0 2 3 4
MET WILD-TYPE 81 22 57 62 97
'MET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.266 (Fisher's exact test), Q value = 0.78

Table S142.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
MET MUTATED 5 9 3
MET WILD-TYPE 151 112 56
'MET MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S143.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
MET MUTATED 7 10 4
MET WILD-TYPE 143 175 139
'MET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.626 (Fisher's exact test), Q value = 1

Table S144.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
MET MUTATED 3 6 4 1 0 2 5
MET WILD-TYPE 69 103 86 43 49 44 63
'MET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0849 (Fisher's exact test), Q value = 0.48

Table S145.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
MET MUTATED 9 5 7
MET WILD-TYPE 166 206 83
'MET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.21 (Fisher's exact test), Q value = 0.7

Table S146.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
MET MUTATED 2 9 9 1
MET WILD-TYPE 68 177 122 88
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.97

Table S147.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
MET MUTATED 8 6 5
MET WILD-TYPE 133 176 84
'MET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.169 (Fisher's exact test), Q value = 0.65

Table S148.  Gene #14: 'MET MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
MET MUTATED 2 10 7
MET WILD-TYPE 92 223 78
'GAGE2A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 0.95

Table S149.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
GAGE2A MUTATED 0 5 2 1
GAGE2A WILD-TYPE 65 205 70 130
'GAGE2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S150.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
GAGE2A MUTATED 3 1 2
GAGE2A WILD-TYPE 128 137 159
'GAGE2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S151.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
GAGE2A MUTATED 3 0 0 1 2
GAGE2A WILD-TYPE 86 22 59 64 99
'GAGE2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.482 (Fisher's exact test), Q value = 0.98

Table S152.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
GAGE2A MUTATED 2 2 2
GAGE2A WILD-TYPE 154 119 57
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.89

Table S153.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
GAGE2A MUTATED 1 5 2
GAGE2A WILD-TYPE 149 180 141
'GAGE2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S154.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
GAGE2A MUTATED 0 4 1 1 0 1 1
GAGE2A WILD-TYPE 72 105 89 43 49 45 67
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0689 (Fisher's exact test), Q value = 0.46

Table S155.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
GAGE2A MUTATED 1 3 4
GAGE2A WILD-TYPE 174 208 86
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S156.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
GAGE2A MUTATED 0 3 3 2
GAGE2A WILD-TYPE 70 183 128 87
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S157.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
GAGE2A MUTATED 3 2 0
GAGE2A WILD-TYPE 138 180 89
'GAGE2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 0.84

Table S158.  Gene #15: 'GAGE2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
GAGE2A MUTATED 0 3 2
GAGE2A WILD-TYPE 94 230 83
'SETD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.208 (Fisher's exact test), Q value = 0.7

Table S159.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
SETD2 MUTATED 2 16 7 5
SETD2 WILD-TYPE 63 194 65 126
'SETD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.9

Table S160.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
SETD2 MUTATED 10 6 13
SETD2 WILD-TYPE 121 132 148
'SETD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.611 (Fisher's exact test), Q value = 1

Table S161.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
SETD2 MUTATED 5 3 3 4 5
SETD2 WILD-TYPE 84 19 56 61 96
'SETD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.681 (Fisher's exact test), Q value = 1

Table S162.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
SETD2 MUTATED 11 7 2
SETD2 WILD-TYPE 145 114 57
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.53

Table S163.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
SETD2 MUTATED 12 14 4
SETD2 WILD-TYPE 138 171 139
'SETD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.73

Table S164.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
SETD2 MUTATED 8 7 7 1 0 3 4
SETD2 WILD-TYPE 64 102 83 43 49 43 64
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S165.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
SETD2 MUTATED 13 10 6
SETD2 WILD-TYPE 162 201 84
'SETD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S166.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
SETD2 MUTATED 4 12 7 6
SETD2 WILD-TYPE 66 174 124 83
'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.19

Table S167.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
SETD2 MUTATED 12 6 11
SETD2 WILD-TYPE 129 176 78

Figure S50.  Get High-res Image Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'SETD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.054 (Fisher's exact test), Q value = 0.43

Table S168.  Gene #16: 'SETD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
SETD2 MUTATED 2 18 9
SETD2 WILD-TYPE 92 215 76
'U2AF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.717 (Fisher's exact test), Q value = 1

Table S169.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
U2AF1 MUTATED 1 4 1 5
U2AF1 WILD-TYPE 64 206 71 126
'U2AF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S170.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
U2AF1 MUTATED 3 2 4
U2AF1 WILD-TYPE 128 136 157
'U2AF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.058 (Fisher's exact test), Q value = 0.43

Table S171.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
U2AF1 MUTATED 3 1 0 3 0
U2AF1 WILD-TYPE 86 21 59 62 101
'U2AF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.686 (Fisher's exact test), Q value = 1

Table S172.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
U2AF1 MUTATED 4 3 0
U2AF1 WILD-TYPE 152 118 59
'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0482 (Fisher's exact test), Q value = 0.43

Table S173.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
U2AF1 MUTATED 4 7 0
U2AF1 WILD-TYPE 146 178 143

Figure S51.  Get High-res Image Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'U2AF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.57

Table S174.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
U2AF1 MUTATED 1 7 1 0 0 0 2
U2AF1 WILD-TYPE 71 102 89 44 49 46 66
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00866 (Fisher's exact test), Q value = 0.15

Table S175.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
U2AF1 MUTATED 9 2 0
U2AF1 WILD-TYPE 166 209 90

Figure S52.  Get High-res Image Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'U2AF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S176.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
U2AF1 MUTATED 3 4 3 1
U2AF1 WILD-TYPE 67 182 128 88
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0986 (Fisher's exact test), Q value = 0.52

Table S177.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
U2AF1 MUTATED 6 3 0
U2AF1 WILD-TYPE 135 179 89
'U2AF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.529 (Fisher's exact test), Q value = 1

Table S178.  Gene #17: 'U2AF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
U2AF1 MUTATED 2 4 3
U2AF1 WILD-TYPE 92 229 82
'ERBB2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S179.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ERBB2 MUTATED 0 6 2 3
ERBB2 WILD-TYPE 65 204 70 128
'ERBB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.096 (Fisher's exact test), Q value = 0.51

Table S180.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ERBB2 MUTATED 2 0 5
ERBB2 WILD-TYPE 129 138 156
'ERBB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.172 (Fisher's exact test), Q value = 0.66

Table S181.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ERBB2 MUTATED 3 2 0 3 2
ERBB2 WILD-TYPE 86 20 59 62 99
'ERBB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S182.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ERBB2 MUTATED 5 4 1
ERBB2 WILD-TYPE 151 117 58
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.515 (Fisher's exact test), Q value = 1

Table S183.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ERBB2 MUTATED 2 6 3
ERBB2 WILD-TYPE 148 179 140
'ERBB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.59

Table S184.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ERBB2 MUTATED 3 6 1 1 0 0 0
ERBB2 WILD-TYPE 69 103 89 43 49 46 68
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S185.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ERBB2 MUTATED 5 5 1
ERBB2 WILD-TYPE 170 206 89
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.241 (Fisher's exact test), Q value = 0.75

Table S186.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ERBB2 MUTATED 4 4 2 1
ERBB2 WILD-TYPE 66 182 129 88
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S187.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ERBB2 MUTATED 3 3 0
ERBB2 WILD-TYPE 138 179 89
'ERBB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.73

Table S188.  Gene #18: 'ERBB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ERBB2 MUTATED 3 3 0
ERBB2 WILD-TYPE 91 230 85
'CDKN2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S189.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
CDKN2A MUTATED 3 8 2 3
CDKN2A WILD-TYPE 62 202 70 128
'CDKN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S190.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
CDKN2A MUTATED 3 4 5
CDKN2A WILD-TYPE 128 134 156
'CDKN2A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.821 (Fisher's exact test), Q value = 1

Table S191.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
CDKN2A MUTATED 2 0 1 3 4
CDKN2A WILD-TYPE 87 22 58 62 97
'CDKN2A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S192.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
CDKN2A MUTATED 4 5 1
CDKN2A WILD-TYPE 152 116 58
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0603 (Fisher's exact test), Q value = 0.43

Table S193.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
CDKN2A MUTATED 1 9 6
CDKN2A WILD-TYPE 149 176 137
'CDKN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.207 (Fisher's exact test), Q value = 0.7

Table S194.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
CDKN2A MUTATED 0 6 4 1 0 3 2
CDKN2A WILD-TYPE 72 103 86 43 49 43 66
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S195.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
CDKN2A MUTATED 6 7 3
CDKN2A WILD-TYPE 169 204 87
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.858 (Fisher's exact test), Q value = 1

Table S196.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
CDKN2A MUTATED 2 6 6 2
CDKN2A WILD-TYPE 68 180 125 87
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S197.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
CDKN2A MUTATED 3 4 4
CDKN2A WILD-TYPE 138 178 85
'CDKN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.917 (Fisher's exact test), Q value = 1

Table S198.  Gene #19: 'CDKN2A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
CDKN2A MUTATED 3 6 2
CDKN2A WILD-TYPE 91 227 83
'SRPX MUTATION STATUS' versus 'CN_CNMF'

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

Table S199.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
SRPX MUTATED 2 6 3 3
SRPX WILD-TYPE 63 204 69 128
'SRPX MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.798 (Fisher's exact test), Q value = 1

Table S200.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
SRPX MUTATED 4 4 3
SRPX WILD-TYPE 127 134 158
'SRPX MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S201.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
SRPX MUTATED 2 1 1 1 5
SRPX WILD-TYPE 87 21 58 64 96
'SRPX MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0388 (Fisher's exact test), Q value = 0.37

Table S202.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
SRPX MUTATED 2 3 5
SRPX WILD-TYPE 154 118 54

Figure S53.  Get High-res Image Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SRPX MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S203.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
SRPX MUTATED 6 4 4
SRPX WILD-TYPE 144 181 139
'SRPX MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.911 (Fisher's exact test), Q value = 1

Table S204.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
SRPX MUTATED 3 4 2 0 2 1 2
SRPX WILD-TYPE 69 105 88 44 47 45 66
'SRPX MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S205.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
SRPX MUTATED 3 8 3
SRPX WILD-TYPE 172 203 87
'SRPX MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S206.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
SRPX MUTATED 2 8 2 2
SRPX WILD-TYPE 68 178 129 87
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.775 (Fisher's exact test), Q value = 1

Table S207.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
SRPX MUTATED 4 5 1
SRPX WILD-TYPE 137 177 88
'SRPX MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.304 (Fisher's exact test), Q value = 0.82

Table S208.  Gene #20: 'SRPX MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
SRPX MUTATED 1 5 4
SRPX WILD-TYPE 93 228 81
'ATM MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00019 (Fisher's exact test), Q value = 0.0076

Table S209.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ATM MUTATED 12 16 11 3
ATM WILD-TYPE 53 194 61 128

Figure S54.  Get High-res Image Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ATM MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.001 (Fisher's exact test), Q value = 0.031

Table S210.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ATM MUTATED 2 17 16
ATM WILD-TYPE 129 121 145

Figure S55.  Get High-res Image Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ATM MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.332 (Fisher's exact test), Q value = 0.86

Table S211.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ATM MUTATED 4 1 5 9 9
ATM WILD-TYPE 85 21 54 56 92
'ATM MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S212.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ATM MUTATED 13 11 4
ATM WILD-TYPE 143 110 55
'ATM MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00206 (Fisher's exact test), Q value = 0.056

Table S213.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ATM MUTATED 8 11 23
ATM WILD-TYPE 142 174 120

Figure S56.  Get High-res Image Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'ATM MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00047 (Fisher's exact test), Q value = 0.017

Table S214.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ATM MUTATED 6 6 4 6 13 5 2
ATM WILD-TYPE 66 103 86 38 36 41 66

Figure S57.  Get High-res Image Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ATM MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S215.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ATM MUTATED 14 20 8
ATM WILD-TYPE 161 191 82
'ATM MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0533 (Fisher's exact test), Q value = 0.43

Table S216.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ATM MUTATED 8 23 6 5
ATM WILD-TYPE 62 163 125 84
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.509 (Fisher's exact test), Q value = 1

Table S217.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ATM MUTATED 9 18 8
ATM WILD-TYPE 132 164 81
'ATM MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.915 (Fisher's exact test), Q value = 1

Table S218.  Gene #21: 'ATM MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ATM MUTATED 8 21 6
ATM WILD-TYPE 86 212 79
'TCEAL5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S219.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
TCEAL5 MUTATED 1 4 3 5
TCEAL5 WILD-TYPE 64 206 69 126
'TCEAL5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.663 (Fisher's exact test), Q value = 1

Table S220.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
TCEAL5 MUTATED 4 5 3
TCEAL5 WILD-TYPE 127 133 158
'TCEAL5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.86

Table S221.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
TCEAL5 MUTATED 2 1 2 5 2
TCEAL5 WILD-TYPE 87 21 57 60 99
'TCEAL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S222.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
TCEAL5 MUTATED 5 5 2
TCEAL5 WILD-TYPE 151 116 57
'TCEAL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.936 (Fisher's exact test), Q value = 1

Table S223.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
TCEAL5 MUTATED 4 4 4
TCEAL5 WILD-TYPE 146 181 139
'TCEAL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.866 (Fisher's exact test), Q value = 1

Table S224.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
TCEAL5 MUTATED 3 3 2 1 2 0 1
TCEAL5 WILD-TYPE 69 106 88 43 47 46 67
'TCEAL5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.933 (Fisher's exact test), Q value = 1

Table S225.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
TCEAL5 MUTATED 4 6 3
TCEAL5 WILD-TYPE 171 205 87
'TCEAL5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S226.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
TCEAL5 MUTATED 1 4 4 4
TCEAL5 WILD-TYPE 69 182 127 85
'TCEAL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S227.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
TCEAL5 MUTATED 5 4 3
TCEAL5 WILD-TYPE 136 178 86
'TCEAL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S228.  Gene #22: 'TCEAL5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
TCEAL5 MUTATED 2 9 1
TCEAL5 WILD-TYPE 92 224 84
'PPP3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.926 (Fisher's exact test), Q value = 1

Table S229.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
PPP3CA MUTATED 2 6 1 3
PPP3CA WILD-TYPE 63 204 71 128
'PPP3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.82

Table S230.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
PPP3CA MUTATED 1 4 6
PPP3CA WILD-TYPE 130 134 155
'PPP3CA MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S231.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
PPP3CA MUTATED 2 1 2 2 1
PPP3CA WILD-TYPE 87 21 57 63 100
'PPP3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S232.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
PPP3CA MUTATED 5 2 1
PPP3CA WILD-TYPE 151 119 58
'PPP3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.47 (Fisher's exact test), Q value = 0.97

Table S233.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
PPP3CA MUTATED 2 5 5
PPP3CA WILD-TYPE 148 180 138
'PPP3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0154 (Fisher's exact test), Q value = 0.22

Table S234.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
PPP3CA MUTATED 1 3 3 5 0 0 0
PPP3CA WILD-TYPE 71 106 87 39 49 46 68

Figure S58.  Get High-res Image Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PPP3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.142 (Fisher's exact test), Q value = 0.6

Table S235.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
PPP3CA MUTATED 2 9 1
PPP3CA WILD-TYPE 173 202 89
'PPP3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.242 (Fisher's exact test), Q value = 0.75

Table S236.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
PPP3CA MUTATED 1 8 1 2
PPP3CA WILD-TYPE 69 178 130 87
'PPP3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S237.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
PPP3CA MUTATED 3 7 1
PPP3CA WILD-TYPE 138 175 88
'PPP3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.77

Table S238.  Gene #23: 'PPP3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
PPP3CA MUTATED 3 8 0
PPP3CA WILD-TYPE 91 225 85
'FCRLA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.174 (Fisher's exact test), Q value = 0.66

Table S239.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
FCRLA MUTATED 4 6 0 5
FCRLA WILD-TYPE 61 204 72 126
'FCRLA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S240.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
FCRLA MUTATED 4 4 7
FCRLA WILD-TYPE 127 134 154
'FCRLA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.845 (Fisher's exact test), Q value = 1

Table S241.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
FCRLA MUTATED 3 1 1 3 3
FCRLA WILD-TYPE 86 21 58 62 98
'FCRLA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.332 (Fisher's exact test), Q value = 0.86

Table S242.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
FCRLA MUTATED 6 5 0
FCRLA WILD-TYPE 150 116 59
'FCRLA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S243.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
FCRLA MUTATED 4 7 4
FCRLA WILD-TYPE 146 178 139
'FCRLA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.9

Table S244.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
FCRLA MUTATED 1 5 1 0 3 2 3
FCRLA WILD-TYPE 71 104 89 44 46 44 65
'FCRLA MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S245.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
FCRLA MUTATED 5 7 3
FCRLA WILD-TYPE 170 204 87
'FCRLA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S246.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
FCRLA MUTATED 3 6 3 3
FCRLA WILD-TYPE 67 180 128 86
'FCRLA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.643 (Fisher's exact test), Q value = 1

Table S247.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
FCRLA MUTATED 4 8 2
FCRLA WILD-TYPE 137 174 87
'FCRLA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.199 (Fisher's exact test), Q value = 0.7

Table S248.  Gene #24: 'FCRLA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
FCRLA MUTATED 1 8 5
FCRLA WILD-TYPE 93 225 80
'ARID2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S249.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ARID2 MUTATED 3 9 5 7
ARID2 WILD-TYPE 62 201 67 124
'ARID2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S250.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ARID2 MUTATED 5 6 10
ARID2 WILD-TYPE 126 132 151
'ARID2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S251.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ARID2 MUTATED 4 0 4 2 5
ARID2 WILD-TYPE 85 22 55 63 96
'ARID2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S252.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ARID2 MUTATED 7 6 2
ARID2 WILD-TYPE 149 115 57
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.138 (Fisher's exact test), Q value = 0.59

Table S253.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ARID2 MUTATED 6 14 4
ARID2 WILD-TYPE 144 171 139
'ARID2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0918 (Fisher's exact test), Q value = 0.5

Table S254.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ARID2 MUTATED 1 5 6 5 0 4 3
ARID2 WILD-TYPE 71 104 84 39 49 42 65
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0791 (Fisher's exact test), Q value = 0.48

Table S255.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ARID2 MUTATED 4 15 5
ARID2 WILD-TYPE 171 196 85
'ARID2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.8

Table S256.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ARID2 MUTATED 3 13 3 5
ARID2 WILD-TYPE 67 173 128 84
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.126 (Fisher's exact test), Q value = 0.57

Table S257.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ARID2 MUTATED 3 9 7
ARID2 WILD-TYPE 138 173 82
'ARID2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.385 (Fisher's exact test), Q value = 0.91

Table S258.  Gene #25: 'ARID2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ARID2 MUTATED 3 14 2
ARID2 WILD-TYPE 91 219 83
'APC MUTATION STATUS' versus 'CN_CNMF'

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

Table S259.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
APC MUTATED 3 8 4 5
APC WILD-TYPE 62 202 68 126
'APC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.642 (Fisher's exact test), Q value = 1

Table S260.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
APC MUTATED 5 6 4
APC WILD-TYPE 126 132 157
'APC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S261.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
APC MUTATED 5 1 3 3 3
APC WILD-TYPE 84 21 56 62 98
'APC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S262.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
APC MUTATED 8 5 2
APC WILD-TYPE 148 116 57
'APC MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0861 (Fisher's exact test), Q value = 0.49

Table S263.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
APC MUTATED 2 11 7
APC WILD-TYPE 148 174 136
'APC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.222 (Fisher's exact test), Q value = 0.73

Table S264.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
APC MUTATED 1 4 7 2 1 4 1
APC WILD-TYPE 71 105 83 42 48 42 67
'APC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.063 (Fisher's exact test), Q value = 0.43

Table S265.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
APC MUTATED 5 14 1
APC WILD-TYPE 170 197 89
'APC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0516 (Fisher's exact test), Q value = 0.43

Table S266.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
APC MUTATED 0 11 3 6
APC WILD-TYPE 70 175 128 83
'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S267.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
APC MUTATED 4 6 4
APC WILD-TYPE 137 176 85
'APC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.79

Table S268.  Gene #26: 'APC MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
APC MUTATED 2 11 1
APC WILD-TYPE 92 222 84
'ZEB1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S269.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
ZEB1 MUTATED 1 2 0 1
ZEB1 WILD-TYPE 4 5 5 2
'ZEB1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S270.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
ZEB1 MUTATED 1 2 1
ZEB1 WILD-TYPE 6 7 3
'ZEB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S271.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ZEB1 MUTATED 6 12 6 8
ZEB1 WILD-TYPE 59 198 66 123
'ZEB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.689 (Fisher's exact test), Q value = 1

Table S272.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ZEB1 MUTATED 7 11 10
ZEB1 WILD-TYPE 124 127 151
'ZEB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S273.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ZEB1 MUTATED 6 2 3 6 5
ZEB1 WILD-TYPE 83 20 56 59 96
'ZEB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S274.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ZEB1 MUTATED 10 9 3
ZEB1 WILD-TYPE 146 112 56
'ZEB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.97

Table S275.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ZEB1 MUTATED 7 15 9
ZEB1 WILD-TYPE 143 170 134
'ZEB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 0.98

Table S276.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ZEB1 MUTATED 4 9 8 2 3 0 5
ZEB1 WILD-TYPE 68 100 82 42 46 46 63
'ZEB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.506 (Fisher's exact test), Q value = 1

Table S277.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ZEB1 MUTATED 9 17 5
ZEB1 WILD-TYPE 166 194 85
'ZEB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.044 (Fisher's exact test), Q value = 0.41

Table S278.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ZEB1 MUTATED 3 8 8 12
ZEB1 WILD-TYPE 67 178 123 77

Figure S59.  Get High-res Image Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ZEB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S279.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ZEB1 MUTATED 8 12 5
ZEB1 WILD-TYPE 133 170 84
'ZEB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S280.  Gene #27: 'ZEB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ZEB1 MUTATED 5 13 7
ZEB1 WILD-TYPE 89 220 78
'SIP1 MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.55

Table S281.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
SIP1 MUTATED 2 0 0 1
SIP1 WILD-TYPE 3 7 5 2
'SIP1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.55

Table S282.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
SIP1 MUTATED 0 1 2
SIP1 WILD-TYPE 7 8 2
'SIP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0662 (Fisher's exact test), Q value = 0.45

Table S283.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
SIP1 MUTATED 0 0 2 2
SIP1 WILD-TYPE 65 210 70 129
'SIP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 0.97

Table S284.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
SIP1 MUTATED 2 0 0 1 0
SIP1 WILD-TYPE 87 22 59 64 101
'SIP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S285.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
SIP1 MUTATED 2 1 0
SIP1 WILD-TYPE 154 120 59
'SIP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S286.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
SIP1 MUTATED 1 2 1
SIP1 WILD-TYPE 149 183 142
'SIP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.978 (Fisher's exact test), Q value = 1

Table S287.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
SIP1 MUTATED 1 2 1 0 0 0 0
SIP1 WILD-TYPE 71 107 89 44 49 46 68
'SIP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 0.92

Table S288.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
SIP1 MUTATED 3 1 0
SIP1 WILD-TYPE 172 210 90
'SIP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.6

Table S289.  Gene #28: 'SIP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
SIP1 MUTATED 2 1 0 1
SIP1 WILD-TYPE 68 185 131 88
'SLC4A3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S290.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
SLC4A3 MUTATED 2 8 3 5
SLC4A3 WILD-TYPE 63 202 69 126
'SLC4A3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.9

Table S291.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
SLC4A3 MUTATED 3 8 7
SLC4A3 WILD-TYPE 128 130 154
'SLC4A3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.66

Table S292.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
SLC4A3 MUTATED 5 1 1 6 2
SLC4A3 WILD-TYPE 84 21 58 59 99
'SLC4A3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0583 (Fisher's exact test), Q value = 0.43

Table S293.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
SLC4A3 MUTATED 6 9 0
SLC4A3 WILD-TYPE 150 112 59
'SLC4A3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.13 (Fisher's exact test), Q value = 0.58

Table S294.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
SLC4A3 MUTATED 2 10 6
SLC4A3 WILD-TYPE 148 175 137
'SLC4A3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.96

Table S295.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
SLC4A3 MUTATED 0 6 5 1 2 2 2
SLC4A3 WILD-TYPE 72 103 85 43 47 44 66
'SLC4A3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.146 (Fisher's exact test), Q value = 0.6

Table S296.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
SLC4A3 MUTATED 5 12 1
SLC4A3 WILD-TYPE 170 199 89
'SLC4A3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.752 (Fisher's exact test), Q value = 1

Table S297.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
SLC4A3 MUTATED 3 8 3 4
SLC4A3 WILD-TYPE 67 178 128 85
'SLC4A3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.344 (Fisher's exact test), Q value = 0.87

Table S298.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
SLC4A3 MUTATED 3 10 4
SLC4A3 WILD-TYPE 138 172 85
'SLC4A3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00348 (Fisher's exact test), Q value = 0.078

Table S299.  Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
SLC4A3 MUTATED 1 16 0
SLC4A3 WILD-TYPE 93 217 85

Figure S60.  Get High-res Image Gene #29: 'SLC4A3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'STK19 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S300.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
STK19 MUTATED 1 2 0 2
STK19 WILD-TYPE 64 208 72 129
'STK19 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S301.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
STK19 MUTATED 1 2 2
STK19 WILD-TYPE 130 136 159
'STK19 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.823 (Fisher's exact test), Q value = 1

Table S302.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
STK19 MUTATED 1 0 0 0 2
STK19 WILD-TYPE 88 22 59 65 99
'STK19 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.588 (Fisher's exact test), Q value = 1

Table S303.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
STK19 MUTATED 1 1 1
STK19 WILD-TYPE 155 120 58
'STK19 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.39 (Fisher's exact test), Q value = 0.91

Table S304.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
STK19 MUTATED 2 3 0
STK19 WILD-TYPE 148 182 143
'STK19 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.976 (Fisher's exact test), Q value = 1

Table S305.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
STK19 MUTATED 1 1 1 0 0 1 1
STK19 WILD-TYPE 71 108 89 44 49 45 67
'STK19 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.848 (Fisher's exact test), Q value = 1

Table S306.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
STK19 MUTATED 1 3 1
STK19 WILD-TYPE 174 208 89
'STK19 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S307.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
STK19 MUTATED 0 3 2 0
STK19 WILD-TYPE 70 183 129 89
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0555 (Fisher's exact test), Q value = 0.43

Table S308.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
STK19 MUTATED 0 5 0
STK19 WILD-TYPE 141 177 89
'STK19 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S309.  Gene #30: 'STK19 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
STK19 MUTATED 1 4 0
STK19 WILD-TYPE 93 229 85
'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.8 (Fisher's exact test), Q value = 1

Table S310.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
NUDT11 MUTATED 1 3 0 1
NUDT11 WILD-TYPE 64 207 72 130
'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S311.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
NUDT11 MUTATED 1 2 2
NUDT11 WILD-TYPE 130 136 159
'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S312.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
NUDT11 MUTATED 1 0 2 0 1
NUDT11 WILD-TYPE 88 22 57 65 100
'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S313.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
NUDT11 MUTATED 2 1 1
NUDT11 WILD-TYPE 154 120 58
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S314.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
NUDT11 MUTATED 2 1 1
NUDT11 WILD-TYPE 148 184 142
'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.82

Table S315.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
NUDT11 MUTATED 0 1 0 1 0 0 2
NUDT11 WILD-TYPE 72 108 90 43 49 46 66
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.067 (Fisher's exact test), Q value = 0.45

Table S316.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
NUDT11 MUTATED 4 0 1
NUDT11 WILD-TYPE 171 211 89
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.73

Table S317.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
NUDT11 MUTATED 2 1 2 0
NUDT11 WILD-TYPE 68 185 129 89
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S318.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
NUDT11 MUTATED 1 2 1
NUDT11 WILD-TYPE 140 180 88
'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.146 (Fisher's exact test), Q value = 0.6

Table S319.  Gene #31: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
NUDT11 MUTATED 1 1 2
NUDT11 WILD-TYPE 93 232 83
'SLAMF9 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00899 (Fisher's exact test), Q value = 0.15

Table S320.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
SLAMF9 MUTATED 1 1 2 8
SLAMF9 WILD-TYPE 64 209 70 123

Figure S61.  Get High-res Image Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'SLAMF9 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0404 (Fisher's exact test), Q value = 0.39

Table S321.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
SLAMF9 MUTATED 0 6 5
SLAMF9 WILD-TYPE 131 132 156

Figure S62.  Get High-res Image Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'SLAMF9 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 1

Table S322.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
SLAMF9 MUTATED 4 0 2 3 3
SLAMF9 WILD-TYPE 85 22 57 62 98
'SLAMF9 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S323.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
SLAMF9 MUTATED 6 4 2
SLAMF9 WILD-TYPE 150 117 57
'SLAMF9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.2 (Fisher's exact test), Q value = 0.7

Table S324.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
SLAMF9 MUTATED 1 6 5
SLAMF9 WILD-TYPE 149 179 138
'SLAMF9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S325.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
SLAMF9 MUTATED 2 4 4 0 1 1 0
SLAMF9 WILD-TYPE 70 105 86 44 48 45 68
'SLAMF9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0824 (Fisher's exact test), Q value = 0.48

Table S326.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
SLAMF9 MUTATED 1 8 3
SLAMF9 WILD-TYPE 174 203 87
'SLAMF9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0122 (Fisher's exact test), Q value = 0.19

Table S327.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
SLAMF9 MUTATED 0 9 0 3
SLAMF9 WILD-TYPE 70 177 131 86

Figure S63.  Get High-res Image Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'SLAMF9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S328.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
SLAMF9 MUTATED 4 3 3
SLAMF9 WILD-TYPE 137 179 86
'SLAMF9 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S329.  Gene #32: 'SLAMF9 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
SLAMF9 MUTATED 1 7 2
SLAMF9 WILD-TYPE 93 226 83
'DNMT3A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S330.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
DNMT3A MUTATED 3 9 4 3
DNMT3A WILD-TYPE 62 201 68 128
'DNMT3A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.486 (Fisher's exact test), Q value = 0.98

Table S331.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
DNMT3A MUTATED 6 8 5
DNMT3A WILD-TYPE 125 130 156
'DNMT3A MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.576 (Fisher's exact test), Q value = 1

Table S332.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
DNMT3A MUTATED 3 1 0 2 4
DNMT3A WILD-TYPE 86 21 59 63 97
'DNMT3A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.81

Table S333.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
DNMT3A MUTATED 3 6 1
DNMT3A WILD-TYPE 153 115 58
'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S334.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
DNMT3A MUTATED 4 8 7
DNMT3A WILD-TYPE 146 177 136
'DNMT3A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S335.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
DNMT3A MUTATED 3 3 5 1 2 4 1
DNMT3A WILD-TYPE 69 106 85 43 47 42 67
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.338 (Fisher's exact test), Q value = 0.87

Table S336.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
DNMT3A MUTATED 4 11 4
DNMT3A WILD-TYPE 171 200 86
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.111 (Fisher's exact test), Q value = 0.54

Table S337.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
DNMT3A MUTATED 2 5 4 8
DNMT3A WILD-TYPE 68 181 127 81
'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00913 (Fisher's exact test), Q value = 0.15

Table S338.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
DNMT3A MUTATED 1 13 4
DNMT3A WILD-TYPE 140 169 85

Figure S64.  Get High-res Image Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'DNMT3A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00831 (Fisher's exact test), Q value = 0.15

Table S339.  Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
DNMT3A MUTATED 0 16 2
DNMT3A WILD-TYPE 94 217 83

Figure S65.  Get High-res Image Gene #33: 'DNMT3A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CTNNB1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 0.95

Table S340.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
CTNNB1 MUTATED 5 8 2 4
CTNNB1 WILD-TYPE 60 202 70 127
'CTNNB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.79

Table S341.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
CTNNB1 MUTATED 2 6 8
CTNNB1 WILD-TYPE 129 132 153
'CTNNB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0347 (Fisher's exact test), Q value = 0.35

Table S342.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
CTNNB1 MUTATED 1 1 6 1 2
CTNNB1 WILD-TYPE 88 21 53 64 99

Figure S66.  Get High-res Image Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'CTNNB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 0.77

Table S343.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
CTNNB1 MUTATED 8 2 1
CTNNB1 WILD-TYPE 148 119 58
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.78

Table S344.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
CTNNB1 MUTATED 4 6 9
CTNNB1 WILD-TYPE 146 179 134
'CTNNB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.408 (Fisher's exact test), Q value = 0.92

Table S345.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
CTNNB1 MUTATED 4 2 5 4 1 1 2
CTNNB1 WILD-TYPE 68 107 85 40 48 45 66
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0269 (Fisher's exact test), Q value = 0.3

Table S346.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
CTNNB1 MUTATED 6 13 0
CTNNB1 WILD-TYPE 169 198 90

Figure S67.  Get High-res Image Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S347.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
CTNNB1 MUTATED 2 8 4 5
CTNNB1 WILD-TYPE 68 178 127 84
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.264 (Fisher's exact test), Q value = 0.78

Table S348.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
CTNNB1 MUTATED 2 8 1
CTNNB1 WILD-TYPE 139 174 88
'CTNNB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S349.  Gene #34: 'CTNNB1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
CTNNB1 MUTATED 3 7 1
CTNNB1 WILD-TYPE 91 226 84
'PTPRU MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0138 (Fisher's exact test), Q value = 0.2

Table S350.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
PTPRU MUTATED 2 3 2 11
PTPRU WILD-TYPE 63 207 70 120

Figure S68.  Get High-res Image Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PTPRU MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.54

Table S351.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
PTPRU MUTATED 1 5 8
PTPRU WILD-TYPE 130 133 153
'PTPRU MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.103 (Fisher's exact test), Q value = 0.53

Table S352.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
PTPRU MUTATED 3 3 2 5 2
PTPRU WILD-TYPE 86 19 57 60 99
'PTPRU MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0261 (Fisher's exact test), Q value = 0.3

Table S353.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
PTPRU MUTATED 5 10 0
PTPRU WILD-TYPE 151 111 59

Figure S69.  Get High-res Image Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'PTPRU MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0112 (Fisher's exact test), Q value = 0.18

Table S354.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
PTPRU MUTATED 1 12 5
PTPRU WILD-TYPE 149 173 138

Figure S70.  Get High-res Image Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PTPRU MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.061 (Fisher's exact test), Q value = 0.43

Table S355.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
PTPRU MUTATED 2 6 8 0 1 1 0
PTPRU WILD-TYPE 70 103 82 44 48 45 68
'PTPRU MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00296 (Fisher's exact test), Q value = 0.073

Table S356.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
PTPRU MUTATED 1 14 2
PTPRU WILD-TYPE 174 197 88

Figure S71.  Get High-res Image Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PTPRU MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00739 (Fisher's exact test), Q value = 0.14

Table S357.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
PTPRU MUTATED 0 9 1 7
PTPRU WILD-TYPE 70 177 130 82

Figure S72.  Get High-res Image Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PTPRU MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S358.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
PTPRU MUTATED 4 6 3
PTPRU WILD-TYPE 137 176 86
'PTPRU MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.69

Table S359.  Gene #35: 'PTPRU MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
PTPRU MUTATED 1 11 1
PTPRU WILD-TYPE 93 222 84
'PIK3CA MUTATION STATUS' versus 'CN_CNMF'

P value = 0.368 (Fisher's exact test), Q value = 0.9

Table S360.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
PIK3CA MUTATED 2 15 6 5
PIK3CA WILD-TYPE 63 195 66 126
'PIK3CA MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 0.82

Table S361.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
PIK3CA MUTATED 10 9 6
PIK3CA WILD-TYPE 121 129 155
'PIK3CA MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.15 (Fisher's exact test), Q value = 0.61

Table S362.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
PIK3CA MUTATED 2 2 2 5 10
PIK3CA WILD-TYPE 87 20 57 60 91
'PIK3CA MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.58

Table S363.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
PIK3CA MUTATED 7 7 7
PIK3CA WILD-TYPE 149 114 52
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0504 (Fisher's exact test), Q value = 0.43

Table S364.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
PIK3CA MUTATED 10 15 3
PIK3CA WILD-TYPE 140 170 140
'PIK3CA MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0249 (Fisher's exact test), Q value = 0.3

Table S365.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
PIK3CA MUTATED 6 5 12 1 0 2 2
PIK3CA WILD-TYPE 66 104 78 43 49 44 66

Figure S73.  Get High-res Image Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.874 (Fisher's exact test), Q value = 1

Table S366.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
PIK3CA MUTATED 9 13 6
PIK3CA WILD-TYPE 166 198 84
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S367.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
PIK3CA MUTATED 2 10 10 6
PIK3CA WILD-TYPE 68 176 121 83
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.62

Table S368.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
PIK3CA MUTATED 10 6 7
PIK3CA WILD-TYPE 131 176 82
'PIK3CA MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.164 (Fisher's exact test), Q value = 0.64

Table S369.  Gene #36: 'PIK3CA MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
PIK3CA MUTATED 2 14 7
PIK3CA WILD-TYPE 92 219 78
'ZNF608 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.183 (Fisher's exact test), Q value = 0.68

Table S370.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ZNF608 MUTATED 3 3 2 1
ZNF608 WILD-TYPE 62 207 70 130
'ZNF608 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S371.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ZNF608 MUTATED 3 4 2
ZNF608 WILD-TYPE 128 134 159
'ZNF608 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.233 (Fisher's exact test), Q value = 0.73

Table S372.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ZNF608 MUTATED 0 0 0 1 4
ZNF608 WILD-TYPE 89 22 59 64 97
'ZNF608 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S373.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ZNF608 MUTATED 2 2 1
ZNF608 WILD-TYPE 154 119 58
'ZNF608 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.199 (Fisher's exact test), Q value = 0.7

Table S374.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ZNF608 MUTATED 1 3 5
ZNF608 WILD-TYPE 149 182 138
'ZNF608 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00889 (Fisher's exact test), Q value = 0.15

Table S375.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ZNF608 MUTATED 1 0 1 2 4 1 0
ZNF608 WILD-TYPE 71 109 89 42 45 45 68

Figure S74.  Get High-res Image Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'ZNF608 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 1

Table S376.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ZNF608 MUTATED 2 6 1
ZNF608 WILD-TYPE 173 205 89
'ZNF608 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S377.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ZNF608 MUTATED 0 4 2 3
ZNF608 WILD-TYPE 70 182 129 86
'ZNF608 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S378.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ZNF608 MUTATED 2 4 3
ZNF608 WILD-TYPE 139 178 86
'ZNF608 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.374 (Fisher's exact test), Q value = 0.9

Table S379.  Gene #37: 'ZNF608 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ZNF608 MUTATED 2 7 0
ZNF608 WILD-TYPE 92 226 85
'STIM1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0154 (Fisher's exact test), Q value = 0.22

Table S380.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
STIM1 MUTATED 0 2 0 7
STIM1 WILD-TYPE 65 208 72 124

Figure S75.  Get High-res Image Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'STIM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S381.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
STIM1 MUTATED 2 3 3
STIM1 WILD-TYPE 129 135 158
'STIM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S382.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
STIM1 MUTATED 2 0 1 2 1
STIM1 WILD-TYPE 87 22 58 63 100
'STIM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S383.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
STIM1 MUTATED 2 3 1
STIM1 WILD-TYPE 154 118 58
'STIM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S384.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
STIM1 MUTATED 2 5 2
STIM1 WILD-TYPE 148 180 141
'STIM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.265 (Fisher's exact test), Q value = 0.78

Table S385.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
STIM1 MUTATED 1 5 3 0 0 0 0
STIM1 WILD-TYPE 71 104 87 44 49 46 68
'STIM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.55

Table S386.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
STIM1 MUTATED 2 7 0
STIM1 WILD-TYPE 173 204 90
'STIM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.191 (Fisher's exact test), Q value = 0.69

Table S387.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
STIM1 MUTATED 2 5 0 2
STIM1 WILD-TYPE 68 181 131 87
'STIM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 0.95

Table S388.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
STIM1 MUTATED 1 5 1
STIM1 WILD-TYPE 140 177 88
'STIM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S389.  Gene #38: 'STIM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
STIM1 MUTATED 1 5 1
STIM1 WILD-TYPE 93 228 84
'EMG1 MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S390.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
EMG1 MUTATED 1 1 1 0
EMG1 WILD-TYPE 4 6 4 3
'EMG1 MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S391.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
EMG1 MUTATED 2 1 0
EMG1 WILD-TYPE 5 8 4
'EMG1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S392.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
EMG1 MUTATED 0 4 0 1
EMG1 WILD-TYPE 65 206 72 130
'EMG1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.401 (Fisher's exact test), Q value = 0.92

Table S393.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
EMG1 MUTATED 2 0 1
EMG1 WILD-TYPE 129 138 160
'EMG1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S394.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
EMG1 MUTATED 2 0 0 0 1
EMG1 WILD-TYPE 87 22 59 65 100
'EMG1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.295 (Fisher's exact test), Q value = 0.81

Table S395.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
EMG1 MUTATED 3 0 0
EMG1 WILD-TYPE 153 121 59
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 0.47

Table S396.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
EMG1 MUTATED 4 1 0
EMG1 WILD-TYPE 146 184 143
'EMG1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.262 (Fisher's exact test), Q value = 0.78

Table S397.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
EMG1 MUTATED 3 1 0 0 0 0 1
EMG1 WILD-TYPE 69 108 90 44 49 46 67
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.71

Table S398.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
EMG1 MUTATED 4 1 0
EMG1 WILD-TYPE 171 210 90
'EMG1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 0.9

Table S399.  Gene #39: 'EMG1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
EMG1 MUTATED 2 2 1 0
EMG1 WILD-TYPE 68 184 130 89
'PHKA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00124 (Fisher's exact test), Q value = 0.037

Table S400.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
PHKA1 MUTATED 2 1 0 9
PHKA1 WILD-TYPE 63 209 72 122

Figure S76.  Get High-res Image Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'PHKA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.345 (Fisher's exact test), Q value = 0.87

Table S401.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
PHKA1 MUTATED 2 6 3
PHKA1 WILD-TYPE 129 132 158
'PHKA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.693 (Fisher's exact test), Q value = 1

Table S402.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
PHKA1 MUTATED 2 1 2 1 5
PHKA1 WILD-TYPE 87 21 57 64 96
'PHKA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.781 (Fisher's exact test), Q value = 1

Table S403.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
PHKA1 MUTATED 5 5 1
PHKA1 WILD-TYPE 151 116 58
'PHKA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.58

Table S404.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
PHKA1 MUTATED 1 5 6
PHKA1 WILD-TYPE 149 180 137
'PHKA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.355 (Fisher's exact test), Q value = 0.89

Table S405.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
PHKA1 MUTATED 1 6 3 0 1 1 0
PHKA1 WILD-TYPE 71 103 87 44 48 45 68
'PHKA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.92

Table S406.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
PHKA1 MUTATED 3 8 1
PHKA1 WILD-TYPE 172 203 89
'PHKA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.279 (Fisher's exact test), Q value = 0.79

Table S407.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
PHKA1 MUTATED 1 6 1 4
PHKA1 WILD-TYPE 69 180 130 85
'PHKA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.93

Table S408.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
PHKA1 MUTATED 2 7 2
PHKA1 WILD-TYPE 139 175 87
'PHKA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0505 (Fisher's exact test), Q value = 0.43

Table S409.  Gene #40: 'PHKA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
PHKA1 MUTATED 0 10 1
PHKA1 WILD-TYPE 94 223 84
'PAK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.88

Table S410.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
PAK1 MUTATED 0 6 2 1
PAK1 WILD-TYPE 65 204 70 130
'PAK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S411.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
PAK1 MUTATED 3 4 2
PAK1 WILD-TYPE 128 134 159
'PAK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.81

Table S412.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
PAK1 MUTATED 1 1 3 1 1
PAK1 WILD-TYPE 88 21 56 64 100
'PAK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S413.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
PAK1 MUTATED 4 2 1
PAK1 WILD-TYPE 152 119 58
'PAK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.82

Table S414.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
PAK1 MUTATED 2 2 5
PAK1 WILD-TYPE 148 183 138
'PAK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.255 (Fisher's exact test), Q value = 0.77

Table S415.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
PAK1 MUTATED 1 0 2 2 1 2 1
PAK1 WILD-TYPE 71 109 88 42 48 44 67
'PAK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.912 (Fisher's exact test), Q value = 1

Table S416.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
PAK1 MUTATED 4 4 1
PAK1 WILD-TYPE 171 207 89
'PAK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S417.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
PAK1 MUTATED 2 3 2 2
PAK1 WILD-TYPE 68 183 129 87
'PAK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S418.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
PAK1 MUTATED 3 4 2
PAK1 WILD-TYPE 138 178 87
'PAK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S419.  Gene #41: 'PAK1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
PAK1 MUTATED 2 5 2
PAK1 WILD-TYPE 92 228 83
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0765 (Fisher's exact test), Q value = 0.48

Table S420.  Gene #42: 'NRAS MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
NRAS MUTATED 0 0 0 3
NRAS WILD-TYPE 65 210 72 128
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S421.  Gene #42: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
NRAS MUTATED 0 3 0
NRAS WILD-TYPE 150 182 143
'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.895 (Fisher's exact test), Q value = 1

Table S422.  Gene #42: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
NRAS MUTATED 0 2 1 0 0 0 0
NRAS WILD-TYPE 72 107 89 44 49 46 68
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.305 (Fisher's exact test), Q value = 0.82

Table S423.  Gene #42: 'NRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
NRAS MUTATED 0 3 0
NRAS WILD-TYPE 175 208 90
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.35 (Fisher's exact test), Q value = 0.88

Table S424.  Gene #42: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
NRAS MUTATED 0 3 0 0
NRAS WILD-TYPE 70 183 131 89
'G3BP1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.66

Table S425.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
G3BP1 MUTATED 3 4 0 1
G3BP1 WILD-TYPE 62 206 72 130
'G3BP1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S426.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
G3BP1 MUTATED 2 1 1
G3BP1 WILD-TYPE 129 137 160
'G3BP1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.931 (Fisher's exact test), Q value = 1

Table S427.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
G3BP1 MUTATED 1 0 1 2 2
G3BP1 WILD-TYPE 88 22 58 63 99
'G3BP1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.334 (Fisher's exact test), Q value = 0.86

Table S428.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
G3BP1 MUTATED 2 4 0
G3BP1 WILD-TYPE 154 117 59
'G3BP1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S429.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
G3BP1 MUTATED 2 2 4
G3BP1 WILD-TYPE 148 183 139
'G3BP1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S430.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
G3BP1 MUTATED 0 3 2 1 1 0 1
G3BP1 WILD-TYPE 72 106 88 43 48 46 67
'G3BP1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S431.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
G3BP1 MUTATED 3 3 2
G3BP1 WILD-TYPE 172 208 88
'G3BP1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S432.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
G3BP1 MUTATED 1 2 3 2
G3BP1 WILD-TYPE 69 184 128 87
'G3BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.687 (Fisher's exact test), Q value = 1

Table S433.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
G3BP1 MUTATED 2 1 1
G3BP1 WILD-TYPE 139 181 88
'G3BP1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S434.  Gene #43: 'G3BP1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
G3BP1 MUTATED 0 3 1
G3BP1 WILD-TYPE 94 230 84
'TRERF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.157 (Fisher's exact test), Q value = 0.62

Table S435.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
TRERF1 MUTATED 2 4 4 8
TRERF1 WILD-TYPE 63 206 68 123
'TRERF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0598 (Fisher's exact test), Q value = 0.43

Table S436.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
TRERF1 MUTATED 1 8 7
TRERF1 WILD-TYPE 130 130 154
'TRERF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.81

Table S437.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
TRERF1 MUTATED 1 1 4 1 4
TRERF1 WILD-TYPE 88 21 55 64 97
'TRERF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.654 (Fisher's exact test), Q value = 1

Table S438.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
TRERF1 MUTATED 5 3 3
TRERF1 WILD-TYPE 151 118 56
'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0111 (Fisher's exact test), Q value = 0.18

Table S439.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
TRERF1 MUTATED 1 12 5
TRERF1 WILD-TYPE 149 173 138

Figure S77.  Get High-res Image Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TRERF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.307 (Fisher's exact test), Q value = 0.82

Table S440.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
TRERF1 MUTATED 1 5 5 1 0 4 2
TRERF1 WILD-TYPE 71 104 85 43 49 42 66
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0692 (Fisher's exact test), Q value = 0.46

Table S441.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
TRERF1 MUTATED 3 13 2
TRERF1 WILD-TYPE 172 198 88
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.298 (Fisher's exact test), Q value = 0.82

Table S442.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
TRERF1 MUTATED 1 11 3 3
TRERF1 WILD-TYPE 69 175 128 86
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S443.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
TRERF1 MUTATED 4 9 2
TRERF1 WILD-TYPE 137 173 87
'TRERF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.7

Table S444.  Gene #44: 'TRERF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
TRERF1 MUTATED 1 12 2
TRERF1 WILD-TYPE 93 221 83
'CACNA1F MUTATION STATUS' versus 'CN_CNMF'

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

Table S445.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
CACNA1F MUTATED 3 12 4 8
CACNA1F WILD-TYPE 62 198 68 123
'CACNA1F MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S446.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
CACNA1F MUTATED 7 9 10
CACNA1F WILD-TYPE 124 129 151
'CACNA1F MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.7

Table S447.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
CACNA1F MUTATED 6 3 1 5 4
CACNA1F WILD-TYPE 83 19 58 60 97
'CACNA1F MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S448.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
CACNA1F MUTATED 8 7 4
CACNA1F WILD-TYPE 148 114 55
'CACNA1F MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S449.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
CACNA1F MUTATED 8 13 6
CACNA1F WILD-TYPE 142 172 137
'CACNA1F MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.52

Table S450.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
CACNA1F MUTATED 1 5 7 1 1 5 7
CACNA1F WILD-TYPE 71 104 83 43 48 41 61
'CACNA1F MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00784 (Fisher's exact test), Q value = 0.15

Table S451.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
CACNA1F MUTATED 10 17 0
CACNA1F WILD-TYPE 165 194 90

Figure S78.  Get High-res Image Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'CACNA1F MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.992 (Fisher's exact test), Q value = 1

Table S452.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
CACNA1F MUTATED 4 10 8 5
CACNA1F WILD-TYPE 66 176 123 84
'CACNA1F MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S453.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
CACNA1F MUTATED 8 14 4
CACNA1F WILD-TYPE 133 168 85
'CACNA1F MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S454.  Gene #45: 'CACNA1F MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
CACNA1F MUTATED 4 16 6
CACNA1F WILD-TYPE 90 217 79
'NFE2L2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S455.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
NFE2L2 MUTATED 2 8 1 2
NFE2L2 WILD-TYPE 63 202 71 129
'NFE2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S456.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
NFE2L2 MUTATED 2 5 5
NFE2L2 WILD-TYPE 129 133 156
'NFE2L2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.271 (Fisher's exact test), Q value = 0.78

Table S457.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
NFE2L2 MUTATED 1 2 2 1 2
NFE2L2 WILD-TYPE 88 20 57 64 99
'NFE2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 0.77

Table S458.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
NFE2L2 MUTATED 6 1 1
NFE2L2 WILD-TYPE 150 120 58
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0746 (Fisher's exact test), Q value = 0.47

Table S459.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
NFE2L2 MUTATED 1 5 7
NFE2L2 WILD-TYPE 149 180 136
'NFE2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0383 (Fisher's exact test), Q value = 0.37

Table S460.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
NFE2L2 MUTATED 0 2 3 3 0 4 1
NFE2L2 WILD-TYPE 72 107 87 41 49 42 67

Figure S79.  Get High-res Image Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S461.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
NFE2L2 MUTATED 4 6 2
NFE2L2 WILD-TYPE 171 205 88
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.7

Table S462.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
NFE2L2 MUTATED 2 8 1 1
NFE2L2 WILD-TYPE 68 178 130 88
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S463.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
NFE2L2 MUTATED 2 6 2
NFE2L2 WILD-TYPE 139 176 87
'NFE2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S464.  Gene #46: 'NFE2L2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
NFE2L2 MUTATED 3 6 1
NFE2L2 WILD-TYPE 91 227 84
'RPL5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S465.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
RPL5 MUTATED 1 4 1 2
RPL5 WILD-TYPE 64 206 71 129
'RPL5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S466.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
RPL5 MUTATED 3 3 2
RPL5 WILD-TYPE 128 135 159
'RPL5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.902 (Fisher's exact test), Q value = 1

Table S467.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
RPL5 MUTATED 1 0 2 1 2
RPL5 WILD-TYPE 88 22 57 64 99
'RPL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.129 (Fisher's exact test), Q value = 0.58

Table S468.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
RPL5 MUTATED 5 0 1
RPL5 WILD-TYPE 151 121 58
'RPL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.738 (Fisher's exact test), Q value = 1

Table S469.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
RPL5 MUTATED 3 2 3
RPL5 WILD-TYPE 147 183 140
'RPL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S470.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
RPL5 MUTATED 1 1 2 2 0 1 1
RPL5 WILD-TYPE 71 108 88 42 49 45 67
'RPL5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.93

Table S471.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
RPL5 MUTATED 2 3 3
RPL5 WILD-TYPE 173 208 87
'RPL5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.367 (Fisher's exact test), Q value = 0.9

Table S472.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
RPL5 MUTATED 0 2 3 3
RPL5 WILD-TYPE 70 184 128 86
'RPL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 0.97

Table S473.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
RPL5 MUTATED 1 5 2
RPL5 WILD-TYPE 140 177 87
'RPL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S474.  Gene #47: 'RPL5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
RPL5 MUTATED 2 5 1
RPL5 WILD-TYPE 92 228 84
'STRA8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0047 (Fisher's exact test), Q value = 0.1

Table S475.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
STRA8 MUTATED 2 0 4 2
STRA8 WILD-TYPE 63 210 68 129

Figure S80.  Get High-res Image Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'STRA8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0766 (Fisher's exact test), Q value = 0.48

Table S476.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
STRA8 MUTATED 0 4 1
STRA8 WILD-TYPE 131 134 160
'STRA8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00851 (Fisher's exact test), Q value = 0.15

Table S477.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
STRA8 MUTATED 0 0 0 5 1
STRA8 WILD-TYPE 89 22 59 60 100

Figure S81.  Get High-res Image Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'STRA8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.28

Table S478.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
STRA8 MUTATED 0 5 1
STRA8 WILD-TYPE 156 116 58

Figure S82.  Get High-res Image Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'STRA8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.105 (Fisher's exact test), Q value = 0.53

Table S479.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
STRA8 MUTATED 0 5 3
STRA8 WILD-TYPE 150 180 140
'STRA8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0338 (Fisher's exact test), Q value = 0.35

Table S480.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
STRA8 MUTATED 0 1 4 0 3 0 0
STRA8 WILD-TYPE 72 108 86 44 46 46 68

Figure S83.  Get High-res Image Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'STRA8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0128 (Fisher's exact test), Q value = 0.19

Table S481.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
STRA8 MUTATED 0 7 0
STRA8 WILD-TYPE 175 204 90

Figure S84.  Get High-res Image Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'STRA8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 0.55

Table S482.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
STRA8 MUTATED 0 4 0 3
STRA8 WILD-TYPE 70 182 131 86
'STRA8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S483.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
STRA8 MUTATED 3 2 0
STRA8 WILD-TYPE 138 180 89
'STRA8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.24 (Fisher's exact test), Q value = 0.75

Table S484.  Gene #48: 'STRA8 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
STRA8 MUTATED 0 5 0
STRA8 WILD-TYPE 94 228 85
'NLRP6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.58

Table S485.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
NLRP6 MUTATED 0 3 4 3
NLRP6 WILD-TYPE 65 207 68 128
'NLRP6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 0.95

Table S486.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
NLRP6 MUTATED 1 3 5
NLRP6 WILD-TYPE 130 135 156
'NLRP6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0263 (Fisher's exact test), Q value = 0.3

Table S487.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
NLRP6 MUTATED 1 0 0 4 0
NLRP6 WILD-TYPE 88 22 59 61 101

Figure S85.  Get High-res Image Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'NLRP6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.165 (Fisher's exact test), Q value = 0.64

Table S488.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
NLRP6 MUTATED 1 4 0
NLRP6 WILD-TYPE 155 117 59
'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S489.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
NLRP6 MUTATED 3 3 4
NLRP6 WILD-TYPE 147 182 139
'NLRP6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0187 (Fisher's exact test), Q value = 0.25

Table S490.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
NLRP6 MUTATED 1 0 2 0 4 0 3
NLRP6 WILD-TYPE 71 109 88 44 45 46 65

Figure S86.  Get High-res Image Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.137 (Fisher's exact test), Q value = 0.59

Table S491.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
NLRP6 MUTATED 1 7 2
NLRP6 WILD-TYPE 174 204 88
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0778 (Fisher's exact test), Q value = 0.48

Table S492.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
NLRP6 MUTATED 1 5 0 4
NLRP6 WILD-TYPE 69 181 131 85
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S493.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
NLRP6 MUTATED 2 4 3
NLRP6 WILD-TYPE 139 178 86
'NLRP6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0907 (Fisher's exact test), Q value = 0.49

Table S494.  Gene #49: 'NLRP6 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
NLRP6 MUTATED 0 5 4
NLRP6 WILD-TYPE 94 228 81
'FAM65C MUTATION STATUS' versus 'CN_CNMF'

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

Table S495.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
FAM65C MUTATED 1 8 3 2
FAM65C WILD-TYPE 64 202 69 129
'FAM65C MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S496.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
FAM65C MUTATED 3 4 6
FAM65C WILD-TYPE 128 134 155
'FAM65C MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0573 (Fisher's exact test), Q value = 0.43

Table S497.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
FAM65C MUTATED 0 1 2 0 5
FAM65C WILD-TYPE 89 21 57 65 96
'FAM65C MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0542 (Fisher's exact test), Q value = 0.43

Table S498.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
FAM65C MUTATED 3 1 4
FAM65C WILD-TYPE 153 120 55
'FAM65C MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S499.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
FAM65C MUTATED 5 5 4
FAM65C WILD-TYPE 145 180 139
'FAM65C MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S500.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
FAM65C MUTATED 2 5 3 1 1 2 0
FAM65C WILD-TYPE 70 104 87 43 48 44 68
'FAM65C MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.54

Table S501.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
FAM65C MUTATED 2 10 2
FAM65C WILD-TYPE 173 201 88
'FAM65C MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.48 (Fisher's exact test), Q value = 0.98

Table S502.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
FAM65C MUTATED 1 7 2 4
FAM65C WILD-TYPE 69 179 129 85
'FAM65C MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S503.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
FAM65C MUTATED 4 4 3
FAM65C WILD-TYPE 137 178 86
'FAM65C MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.58

Table S504.  Gene #50: 'FAM65C MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
FAM65C MUTATED 0 9 2
FAM65C WILD-TYPE 94 224 83
'WDR66 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0547 (Fisher's exact test), Q value = 0.43

Table S505.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
WDR66 MUTATED 3 2 2 7
WDR66 WILD-TYPE 62 208 70 124
'WDR66 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0454 (Fisher's exact test), Q value = 0.42

Table S506.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
WDR66 MUTATED 1 8 3
WDR66 WILD-TYPE 130 130 158

Figure S87.  Get High-res Image Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'WDR66 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00342 (Fisher's exact test), Q value = 0.078

Table S507.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
WDR66 MUTATED 0 0 5 5 1
WDR66 WILD-TYPE 89 22 54 60 100

Figure S88.  Get High-res Image Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'WDR66 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.104 (Fisher's exact test), Q value = 0.53

Table S508.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
WDR66 MUTATED 4 7 0
WDR66 WILD-TYPE 152 114 59
'WDR66 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S509.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
WDR66 MUTATED 4 4 6
WDR66 WILD-TYPE 146 181 137
'WDR66 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.491 (Fisher's exact test), Q value = 0.99

Table S510.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
WDR66 MUTATED 2 1 4 0 2 2 3
WDR66 WILD-TYPE 70 108 86 44 47 44 65
'WDR66 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.62

Table S511.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
WDR66 MUTATED 3 10 1
WDR66 WILD-TYPE 172 201 89
'WDR66 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S512.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
WDR66 MUTATED 1 8 2 3
WDR66 WILD-TYPE 69 178 129 86
'WDR66 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.128 (Fisher's exact test), Q value = 0.57

Table S513.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
WDR66 MUTATED 4 8 0
WDR66 WILD-TYPE 137 174 89
'WDR66 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.159 (Fisher's exact test), Q value = 0.62

Table S514.  Gene #51: 'WDR66 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
WDR66 MUTATED 4 8 0
WDR66 WILD-TYPE 90 225 85
'RIT1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0315 (Fisher's exact test), Q value = 0.33

Table S515.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
RIT1 MUTATED 1 3 4 0
RIT1 WILD-TYPE 64 207 68 131

Figure S89.  Get High-res Image Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'RIT1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S516.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
RIT1 MUTATED 1 2 3
RIT1 WILD-TYPE 130 136 158
'RIT1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.363 (Fisher's exact test), Q value = 0.89

Table S517.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
RIT1 MUTATED 0 1 1 1 2
RIT1 WILD-TYPE 89 21 58 64 99
'RIT1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S518.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
RIT1 MUTATED 2 2 1
RIT1 WILD-TYPE 154 119 58
'RIT1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S519.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
RIT1 MUTATED 2 3 3
RIT1 WILD-TYPE 148 182 140
'RIT1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.66

Table S520.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
RIT1 MUTATED 0 2 0 2 1 2 1
RIT1 WILD-TYPE 72 107 90 42 48 44 67
'RIT1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.269 (Fisher's exact test), Q value = 0.78

Table S521.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
RIT1 MUTATED 2 2 3
RIT1 WILD-TYPE 173 209 87
'RIT1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S522.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
RIT1 MUTATED 1 3 2 1
RIT1 WILD-TYPE 69 183 129 88
'RIT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S523.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
RIT1 MUTATED 3 3 0
RIT1 WILD-TYPE 138 179 89
'RIT1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.27 (Fisher's exact test), Q value = 0.78

Table S524.  Gene #52: 'RIT1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
RIT1 MUTATED 3 2 1
RIT1 WILD-TYPE 91 231 84
'TGFBR3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S525.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
TGFBR3 MUTATED 3 5 1 5
TGFBR3 WILD-TYPE 62 205 71 126
'TGFBR3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S526.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
TGFBR3 MUTATED 3 6 5
TGFBR3 WILD-TYPE 128 132 156
'TGFBR3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.799 (Fisher's exact test), Q value = 1

Table S527.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
TGFBR3 MUTATED 2 0 2 3 2
TGFBR3 WILD-TYPE 87 22 57 62 99
'TGFBR3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.59

Table S528.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
TGFBR3 MUTATED 2 6 1
TGFBR3 WILD-TYPE 154 115 58
'TGFBR3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 0.91

Table S529.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
TGFBR3 MUTATED 2 7 5
TGFBR3 WILD-TYPE 148 178 138
'TGFBR3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.73

Table S530.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
TGFBR3 MUTATED 1 6 1 0 2 3 1
TGFBR3 WILD-TYPE 71 103 89 44 47 43 67
'TGFBR3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0448 (Fisher's exact test), Q value = 0.41

Table S531.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
TGFBR3 MUTATED 2 11 1
TGFBR3 WILD-TYPE 173 200 89

Figure S90.  Get High-res Image Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TGFBR3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.203 (Fisher's exact test), Q value = 0.7

Table S532.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
TGFBR3 MUTATED 2 9 1 2
TGFBR3 WILD-TYPE 68 177 130 87
'TGFBR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.198 (Fisher's exact test), Q value = 0.7

Table S533.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
TGFBR3 MUTATED 2 9 2
TGFBR3 WILD-TYPE 139 173 87
'TGFBR3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.28

Table S534.  Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
TGFBR3 MUTATED 0 12 1
TGFBR3 WILD-TYPE 94 221 84

Figure S91.  Get High-res Image Gene #53: 'TGFBR3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CXCR7 MUTATION STATUS' versus 'CN_CNMF'

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

Table S535.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
CXCR7 MUTATED 2 3 2 3
CXCR7 WILD-TYPE 63 207 70 128
'CXCR7 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S536.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
CXCR7 MUTATED 2 4 4
CXCR7 WILD-TYPE 129 134 157
'CXCR7 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S537.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
CXCR7 MUTATED 1 1 2 1 2
CXCR7 WILD-TYPE 88 21 57 64 99
'CXCR7 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.19 (Fisher's exact test), Q value = 0.69

Table S538.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
CXCR7 MUTATED 2 5 0
CXCR7 WILD-TYPE 154 116 59
'CXCR7 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.669 (Fisher's exact test), Q value = 1

Table S539.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
CXCR7 MUTATED 2 5 3
CXCR7 WILD-TYPE 148 180 140
'CXCR7 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S540.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
CXCR7 MUTATED 0 3 1 1 2 1 2
CXCR7 WILD-TYPE 72 106 89 43 47 45 66
'CXCR7 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.337 (Fisher's exact test), Q value = 0.87

Table S541.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
CXCR7 MUTATED 4 6 0
CXCR7 WILD-TYPE 171 205 90
'CXCR7 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.657 (Fisher's exact test), Q value = 1

Table S542.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
CXCR7 MUTATED 0 4 4 2
CXCR7 WILD-TYPE 70 182 127 87
'CXCR7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S543.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
CXCR7 MUTATED 3 4 2
CXCR7 WILD-TYPE 138 178 87
'CXCR7 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S544.  Gene #54: 'CXCR7 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
CXCR7 MUTATED 1 7 1
CXCR7 WILD-TYPE 93 226 84
'GAN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.479 (Fisher's exact test), Q value = 0.98

Table S545.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
GAN MUTATED 0 7 1 2
GAN WILD-TYPE 65 203 71 129
'GAN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S546.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
GAN MUTATED 3 2 3
GAN WILD-TYPE 128 136 158
'GAN MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S547.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
GAN MUTATED 3 1 2 1 3
GAN WILD-TYPE 86 21 57 64 98
'GAN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S548.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
GAN MUTATED 4 4 2
GAN WILD-TYPE 152 117 57
'GAN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S549.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
GAN MUTATED 3 3 4
GAN WILD-TYPE 147 182 139
'GAN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.405 (Fisher's exact test), Q value = 0.92

Table S550.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
GAN MUTATED 3 3 1 1 0 2 0
GAN WILD-TYPE 69 106 89 43 49 44 68
'GAN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S551.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
GAN MUTATED 2 6 2
GAN WILD-TYPE 173 205 88
'GAN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.792 (Fisher's exact test), Q value = 1

Table S552.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
GAN MUTATED 1 4 2 3
GAN WILD-TYPE 69 182 129 86
'GAN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S553.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
GAN MUTATED 3 3 1
GAN WILD-TYPE 138 179 88
'GAN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.767 (Fisher's exact test), Q value = 1

Table S554.  Gene #55: 'GAN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
GAN MUTATED 1 4 2
GAN WILD-TYPE 93 229 83
'TMEM49 MUTATION STATUS' versus 'CN_CNMF'

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

Table S555.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
TMEM49 MUTATED 0 2 0 3
TMEM49 WILD-TYPE 65 208 72 128
'TMEM49 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.74

Table S556.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
TMEM49 MUTATED 3 0 2
TMEM49 WILD-TYPE 128 138 159
'TMEM49 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.934 (Fisher's exact test), Q value = 1

Table S557.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
TMEM49 MUTATED 1 0 0 1 2
TMEM49 WILD-TYPE 88 22 59 64 99
'TMEM49 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0907 (Fisher's exact test), Q value = 0.49

Table S558.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
TMEM49 MUTATED 0 3 1
TMEM49 WILD-TYPE 156 118 58
'TMEM49 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.281 (Fisher's exact test), Q value = 0.79

Table S559.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
TMEM49 MUTATED 3 2 0
TMEM49 WILD-TYPE 147 183 143
'TMEM49 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.22 (Fisher's exact test), Q value = 0.73

Table S560.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
TMEM49 MUTATED 1 1 0 0 0 0 3
TMEM49 WILD-TYPE 71 108 90 44 49 46 65
'TMEM49 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 0.94

Table S561.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
TMEM49 MUTATED 1 2 2
TMEM49 WILD-TYPE 174 209 88
'TMEM49 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.467 (Fisher's exact test), Q value = 0.97

Table S562.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
TMEM49 MUTATED 0 2 3 0
TMEM49 WILD-TYPE 70 184 128 89
'TMEM49 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S563.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
TMEM49 MUTATED 1 2 2
TMEM49 WILD-TYPE 140 180 87
'TMEM49 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 0.92

Table S564.  Gene #56: 'TMEM49 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
TMEM49 MUTATED 1 2 2
TMEM49 WILD-TYPE 93 231 83
'HSPA8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.62

Table S565.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
HSPA8 MUTATED 0 2 2 5
HSPA8 WILD-TYPE 65 208 70 126
'HSPA8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.7

Table S566.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
HSPA8 MUTATED 0 3 4
HSPA8 WILD-TYPE 131 135 157
'HSPA8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.426 (Fisher's exact test), Q value = 0.94

Table S567.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
HSPA8 MUTATED 1 0 2 3 1
HSPA8 WILD-TYPE 88 22 57 62 100
'HSPA8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S568.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
HSPA8 MUTATED 3 3 1
HSPA8 WILD-TYPE 153 118 58
'HSPA8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S569.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
HSPA8 MUTATED 2 5 2
HSPA8 WILD-TYPE 148 180 141
'HSPA8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.223 (Fisher's exact test), Q value = 0.73

Table S570.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
HSPA8 MUTATED 0 2 5 0 0 1 1
HSPA8 WILD-TYPE 72 107 85 44 49 45 67
'HSPA8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00535 (Fisher's exact test), Q value = 0.11

Table S571.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
HSPA8 MUTATED 0 8 0
HSPA8 WILD-TYPE 175 203 90

Figure S92.  Get High-res Image Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'HSPA8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.157 (Fisher's exact test), Q value = 0.62

Table S572.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
HSPA8 MUTATED 0 2 2 4
HSPA8 WILD-TYPE 70 184 129 85
'HSPA8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.294 (Fisher's exact test), Q value = 0.81

Table S573.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
HSPA8 MUTATED 4 3 0
HSPA8 WILD-TYPE 137 179 89
'HSPA8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S574.  Gene #57: 'HSPA8 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
HSPA8 MUTATED 1 5 1
HSPA8 WILD-TYPE 93 228 84
'CD244 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.26 (Fisher's exact test), Q value = 0.78

Table S575.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
CD244 MUTATED 0 4 3 5
CD244 WILD-TYPE 65 206 69 126
'CD244 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S576.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
CD244 MUTATED 4 5 3
CD244 WILD-TYPE 127 133 158
'CD244 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.63 (Fisher's exact test), Q value = 1

Table S577.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
CD244 MUTATED 2 0 0 1 4
CD244 WILD-TYPE 87 22 59 64 97
'CD244 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S578.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
CD244 MUTATED 3 2 2
CD244 WILD-TYPE 153 119 57
'CD244 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.9

Table S579.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
CD244 MUTATED 2 7 3
CD244 WILD-TYPE 148 178 140
'CD244 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.78

Table S580.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
CD244 MUTATED 0 2 5 1 0 2 2
CD244 WILD-TYPE 72 107 85 43 49 44 66
'CD244 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0747 (Fisher's exact test), Q value = 0.47

Table S581.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
CD244 MUTATED 3 9 0
CD244 WILD-TYPE 172 202 90
'CD244 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0142 (Fisher's exact test), Q value = 0.21

Table S582.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
CD244 MUTATED 3 2 1 6
CD244 WILD-TYPE 67 184 130 83

Figure S93.  Get High-res Image Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'CD244 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S583.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
CD244 MUTATED 4 5 2
CD244 WILD-TYPE 137 177 87
'CD244 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S584.  Gene #58: 'CD244 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
CD244 MUTATED 1 8 2
CD244 WILD-TYPE 93 225 83
'KIF18B MUTATION STATUS' versus 'MRNA_CNMF'

P value = 0.289 (Fisher's exact test), Q value = 0.81

Table S585.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
KIF18B MUTATED 0 2 0 1
KIF18B WILD-TYPE 5 5 5 2
'KIF18B MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

P value = 0.391 (Fisher's exact test), Q value = 0.91

Table S586.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
KIF18B MUTATED 0 2 1
KIF18B WILD-TYPE 7 7 3
'KIF18B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0461 (Fisher's exact test), Q value = 0.42

Table S587.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
KIF18B MUTATED 2 0 1 1
KIF18B WILD-TYPE 63 210 71 130

Figure S94.  Get High-res Image Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KIF18B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.89

Table S588.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
KIF18B MUTATED 1 1 0 0 1
KIF18B WILD-TYPE 88 21 59 65 100
'KIF18B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.126 (Fisher's exact test), Q value = 0.57

Table S589.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
KIF18B MUTATED 0 3 0
KIF18B WILD-TYPE 156 118 59
'KIF18B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S590.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
KIF18B MUTATED 0 2 2
KIF18B WILD-TYPE 150 183 141
'KIF18B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S591.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
KIF18B MUTATED 0 2 2 0 0 0 0
KIF18B WILD-TYPE 72 107 88 44 49 46 68
'KIF18B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S592.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
KIF18B MUTATED 1 2 1
KIF18B WILD-TYPE 174 209 89
'KIF18B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.454 (Fisher's exact test), Q value = 0.96

Table S593.  Gene #59: 'KIF18B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
KIF18B MUTATED 0 1 1 2
KIF18B WILD-TYPE 70 185 130 87
'PDE6A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.326 (Fisher's exact test), Q value = 0.85

Table S594.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
PDE6A MUTATED 3 4 4 5
PDE6A WILD-TYPE 62 206 68 126
'PDE6A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 0.92

Table S595.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
PDE6A MUTATED 2 6 4
PDE6A WILD-TYPE 129 132 157
'PDE6A MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S596.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
PDE6A MUTATED 2 0 2 2 3
PDE6A WILD-TYPE 87 22 57 63 98
'PDE6A MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.119 (Fisher's exact test), Q value = 0.55

Table S597.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
PDE6A MUTATED 3 6 0
PDE6A WILD-TYPE 153 115 59
'PDE6A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0246 (Fisher's exact test), Q value = 0.3

Table S598.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
PDE6A MUTATED 1 6 9
PDE6A WILD-TYPE 149 179 134

Figure S95.  Get High-res Image Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'PDE6A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.3

Table S599.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
PDE6A MUTATED 2 1 4 1 5 3 0
PDE6A WILD-TYPE 70 108 86 43 44 43 68

Figure S96.  Get High-res Image Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'PDE6A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0185 (Fisher's exact test), Q value = 0.25

Table S600.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
PDE6A MUTATED 1 11 3
PDE6A WILD-TYPE 174 200 87

Figure S97.  Get High-res Image Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'PDE6A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0297 (Fisher's exact test), Q value = 0.32

Table S601.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
PDE6A MUTATED 1 6 1 7
PDE6A WILD-TYPE 69 180 130 82

Figure S98.  Get High-res Image Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'PDE6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S602.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
PDE6A MUTATED 3 7 2
PDE6A WILD-TYPE 138 175 87
'PDE6A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.574 (Fisher's exact test), Q value = 1

Table S603.  Gene #60: 'PDE6A MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
PDE6A MUTATED 2 9 1
PDE6A WILD-TYPE 92 224 84
'CHRND MUTATION STATUS' versus 'CN_CNMF'

P value = 0.159 (Fisher's exact test), Q value = 0.62

Table S604.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
CHRND MUTATED 1 4 3 8
CHRND WILD-TYPE 64 206 69 123
'CHRND MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S605.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
CHRND MUTATED 2 5 6
CHRND WILD-TYPE 129 133 155
'CHRND MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.58

Table S606.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
CHRND MUTATED 3 1 0 5 2
CHRND WILD-TYPE 86 21 59 60 99
'CHRND MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.093 (Fisher's exact test), Q value = 0.5

Table S607.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
CHRND MUTATED 2 7 2
CHRND WILD-TYPE 154 114 57
'CHRND MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.405 (Fisher's exact test), Q value = 0.92

Table S608.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
CHRND MUTATED 3 6 7
CHRND WILD-TYPE 147 179 136
'CHRND MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.204 (Fisher's exact test), Q value = 0.7

Table S609.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
CHRND MUTATED 0 4 2 1 4 1 4
CHRND WILD-TYPE 72 105 88 43 45 45 64
'CHRND MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.398 (Fisher's exact test), Q value = 0.92

Table S610.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
CHRND MUTATED 4 10 2
CHRND WILD-TYPE 171 201 88
'CHRND MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 0.55

Table S611.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
CHRND MUTATED 1 5 3 7
CHRND WILD-TYPE 69 181 128 82
'CHRND MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S612.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
CHRND MUTATED 3 5 4
CHRND WILD-TYPE 138 177 85
'CHRND MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.572 (Fisher's exact test), Q value = 1

Table S613.  Gene #61: 'CHRND MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
CHRND MUTATED 2 9 1
CHRND WILD-TYPE 92 224 84
'KLK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0375 (Fisher's exact test), Q value = 0.37

Table S614.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
KLK1 MUTATED 4 2 0 2
KLK1 WILD-TYPE 61 208 72 129

Figure S99.  Get High-res Image Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'KLK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0794 (Fisher's exact test), Q value = 0.48

Table S615.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
KLK1 MUTATED 0 5 3
KLK1 WILD-TYPE 131 133 158
'KLK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.568 (Fisher's exact test), Q value = 1

Table S616.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
KLK1 MUTATED 0 0 0 1 2
KLK1 WILD-TYPE 89 22 59 64 99
'KLK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0385 (Fisher's exact test), Q value = 0.37

Table S617.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
KLK1 MUTATED 0 1 2
KLK1 WILD-TYPE 156 120 57

Figure S100.  Get High-res Image Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'KLK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S618.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
KLK1 MUTATED 1 4 3
KLK1 WILD-TYPE 149 181 140
'KLK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.648 (Fisher's exact test), Q value = 1

Table S619.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
KLK1 MUTATED 1 4 2 0 1 0 0
KLK1 WILD-TYPE 71 105 88 44 48 46 68
'KLK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.196 (Fisher's exact test), Q value = 0.7

Table S620.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
KLK1 MUTATED 2 6 0
KLK1 WILD-TYPE 173 205 90
'KLK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.225 (Fisher's exact test), Q value = 0.73

Table S621.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
KLK1 MUTATED 1 5 0 2
KLK1 WILD-TYPE 69 181 131 87
'KLK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.206 (Fisher's exact test), Q value = 0.7

Table S622.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
KLK1 MUTATED 2 6 0
KLK1 WILD-TYPE 139 176 89
'KLK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.23 (Fisher's exact test), Q value = 0.73

Table S623.  Gene #62: 'KLK1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
KLK1 MUTATED 0 7 1
KLK1 WILD-TYPE 94 226 84
'KLHL5 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.418 (Fisher's exact test), Q value = 0.93

Table S624.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
KLHL5 MUTATED 0 6 3 5
KLHL5 WILD-TYPE 65 204 69 126
'KLHL5 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.937 (Fisher's exact test), Q value = 1

Table S625.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
KLHL5 MUTATED 3 4 5
KLHL5 WILD-TYPE 128 134 156
'KLHL5 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S626.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
KLHL5 MUTATED 2 1 1 3 3
KLHL5 WILD-TYPE 87 21 58 62 98
'KLHL5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0862 (Fisher's exact test), Q value = 0.49

Table S627.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
KLHL5 MUTATED 2 4 4
KLHL5 WILD-TYPE 154 117 55
'KLHL5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.433 (Fisher's exact test), Q value = 0.95

Table S628.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
KLHL5 MUTATED 6 6 2
KLHL5 WILD-TYPE 144 179 141
'KLHL5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S629.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
KLHL5 MUTATED 1 4 3 1 0 2 3
KLHL5 WILD-TYPE 71 105 87 43 49 44 65
'KLHL5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S630.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
KLHL5 MUTATED 5 7 2
KLHL5 WILD-TYPE 170 204 88
'KLHL5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S631.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
KLHL5 MUTATED 1 5 6 2
KLHL5 WILD-TYPE 69 181 125 87
'KLHL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.674 (Fisher's exact test), Q value = 1

Table S632.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
KLHL5 MUTATED 4 6 1
KLHL5 WILD-TYPE 137 176 88
'KLHL5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S633.  Gene #63: 'KLHL5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
KLHL5 MUTATED 3 7 1
KLHL5 WILD-TYPE 91 226 84
'DSC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S634.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
DSC2 MUTATED 1 8 4 7
DSC2 WILD-TYPE 64 202 68 124
'DSC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0755 (Fisher's exact test), Q value = 0.47

Table S635.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
DSC2 MUTATED 2 5 11
DSC2 WILD-TYPE 129 133 150
'DSC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00317 (Fisher's exact test), Q value = 0.076

Table S636.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
DSC2 MUTATED 0 3 1 2 9
DSC2 WILD-TYPE 89 19 58 63 92

Figure S101.  Get High-res Image Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'DSC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00444 (Fisher's exact test), Q value = 0.096

Table S637.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
DSC2 MUTATED 7 1 7
DSC2 WILD-TYPE 149 120 52

Figure S102.  Get High-res Image Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'DSC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S638.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
DSC2 MUTATED 5 10 5
DSC2 WILD-TYPE 145 175 138
'DSC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S639.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
DSC2 MUTATED 4 6 4 2 2 1 1
DSC2 WILD-TYPE 68 103 86 42 47 45 67
'DSC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.191 (Fisher's exact test), Q value = 0.69

Table S640.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
DSC2 MUTATED 6 7 7
DSC2 WILD-TYPE 169 204 83
'DSC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.87

Table S641.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
DSC2 MUTATED 2 7 4 7
DSC2 WILD-TYPE 68 179 127 82
'DSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0624 (Fisher's exact test), Q value = 0.43

Table S642.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
DSC2 MUTATED 8 3 6
DSC2 WILD-TYPE 133 179 83
'DSC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.66

Table S643.  Gene #64: 'DSC2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
DSC2 MUTATED 1 11 5
DSC2 WILD-TYPE 93 222 80
'RNF160 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.62

Table S644.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
RNF160 MUTATED 4 4 4 3
RNF160 WILD-TYPE 61 206 68 128
'RNF160 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.102 (Fisher's exact test), Q value = 0.53

Table S645.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
RNF160 MUTATED 1 4 8
RNF160 WILD-TYPE 130 134 153
'RNF160 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0217 (Fisher's exact test), Q value = 0.28

Table S646.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
RNF160 MUTATED 0 1 0 4 6
RNF160 WILD-TYPE 89 21 59 61 95

Figure S103.  Get High-res Image Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

'RNF160 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.128 (Fisher's exact test), Q value = 0.57

Table S647.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
RNF160 MUTATED 2 6 3
RNF160 WILD-TYPE 154 115 56
'RNF160 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.021 (Fisher's exact test), Q value = 0.28

Table S648.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
RNF160 MUTATED 1 11 3
RNF160 WILD-TYPE 149 174 140

Figure S104.  Get High-res Image Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'RNF160 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 0.92

Table S649.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
RNF160 MUTATED 1 6 4 1 1 2 0
RNF160 WILD-TYPE 71 103 86 43 48 44 68
'RNF160 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.9

Table S650.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
RNF160 MUTATED 3 8 4
RNF160 WILD-TYPE 172 203 86
'RNF160 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.209 (Fisher's exact test), Q value = 0.7

Table S651.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
RNF160 MUTATED 2 9 1 3
RNF160 WILD-TYPE 68 177 130 86
'RNF160 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S652.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
RNF160 MUTATED 4 6 3
RNF160 WILD-TYPE 137 176 86
'RNF160 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.92

Table S653.  Gene #65: 'RNF160 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
RNF160 MUTATED 2 10 1
RNF160 WILD-TYPE 92 223 84
'AIFM1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S654.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
AIFM1 MUTATED 2 4 1 5
AIFM1 WILD-TYPE 63 206 71 126
'AIFM1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.86

Table S655.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
AIFM1 MUTATED 3 2 7
AIFM1 WILD-TYPE 128 136 154
'AIFM1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.119 (Fisher's exact test), Q value = 0.55

Table S656.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
AIFM1 MUTATED 0 0 1 2 6
AIFM1 WILD-TYPE 89 22 58 63 95
'AIFM1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0653 (Fisher's exact test), Q value = 0.45

Table S657.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
AIFM1 MUTATED 1 6 2
AIFM1 WILD-TYPE 155 115 57
'AIFM1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S658.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
AIFM1 MUTATED 5 4 3
AIFM1 WILD-TYPE 145 181 140
'AIFM1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.493 (Fisher's exact test), Q value = 0.99

Table S659.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
AIFM1 MUTATED 3 2 1 0 3 1 2
AIFM1 WILD-TYPE 69 107 89 44 46 45 66
'AIFM1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.317 (Fisher's exact test), Q value = 0.84

Table S660.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
AIFM1 MUTATED 2 7 3
AIFM1 WILD-TYPE 173 204 87
'AIFM1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.085 (Fisher's exact test), Q value = 0.48

Table S661.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
AIFM1 MUTATED 0 8 4 0
AIFM1 WILD-TYPE 70 178 127 89
'AIFM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0667 (Fisher's exact test), Q value = 0.45

Table S662.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
AIFM1 MUTATED 1 6 5
AIFM1 WILD-TYPE 140 176 84
'AIFM1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S663.  Gene #66: 'AIFM1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
AIFM1 MUTATED 2 7 3
AIFM1 WILD-TYPE 92 226 82
'DOT1L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.655 (Fisher's exact test), Q value = 1

Table S664.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
DOT1L MUTATED 1 5 2 6
DOT1L WILD-TYPE 64 205 70 125
'DOT1L MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S665.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
DOT1L MUTATED 3 3 7
DOT1L WILD-TYPE 128 135 154
'DOT1L MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0622 (Fisher's exact test), Q value = 0.43

Table S666.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
DOT1L MUTATED 1 2 3 4 1
DOT1L WILD-TYPE 88 20 56 61 100
'DOT1L MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.228 (Fisher's exact test), Q value = 0.73

Table S667.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
DOT1L MUTATED 5 6 0
DOT1L WILD-TYPE 151 115 59
'DOT1L MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S668.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
DOT1L MUTATED 3 6 5
DOT1L WILD-TYPE 147 179 138
'DOT1L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00706 (Fisher's exact test), Q value = 0.14

Table S669.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
DOT1L MUTATED 0 4 0 4 0 3 3
DOT1L WILD-TYPE 72 105 90 40 49 43 65

Figure S105.  Get High-res Image Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'DOT1L MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.774 (Fisher's exact test), Q value = 1

Table S670.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
DOT1L MUTATED 6 5 3
DOT1L WILD-TYPE 169 206 87
'DOT1L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0825 (Fisher's exact test), Q value = 0.48

Table S671.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
DOT1L MUTATED 4 8 1 1
DOT1L WILD-TYPE 66 178 130 88
'DOT1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S672.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
DOT1L MUTATED 6 4 3
DOT1L WILD-TYPE 135 178 86
'DOT1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 0.81

Table S673.  Gene #67: 'DOT1L MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
DOT1L MUTATED 5 7 1
DOT1L WILD-TYPE 89 226 84
'MCM9 MUTATION STATUS' versus 'CN_CNMF'

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

Table S674.  Gene #68: 'MCM9 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
MCM9 MUTATED 0 2 0 1
MCM9 WILD-TYPE 65 208 72 130
'MCM9 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.639 (Fisher's exact test), Q value = 1

Table S675.  Gene #68: 'MCM9 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
MCM9 MUTATED 0 2 1
MCM9 WILD-TYPE 150 183 142
'MCM9 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S676.  Gene #68: 'MCM9 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
MCM9 MUTATED 0 1 1 1 0 0 0
MCM9 WILD-TYPE 72 108 89 43 49 46 68
'MCM9 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S677.  Gene #68: 'MCM9 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
MCM9 MUTATED 1 2 0
MCM9 WILD-TYPE 174 209 90
'MCM9 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.484 (Fisher's exact test), Q value = 0.98

Table S678.  Gene #68: 'MCM9 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
MCM9 MUTATED 1 2 0 0
MCM9 WILD-TYPE 69 184 131 89
'NCKAP1L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.303 (Fisher's exact test), Q value = 0.82

Table S679.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
NCKAP1L MUTATED 4 6 5 4
NCKAP1L WILD-TYPE 61 204 67 127
'NCKAP1L MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.77

Table S680.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
NCKAP1L MUTATED 2 7 7
NCKAP1L WILD-TYPE 129 131 154
'NCKAP1L MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.77 (Fisher's exact test), Q value = 1

Table S681.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
NCKAP1L MUTATED 3 0 4 3 6
NCKAP1L WILD-TYPE 86 22 55 62 95
'NCKAP1L MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S682.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
NCKAP1L MUTATED 6 6 4
NCKAP1L WILD-TYPE 150 115 55
'NCKAP1L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0441 (Fisher's exact test), Q value = 0.41

Table S683.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
NCKAP1L MUTATED 2 7 10
NCKAP1L WILD-TYPE 148 178 133

Figure S106.  Get High-res Image Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'NCKAP1L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.212 (Fisher's exact test), Q value = 0.71

Table S684.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
NCKAP1L MUTATED 0 3 6 3 3 2 2
NCKAP1L WILD-TYPE 72 106 84 41 46 44 66
'NCKAP1L MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.36

Table S685.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
NCKAP1L MUTATED 4 14 1
NCKAP1L WILD-TYPE 171 197 89

Figure S107.  Get High-res Image Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'NCKAP1L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0592 (Fisher's exact test), Q value = 0.43

Table S686.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
NCKAP1L MUTATED 2 7 2 8
NCKAP1L WILD-TYPE 68 179 129 81
'NCKAP1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.463 (Fisher's exact test), Q value = 0.97

Table S687.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
NCKAP1L MUTATED 5 5 5
NCKAP1L WILD-TYPE 136 177 84
'NCKAP1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S688.  Gene #69: 'NCKAP1L MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
NCKAP1L MUTATED 3 10 2
NCKAP1L WILD-TYPE 91 223 83
'ESYT3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S689.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ESYT3 MUTATED 0 5 1 2
ESYT3 WILD-TYPE 65 205 71 129
'ESYT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.352 (Fisher's exact test), Q value = 0.88

Table S690.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ESYT3 MUTATED 4 1 2
ESYT3 WILD-TYPE 127 137 159
'ESYT3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.73

Table S691.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ESYT3 MUTATED 0 0 0 1 4
ESYT3 WILD-TYPE 89 22 59 64 97
'ESYT3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.261 (Fisher's exact test), Q value = 0.78

Table S692.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ESYT3 MUTATED 1 2 2
ESYT3 WILD-TYPE 155 119 57
'ESYT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.403 (Fisher's exact test), Q value = 0.92

Table S693.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ESYT3 MUTATED 2 5 1
ESYT3 WILD-TYPE 148 180 142
'ESYT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S694.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ESYT3 MUTATED 1 3 1 1 0 2 0
ESYT3 WILD-TYPE 71 106 89 43 49 44 68
'ESYT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.466 (Fisher's exact test), Q value = 0.97

Table S695.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ESYT3 MUTATED 3 5 0
ESYT3 WILD-TYPE 172 206 90
'ESYT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.325 (Fisher's exact test), Q value = 0.85

Table S696.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ESYT3 MUTATED 0 5 3 0
ESYT3 WILD-TYPE 70 181 128 89
'ESYT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.251 (Fisher's exact test), Q value = 0.77

Table S697.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ESYT3 MUTATED 2 5 0
ESYT3 WILD-TYPE 139 177 89
'ESYT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 0.92

Table S698.  Gene #70: 'ESYT3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ESYT3 MUTATED 0 5 2
ESYT3 WILD-TYPE 94 228 83
'MIA2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0119 (Fisher's exact test), Q value = 0.19

Table S699.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
MIA2 MUTATED 4 1 2 6
MIA2 WILD-TYPE 61 209 70 125

Figure S108.  Get High-res Image Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'MIA2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.315 (Fisher's exact test), Q value = 0.83

Table S700.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
MIA2 MUTATED 1 5 5
MIA2 WILD-TYPE 130 133 156
'MIA2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S701.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
MIA2 MUTATED 3 0 2 2 2
MIA2 WILD-TYPE 86 22 57 63 99
'MIA2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.6

Table S702.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
MIA2 MUTATED 2 6 1
MIA2 WILD-TYPE 154 115 58
'MIA2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.82

Table S703.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
MIA2 MUTATED 2 5 6
MIA2 WILD-TYPE 148 180 137
'MIA2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.266 (Fisher's exact test), Q value = 0.78

Table S704.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
MIA2 MUTATED 2 2 5 2 2 0 0
MIA2 WILD-TYPE 70 107 85 42 47 46 68
'MIA2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.875 (Fisher's exact test), Q value = 1

Table S705.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
MIA2 MUTATED 4 7 2
MIA2 WILD-TYPE 171 204 88
'MIA2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S706.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
MIA2 MUTATED 2 4 3 4
MIA2 WILD-TYPE 68 182 128 85
'MIA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S707.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
MIA2 MUTATED 4 5 2
MIA2 WILD-TYPE 137 177 87
'MIA2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S708.  Gene #71: 'MIA2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
MIA2 MUTATED 3 7 1
MIA2 WILD-TYPE 91 226 84
'TUBB4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S709.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
TUBB4 MUTATED 3 5 3 6
TUBB4 WILD-TYPE 62 205 69 125
'TUBB4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S710.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
TUBB4 MUTATED 3 6 6
TUBB4 WILD-TYPE 128 132 155
'TUBB4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S711.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
TUBB4 MUTATED 2 0 0 2 4
TUBB4 WILD-TYPE 87 22 59 63 97
'TUBB4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 0.96

Table S712.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
TUBB4 MUTATED 2 4 2
TUBB4 WILD-TYPE 154 117 57
'TUBB4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.747 (Fisher's exact test), Q value = 1

Table S713.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
TUBB4 MUTATED 4 8 5
TUBB4 WILD-TYPE 146 177 138
'TUBB4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.807 (Fisher's exact test), Q value = 1

Table S714.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
TUBB4 MUTATED 1 3 4 2 3 1 3
TUBB4 WILD-TYPE 71 106 86 42 46 45 65
'TUBB4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S715.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
TUBB4 MUTATED 5 9 3
TUBB4 WILD-TYPE 170 202 87
'TUBB4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.451 (Fisher's exact test), Q value = 0.96

Table S716.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
TUBB4 MUTATED 1 8 3 5
TUBB4 WILD-TYPE 69 178 128 84
'TUBB4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S717.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
TUBB4 MUTATED 3 8 3
TUBB4 WILD-TYPE 138 174 86
'TUBB4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.117 (Fisher's exact test), Q value = 0.55

Table S718.  Gene #72: 'TUBB4 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
TUBB4 MUTATED 1 12 1
TUBB4 WILD-TYPE 93 221 84
'ABHD12B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.222 (Fisher's exact test), Q value = 0.73

Table S719.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ABHD12B MUTATED 2 1 1 3
ABHD12B WILD-TYPE 63 209 71 128
'ABHD12B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.73

Table S720.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ABHD12B MUTATED 0 2 4
ABHD12B WILD-TYPE 131 136 157
'ABHD12B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.625 (Fisher's exact test), Q value = 1

Table S721.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ABHD12B MUTATED 1 0 1 1 0
ABHD12B WILD-TYPE 88 22 58 64 101
'ABHD12B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S722.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ABHD12B MUTATED 2 1 0
ABHD12B WILD-TYPE 154 120 59
'ABHD12B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S723.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ABHD12B MUTATED 2 3 2
ABHD12B WILD-TYPE 148 182 141
'ABHD12B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S724.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ABHD12B MUTATED 1 1 2 1 1 1 0
ABHD12B WILD-TYPE 71 108 88 43 48 45 68
'ABHD12B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0821 (Fisher's exact test), Q value = 0.48

Table S725.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ABHD12B MUTATED 0 5 2
ABHD12B WILD-TYPE 175 206 88
'ABHD12B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S726.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ABHD12B MUTATED 0 3 2 2
ABHD12B WILD-TYPE 70 183 129 87
'ABHD12B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S727.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ABHD12B MUTATED 2 2 2
ABHD12B WILD-TYPE 139 180 87
'ABHD12B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.92

Table S728.  Gene #73: 'ABHD12B MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ABHD12B MUTATED 0 4 2
ABHD12B WILD-TYPE 94 229 83
'ANTXR1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S729.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ANTXR1 MUTATED 4 8 2 5
ANTXR1 WILD-TYPE 61 202 70 126
'ANTXR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S730.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ANTXR1 MUTATED 5 4 8
ANTXR1 WILD-TYPE 126 134 153
'ANTXR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.943 (Fisher's exact test), Q value = 1

Table S731.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ANTXR1 MUTATED 3 1 1 2 4
ANTXR1 WILD-TYPE 86 21 58 63 97
'ANTXR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S732.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ANTXR1 MUTATED 6 4 1
ANTXR1 WILD-TYPE 150 117 58
'ANTXR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S733.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ANTXR1 MUTATED 7 8 4
ANTXR1 WILD-TYPE 143 177 139
'ANTXR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S734.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ANTXR1 MUTATED 5 5 2 1 1 1 4
ANTXR1 WILD-TYPE 67 104 88 43 48 45 64
'ANTXR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.485 (Fisher's exact test), Q value = 0.98

Table S735.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ANTXR1 MUTATED 9 7 2
ANTXR1 WILD-TYPE 166 204 88
'ANTXR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S736.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ANTXR1 MUTATED 4 7 5 2
ANTXR1 WILD-TYPE 66 179 126 87
'ANTXR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.721 (Fisher's exact test), Q value = 1

Table S737.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ANTXR1 MUTATED 6 8 2
ANTXR1 WILD-TYPE 135 174 87
'ANTXR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S738.  Gene #74: 'ANTXR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ANTXR1 MUTATED 4 7 5
ANTXR1 WILD-TYPE 90 226 80
'FLCN MUTATION STATUS' versus 'CN_CNMF'

P value = 0.362 (Fisher's exact test), Q value = 0.89

Table S739.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
FLCN MUTATED 0 5 0 4
FLCN WILD-TYPE 65 205 72 127
'FLCN MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.361 (Fisher's exact test), Q value = 0.89

Table S740.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
FLCN MUTATED 1 2 5
FLCN WILD-TYPE 130 136 156
'FLCN MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.73

Table S741.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
FLCN MUTATED 0 0 3 1 2
FLCN WILD-TYPE 89 22 56 64 99
'FLCN MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.861 (Fisher's exact test), Q value = 1

Table S742.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
FLCN MUTATED 2 3 1
FLCN WILD-TYPE 154 118 58
'FLCN MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.838 (Fisher's exact test), Q value = 1

Table S743.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
FLCN MUTATED 2 4 3
FLCN WILD-TYPE 148 181 140
'FLCN MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.802 (Fisher's exact test), Q value = 1

Table S744.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
FLCN MUTATED 1 3 1 1 0 2 1
FLCN WILD-TYPE 71 106 89 43 49 44 67
'FLCN MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S745.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
FLCN MUTATED 5 3 1
FLCN WILD-TYPE 170 208 89
'FLCN MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.476 (Fisher's exact test), Q value = 0.98

Table S746.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
FLCN MUTATED 2 2 4 1
FLCN WILD-TYPE 68 184 127 88
'FLCN MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.307 (Fisher's exact test), Q value = 0.82

Table S747.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
FLCN MUTATED 4 4 0
FLCN WILD-TYPE 137 178 89
'FLCN MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S748.  Gene #75: 'FLCN MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
FLCN MUTATED 2 4 2
FLCN WILD-TYPE 92 229 83
'ZNF556 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.79

Table S749.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ZNF556 MUTATED 3 3 1 5
ZNF556 WILD-TYPE 62 207 71 126
'ZNF556 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.598 (Fisher's exact test), Q value = 1

Table S750.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ZNF556 MUTATED 2 5 4
ZNF556 WILD-TYPE 129 133 157
'ZNF556 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S751.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ZNF556 MUTATED 3 0 0 1 3
ZNF556 WILD-TYPE 86 22 59 64 98
'ZNF556 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S752.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ZNF556 MUTATED 4 2 1
ZNF556 WILD-TYPE 152 119 58
'ZNF556 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.17 (Fisher's exact test), Q value = 0.65

Table S753.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ZNF556 MUTATED 2 8 2
ZNF556 WILD-TYPE 148 177 141
'ZNF556 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.184 (Fisher's exact test), Q value = 0.68

Table S754.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ZNF556 MUTATED 0 3 6 1 0 1 1
ZNF556 WILD-TYPE 72 106 84 43 49 45 67
'ZNF556 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.73

Table S755.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ZNF556 MUTATED 2 6 4
ZNF556 WILD-TYPE 173 205 86
'ZNF556 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S756.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ZNF556 MUTATED 1 5 2 4
ZNF556 WILD-TYPE 69 181 129 85
'ZNF556 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S757.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ZNF556 MUTATED 3 6 2
ZNF556 WILD-TYPE 138 176 87
'ZNF556 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0519 (Fisher's exact test), Q value = 0.43

Table S758.  Gene #76: 'ZNF556 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ZNF556 MUTATED 0 10 1
ZNF556 WILD-TYPE 94 223 84
'ASCL3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.392 (Fisher's exact test), Q value = 0.91

Table S759.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ASCL3 MUTATED 0 2 2 3
ASCL3 WILD-TYPE 65 208 70 128
'ASCL3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.91

Table S760.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ASCL3 MUTATED 0 2 3
ASCL3 WILD-TYPE 131 136 158
'ASCL3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.87

Table S761.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ASCL3 MUTATED 1 1 0 0 2
ASCL3 WILD-TYPE 88 21 59 65 99
'ASCL3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.392 (Fisher's exact test), Q value = 0.91

Table S762.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ASCL3 MUTATED 1 3 0
ASCL3 WILD-TYPE 155 118 59
'ASCL3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.79

Table S763.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ASCL3 MUTATED 1 5 1
ASCL3 WILD-TYPE 149 180 142
'ASCL3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S764.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ASCL3 MUTATED 1 2 2 0 1 1 0
ASCL3 WILD-TYPE 71 107 88 44 48 45 68
'ASCL3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0496 (Fisher's exact test), Q value = 0.43

Table S765.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ASCL3 MUTATED 0 4 3
ASCL3 WILD-TYPE 175 207 87

Figure S109.  Get High-res Image Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'ASCL3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.124 (Fisher's exact test), Q value = 0.57

Table S766.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ASCL3 MUTATED 0 2 1 4
ASCL3 WILD-TYPE 70 184 130 85
'ASCL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S767.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ASCL3 MUTATED 1 3 1
ASCL3 WILD-TYPE 140 179 88
'ASCL3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.502 (Fisher's exact test), Q value = 1

Table S768.  Gene #77: 'ASCL3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ASCL3 MUTATED 2 3 0
ASCL3 WILD-TYPE 92 230 85
'DSG3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0845 (Fisher's exact test), Q value = 0.48

Table S769.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
DSG3 MUTATED 5 8 7 13
DSG3 WILD-TYPE 60 202 65 118
'DSG3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 0.91

Table S770.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
DSG3 MUTATED 6 9 14
DSG3 WILD-TYPE 125 129 147
'DSG3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.7

Table S771.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
DSG3 MUTATED 10 1 2 2 10
DSG3 WILD-TYPE 79 21 57 63 91
'DSG3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S772.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
DSG3 MUTATED 12 8 5
DSG3 WILD-TYPE 144 113 54
'DSG3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.173 (Fisher's exact test), Q value = 0.66

Table S773.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
DSG3 MUTATED 6 17 10
DSG3 WILD-TYPE 144 168 133
'DSG3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S774.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
DSG3 MUTATED 3 12 5 2 3 3 5
DSG3 WILD-TYPE 69 97 85 42 46 43 63
'DSG3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.42 (Fisher's exact test), Q value = 0.93

Table S775.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
DSG3 MUTATED 9 18 5
DSG3 WILD-TYPE 166 193 85
'DSG3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.401 (Fisher's exact test), Q value = 0.92

Table S776.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
DSG3 MUTATED 5 14 5 8
DSG3 WILD-TYPE 65 172 126 81
'DSG3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.765 (Fisher's exact test), Q value = 1

Table S777.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
DSG3 MUTATED 8 14 6
DSG3 WILD-TYPE 133 168 83
'DSG3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.414 (Fisher's exact test), Q value = 0.92

Table S778.  Gene #78: 'DSG3 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
DSG3 MUTATED 7 18 3
DSG3 WILD-TYPE 87 215 82
'C5AR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S779.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
C5AR1 MUTATED 0 2 1 3
C5AR1 WILD-TYPE 65 208 71 128
'C5AR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.292 (Fisher's exact test), Q value = 0.81

Table S780.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
C5AR1 MUTATED 0 3 3
C5AR1 WILD-TYPE 131 135 158
'C5AR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.304 (Fisher's exact test), Q value = 0.82

Table S781.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
C5AR1 MUTATED 0 0 0 2 3
C5AR1 WILD-TYPE 89 22 59 63 98
'C5AR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S782.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
C5AR1 MUTATED 3 2 0
C5AR1 WILD-TYPE 153 119 59
'C5AR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.73

Table S783.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
C5AR1 MUTATED 0 3 3
C5AR1 WILD-TYPE 150 182 140
'C5AR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S784.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
C5AR1 MUTATED 0 3 1 0 1 1 0
C5AR1 WILD-TYPE 72 106 89 44 48 45 68
'C5AR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S785.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
C5AR1 MUTATED 0 4 2
C5AR1 WILD-TYPE 175 207 88
'C5AR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.201 (Fisher's exact test), Q value = 0.7

Table S786.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
C5AR1 MUTATED 0 4 0 2
C5AR1 WILD-TYPE 70 182 131 87
'C5AR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S787.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
C5AR1 MUTATED 2 3 1
C5AR1 WILD-TYPE 139 179 88
'C5AR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.55

Table S788.  Gene #79: 'C5AR1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
C5AR1 MUTATED 0 3 3
C5AR1 WILD-TYPE 94 230 82
'ASXL2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S789.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ASXL2 MUTATED 4 8 2 3
ASXL2 WILD-TYPE 61 202 70 128
'ASXL2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S790.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ASXL2 MUTATED 3 7 6
ASXL2 WILD-TYPE 128 131 155
'ASXL2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S791.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ASXL2 MUTATED 1 1 2 3 5
ASXL2 WILD-TYPE 88 21 57 62 96
'ASXL2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.074 (Fisher's exact test), Q value = 0.47

Table S792.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ASXL2 MUTATED 2 7 3
ASXL2 WILD-TYPE 154 114 56
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.41 (Fisher's exact test), Q value = 0.92

Table S793.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ASXL2 MUTATED 5 5 8
ASXL2 WILD-TYPE 145 180 135
'ASXL2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S794.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ASXL2 MUTATED 1 5 3 3 3 1 2
ASXL2 WILD-TYPE 71 104 87 41 46 45 66
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.9

Table S795.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ASXL2 MUTATED 4 9 5
ASXL2 WILD-TYPE 171 202 85
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.42 (Fisher's exact test), Q value = 0.93

Table S796.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ASXL2 MUTATED 2 7 3 6
ASXL2 WILD-TYPE 68 179 128 83
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.145 (Fisher's exact test), Q value = 0.6

Table S797.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ASXL2 MUTATED 2 10 4
ASXL2 WILD-TYPE 139 172 85
'ASXL2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S798.  Gene #80: 'ASXL2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ASXL2 MUTATED 4 10 2
ASXL2 WILD-TYPE 90 223 83
'DLX5 MUTATION STATUS' versus 'CN_CNMF'

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

Table S799.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
DLX5 MUTATED 2 5 1 5
DLX5 WILD-TYPE 63 205 71 126
'DLX5 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S800.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
DLX5 MUTATED 4 4 4
DLX5 WILD-TYPE 127 134 157
'DLX5 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0901 (Fisher's exact test), Q value = 0.49

Table S801.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
DLX5 MUTATED 3 2 0 3 1
DLX5 WILD-TYPE 86 20 59 62 100
'DLX5 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 0.85

Table S802.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
DLX5 MUTATED 4 5 0
DLX5 WILD-TYPE 152 116 59
'DLX5 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.359 (Fisher's exact test), Q value = 0.89

Table S803.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
DLX5 MUTATED 2 7 4
DLX5 WILD-TYPE 148 178 139
'DLX5 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S804.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
DLX5 MUTATED 1 3 4 0 2 2 1
DLX5 WILD-TYPE 71 106 86 44 47 44 67
'DLX5 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00412 (Fisher's exact test), Q value = 0.091

Table S805.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
DLX5 MUTATED 0 10 3
DLX5 WILD-TYPE 175 201 87

Figure S110.  Get High-res Image Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'DLX5 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.58

Table S806.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
DLX5 MUTATED 0 6 2 5
DLX5 WILD-TYPE 70 180 129 84
'DLX5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.151 (Fisher's exact test), Q value = 0.61

Table S807.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
DLX5 MUTATED 2 9 1
DLX5 WILD-TYPE 139 173 88
'DLX5 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.26 (Fisher's exact test), Q value = 0.78

Table S808.  Gene #81: 'DLX5 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
DLX5 MUTATED 1 10 1
DLX5 WILD-TYPE 93 223 84
'ATAD2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0247 (Fisher's exact test), Q value = 0.3

Table S809.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ATAD2 MUTATED 1 2 5 6
ATAD2 WILD-TYPE 64 208 67 125

Figure S111.  Get High-res Image Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

'ATAD2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0271 (Fisher's exact test), Q value = 0.3

Table S810.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ATAD2 MUTATED 0 6 7
ATAD2 WILD-TYPE 131 132 154

Figure S112.  Get High-res Image Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ATAD2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0969 (Fisher's exact test), Q value = 0.52

Table S811.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ATAD2 MUTATED 1 0 2 5 1
ATAD2 WILD-TYPE 88 22 57 60 100
'ATAD2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.49 (Fisher's exact test), Q value = 0.99

Table S812.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ATAD2 MUTATED 5 4 0
ATAD2 WILD-TYPE 151 117 59
'ATAD2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0552 (Fisher's exact test), Q value = 0.43

Table S813.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ATAD2 MUTATED 1 9 3
ATAD2 WILD-TYPE 149 176 140
'ATAD2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.79

Table S814.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ATAD2 MUTATED 0 4 5 2 1 0 1
ATAD2 WILD-TYPE 72 105 85 42 48 46 67
'ATAD2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 0.9

Table S815.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ATAD2 MUTATED 3 7 4
ATAD2 WILD-TYPE 172 204 86
'ATAD2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0162 (Fisher's exact test), Q value = 0.22

Table S816.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ATAD2 MUTATED 2 6 0 6
ATAD2 WILD-TYPE 68 180 131 83

Figure S113.  Get High-res Image Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

'ATAD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S817.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ATAD2 MUTATED 4 5 4
ATAD2 WILD-TYPE 137 177 85
'ATAD2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.404 (Fisher's exact test), Q value = 0.92

Table S818.  Gene #82: 'ATAD2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ATAD2 MUTATED 2 10 1
ATAD2 WILD-TYPE 92 223 84
'RAF1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S819.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
RAF1 MUTATED 0 3 1 2
RAF1 WILD-TYPE 65 207 71 129
'RAF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S820.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
RAF1 MUTATED 2 2 2
RAF1 WILD-TYPE 129 136 159
'RAF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.67

Table S821.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
RAF1 MUTATED 0 1 0 1 3
RAF1 WILD-TYPE 89 21 59 64 98
'RAF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.075 (Fisher's exact test), Q value = 0.47

Table S822.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
RAF1 MUTATED 1 1 3
RAF1 WILD-TYPE 155 120 56
'RAF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S823.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
RAF1 MUTATED 1 3 2
RAF1 WILD-TYPE 149 182 141
'RAF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.552 (Fisher's exact test), Q value = 1

Table S824.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
RAF1 MUTATED 1 2 1 0 0 2 0
RAF1 WILD-TYPE 71 107 89 44 49 44 68
'RAF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S825.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
RAF1 MUTATED 2 3 1
RAF1 WILD-TYPE 173 208 89
'RAF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.211 (Fisher's exact test), Q value = 0.71

Table S826.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
RAF1 MUTATED 1 1 1 3
RAF1 WILD-TYPE 69 185 130 86
'RAF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0444 (Fisher's exact test), Q value = 0.41

Table S827.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
RAF1 MUTATED 4 0 2
RAF1 WILD-TYPE 137 182 87

Figure S114.  Get High-res Image Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

'RAF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0246 (Fisher's exact test), Q value = 0.3

Table S828.  Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
RAF1 MUTATED 0 2 4
RAF1 WILD-TYPE 94 231 81

Figure S115.  Get High-res Image Gene #83: 'RAF1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'A2M MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0991 (Fisher's exact test), Q value = 0.52

Table S829.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
A2M MUTATED 3 4 5 8
A2M WILD-TYPE 62 206 67 123
'A2M MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.624 (Fisher's exact test), Q value = 1

Table S830.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
A2M MUTATED 3 6 7
A2M WILD-TYPE 128 132 154
'A2M MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.204 (Fisher's exact test), Q value = 0.7

Table S831.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
A2M MUTATED 4 1 0 5 3
A2M WILD-TYPE 85 21 59 60 98
'A2M MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.387 (Fisher's exact test), Q value = 0.91

Table S832.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
A2M MUTATED 4 7 2
A2M WILD-TYPE 152 114 57
'A2M MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0504 (Fisher's exact test), Q value = 0.43

Table S833.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
A2M MUTATED 2 12 6
A2M WILD-TYPE 148 173 137
'A2M MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0511 (Fisher's exact test), Q value = 0.43

Table S834.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
A2M MUTATED 0 6 6 0 4 3 1
A2M WILD-TYPE 72 103 84 44 45 43 67
'A2M MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00525 (Fisher's exact test), Q value = 0.11

Table S835.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
A2M MUTATED 1 12 6
A2M WILD-TYPE 174 199 84

Figure S116.  Get High-res Image Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'A2M MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.135 (Fisher's exact test), Q value = 0.58

Table S836.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
A2M MUTATED 1 11 2 5
A2M WILD-TYPE 69 175 129 84
'A2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.202 (Fisher's exact test), Q value = 0.7

Table S837.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
A2M MUTATED 3 7 6
A2M WILD-TYPE 138 175 83
'A2M MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.132 (Fisher's exact test), Q value = 0.58

Table S838.  Gene #84: 'A2M MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
A2M MUTATED 1 13 2
A2M WILD-TYPE 93 220 83
'SND1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0521 (Fisher's exact test), Q value = 0.43

Table S839.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
SND1 MUTATED 2 3 2 9
SND1 WILD-TYPE 63 207 70 122
'SND1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0594 (Fisher's exact test), Q value = 0.43

Table S840.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
SND1 MUTATED 1 8 6
SND1 WILD-TYPE 130 130 155
'SND1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S841.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
SND1 MUTATED 3 1 1 3 5
SND1 WILD-TYPE 86 21 58 62 96
'SND1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0197 (Fisher's exact test), Q value = 0.26

Table S842.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
SND1 MUTATED 2 6 5
SND1 WILD-TYPE 154 115 54

Figure S117.  Get High-res Image Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

'SND1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0564 (Fisher's exact test), Q value = 0.43

Table S843.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
SND1 MUTATED 1 8 7
SND1 WILD-TYPE 149 177 136
'SND1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0229 (Fisher's exact test), Q value = 0.28

Table S844.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
SND1 MUTATED 0 4 7 0 3 2 0
SND1 WILD-TYPE 72 105 83 44 46 44 68

Figure S118.  Get High-res Image Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

'SND1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0343 (Fisher's exact test), Q value = 0.35

Table S845.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
SND1 MUTATED 2 12 2
SND1 WILD-TYPE 173 199 88

Figure S119.  Get High-res Image Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'SND1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0886 (Fisher's exact test), Q value = 0.49

Table S846.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
SND1 MUTATED 1 10 1 4
SND1 WILD-TYPE 69 176 130 85
'SND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.79

Table S847.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
SND1 MUTATED 4 9 1
SND1 WILD-TYPE 137 173 88
'SND1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0159 (Fisher's exact test), Q value = 0.22

Table S848.  Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
SND1 MUTATED 0 13 1
SND1 WILD-TYPE 94 220 84

Figure S120.  Get High-res Image Gene #85: 'SND1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

'C7ORF36 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 0.96

Table S849.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
C7ORF36 MUTATED 2 2 1 1
C7ORF36 WILD-TYPE 63 208 71 130
'C7ORF36 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S850.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
C7ORF36 MUTATED 0 2 2
C7ORF36 WILD-TYPE 131 136 159
'C7ORF36 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.443 (Fisher's exact test), Q value = 0.95

Table S851.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
C7ORF36 MUTATED 0 0 2 1 2
C7ORF36 WILD-TYPE 89 22 57 64 99
'C7ORF36 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.852 (Fisher's exact test), Q value = 1

Table S852.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
C7ORF36 MUTATED 3 2 0
C7ORF36 WILD-TYPE 153 119 59
'C7ORF36 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.229 (Fisher's exact test), Q value = 0.73

Table S853.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
C7ORF36 MUTATED 0 3 3
C7ORF36 WILD-TYPE 150 182 140
'C7ORF36 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.354 (Fisher's exact test), Q value = 0.88

Table S854.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
C7ORF36 MUTATED 0 2 1 2 1 0 0
C7ORF36 WILD-TYPE 72 107 89 42 48 46 68
'C7ORF36 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S855.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
C7ORF36 MUTATED 2 3 1
C7ORF36 WILD-TYPE 173 208 89
'C7ORF36 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.77

Table S856.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
C7ORF36 MUTATED 2 3 0 1
C7ORF36 WILD-TYPE 68 183 131 88
'C7ORF36 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S857.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
C7ORF36 MUTATED 1 2 1
C7ORF36 WILD-TYPE 140 180 88
'C7ORF36 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S858.  Gene #86: 'C7ORF36 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
C7ORF36 MUTATED 1 2 1
C7ORF36 WILD-TYPE 93 231 84
'HTRA1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.76

Table S859.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
HTRA1 MUTATED 0 3 3 4
HTRA1 WILD-TYPE 65 207 69 127
'HTRA1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.18 (Fisher's exact test), Q value = 0.67

Table S860.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
HTRA1 MUTATED 1 6 3
HTRA1 WILD-TYPE 130 132 158
'HTRA1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.505 (Fisher's exact test), Q value = 1

Table S861.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
HTRA1 MUTATED 2 0 3 1 1
HTRA1 WILD-TYPE 87 22 56 64 100
'HTRA1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.684 (Fisher's exact test), Q value = 1

Table S862.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
HTRA1 MUTATED 4 3 0
HTRA1 WILD-TYPE 152 118 59
'HTRA1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S863.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
HTRA1 MUTATED 3 4 3
HTRA1 WILD-TYPE 147 181 140
'HTRA1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S864.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
HTRA1 MUTATED 1 1 3 2 1 1 1
HTRA1 WILD-TYPE 71 108 87 42 48 45 67
'HTRA1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.841 (Fisher's exact test), Q value = 1

Table S865.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
HTRA1 MUTATED 4 5 1
HTRA1 WILD-TYPE 171 206 89
'HTRA1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0785 (Fisher's exact test), Q value = 0.48

Table S866.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
HTRA1 MUTATED 3 2 1 4
HTRA1 WILD-TYPE 67 184 130 85
'HTRA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S867.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
HTRA1 MUTATED 3 5 2
HTRA1 WILD-TYPE 138 177 87
'HTRA1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.76 (Fisher's exact test), Q value = 1

Table S868.  Gene #87: 'HTRA1 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
HTRA1 MUTATED 3 6 1
HTRA1 WILD-TYPE 91 227 84
'ADAMTS2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.197 (Fisher's exact test), Q value = 0.7

Table S869.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
ADAMTS2 MUTATED 9 12 6 11
ADAMTS2 WILD-TYPE 56 198 66 120
'ADAMTS2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00339 (Fisher's exact test), Q value = 0.078

Table S870.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
ADAMTS2 MUTATED 3 12 20
ADAMTS2 WILD-TYPE 128 126 141

Figure S121.  Get High-res Image Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

'ADAMTS2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.898 (Fisher's exact test), Q value = 1

Table S871.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
ADAMTS2 MUTATED 5 2 5 4 6
ADAMTS2 WILD-TYPE 84 20 54 61 95
'ADAMTS2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.189 (Fisher's exact test), Q value = 0.69

Table S872.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
ADAMTS2 MUTATED 8 12 2
ADAMTS2 WILD-TYPE 148 109 57
'ADAMTS2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 0.97

Table S873.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
ADAMTS2 MUTATED 9 18 11
ADAMTS2 WILD-TYPE 141 167 132
'ADAMTS2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S874.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
ADAMTS2 MUTATED 5 10 7 4 6 3 3
ADAMTS2 WILD-TYPE 67 99 83 40 43 43 65
'ADAMTS2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0818 (Fisher's exact test), Q value = 0.48

Table S875.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
ADAMTS2 MUTATED 9 24 6
ADAMTS2 WILD-TYPE 166 187 84
'ADAMTS2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0502 (Fisher's exact test), Q value = 0.43

Table S876.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
ADAMTS2 MUTATED 8 21 5 5
ADAMTS2 WILD-TYPE 62 165 126 84
'ADAMTS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.109 (Fisher's exact test), Q value = 0.54

Table S877.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
ADAMTS2 MUTATED 6 19 6
ADAMTS2 WILD-TYPE 135 163 83
'ADAMTS2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.793 (Fisher's exact test), Q value = 1

Table S878.  Gene #88: 'ADAMTS2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
ADAMTS2 MUTATED 8 16 7
ADAMTS2 WILD-TYPE 86 217 78
'TAF1L MUTATION STATUS' versus 'MRNA_CNMF'

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

Table S879.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #1: 'MRNA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 5 7 5 3
TAF1L MUTATED 0 2 1 1
TAF1L WILD-TYPE 5 5 4 2
'TAF1L MUTATION STATUS' versus 'MRNA_CHIERARCHICAL'

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

Table S880.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #2: 'MRNA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 7 9 4
TAF1L MUTATED 2 1 1
TAF1L WILD-TYPE 5 8 3
'TAF1L MUTATION STATUS' versus 'CN_CNMF'

P value = 0.343 (Fisher's exact test), Q value = 0.87

Table S881.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
TAF1L MUTATED 10 21 9 10
TAF1L WILD-TYPE 55 189 63 121
'TAF1L MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 0.9

Table S882.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
TAF1L MUTATED 11 19 17
TAF1L WILD-TYPE 120 119 144
'TAF1L MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 0.95

Table S883.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
TAF1L MUTATED 8 2 6 12 10
TAF1L WILD-TYPE 81 20 53 53 91
'TAF1L MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S884.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
TAF1L MUTATED 15 17 6
TAF1L WILD-TYPE 141 104 53
'TAF1L MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0474 (Fisher's exact test), Q value = 0.43

Table S885.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
TAF1L MUTATED 9 20 21
TAF1L WILD-TYPE 141 165 122

Figure S122.  Get High-res Image Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

'TAF1L MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 0.8

Table S886.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
TAF1L MUTATED 3 12 12 7 7 3 6
TAF1L WILD-TYPE 69 97 78 37 42 43 62
'TAF1L MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.33

Table S887.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
TAF1L MUTATED 16 30 4
TAF1L WILD-TYPE 159 181 86

Figure S123.  Get High-res Image Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

'TAF1L MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S888.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
TAF1L MUTATED 7 19 13 11
TAF1L WILD-TYPE 63 167 118 78
'TAF1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.768 (Fisher's exact test), Q value = 1

Table S889.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
TAF1L MUTATED 17 19 8
TAF1L WILD-TYPE 124 163 81
'TAF1L MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S890.  Gene #89: 'TAF1L MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
TAF1L MUTATED 9 28 7
TAF1L WILD-TYPE 85 205 78
'PLEKHB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.182 (Fisher's exact test), Q value = 0.68

Table S891.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #3: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 65 210 72 131
PLEKHB2 MUTATED 0 1 2 3
PLEKHB2 WILD-TYPE 65 209 70 128
'PLEKHB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S892.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #4: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 131 138 161
PLEKHB2 MUTATED 1 2 3
PLEKHB2 WILD-TYPE 130 136 158
'PLEKHB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S893.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #5: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 89 22 59 65 101
PLEKHB2 MUTATED 2 0 0 2 1
PLEKHB2 WILD-TYPE 87 22 59 63 100
'PLEKHB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.411 (Fisher's exact test), Q value = 0.92

Table S894.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #6: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 156 121 59
PLEKHB2 MUTATED 1 3 1
PLEKHB2 WILD-TYPE 155 118 58
'PLEKHB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S895.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #7: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 150 185 143
PLEKHB2 MUTATED 1 3 2
PLEKHB2 WILD-TYPE 149 182 141
'PLEKHB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.357 (Fisher's exact test), Q value = 0.89

Table S896.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #8: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 72 109 90 44 49 46 68
PLEKHB2 MUTATED 0 3 3 0 0 0 0
PLEKHB2 WILD-TYPE 72 106 87 44 49 46 68
'PLEKHB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.581 (Fisher's exact test), Q value = 1

Table S897.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 175 211 90
PLEKHB2 MUTATED 1 4 1
PLEKHB2 WILD-TYPE 174 207 89
'PLEKHB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.55

Table S898.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 70 186 131 89
PLEKHB2 MUTATED 0 3 0 3
PLEKHB2 WILD-TYPE 70 183 131 86
'PLEKHB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S899.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #11: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 141 182 89
PLEKHB2 MUTATED 1 3 2
PLEKHB2 WILD-TYPE 140 179 87
'PLEKHB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.6

Table S900.  Gene #90: 'PLEKHB2 MUTATION STATUS' versus Molecular Subtype #12: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 94 233 85
PLEKHB2 MUTATED 0 6 0
PLEKHB2 WILD-TYPE 94 227 85
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/LUAD-TP/20217687/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/20140677/LUAD-TP.transferedmergedcluster.txt

  • Number of patients = 481

  • Number of significantly mutated genes = 90

  • Number of Molecular subtypes = 12

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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