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 59 genes and 10 molecular subtypes across 147 patients, 29 significant findings detected with P value < 0.05 and Q value < 0.25.

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

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

  • CSGALNACT2 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • CDC27 mutation correlated to 'CN_CNMF'.

  • SP8 mutation correlated to 'MRNASEQ_CHIERARCHICAL'.

  • AHDC1 mutation correlated to 'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • RBM3 mutation correlated to 'CN_CNMF'.

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 59 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 29 significant findings detected.

Clinical
Features 		CN
CNMF 		METHLYATION
CNMF 		RPPA
CNMF 		RPPA
CHIERARCHICAL 		MRNASEQ
CNMF 		MRNASEQ
CHIERARCHICAL 		MIRSEQ
CNMF 		MIRSEQ
CHIERARCHICAL 		MIRSEQ
MATURE
CNMF 		MIRSEQ
MATURE
CHIERARCHICAL
nMutated (%) nWild-Type Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test Fisher's exact test
KIT 26 (18%) 121 0.00444
(0.131) 		1e-05
(0.000656) 		3e-05
(0.00147) 		1e-05
(0.000656) 		1e-05
(0.000656) 		1e-05
(0.000656) 		1e-05
(0.000656) 		1e-05
(0.000656) 		1e-05
(0.000656) 		1e-05
(0.000656)
KRAS 19 (13%) 128 0.00135
(0.0469) 		0.0103
(0.224) 		0.00392
(0.122) 		0.00033
(0.015) 		0.00038
(0.016) 		0.00185
(0.0606) 		1e-05
(0.000656) 		3e-05
(0.00147) 		2e-05
(0.00118) 		0.00062
(0.0229)
AHDC1 4 (3%) 143 0.783
(1.00) 		0.0509
(0.521) 		0.0333
(0.44) 		0.108
(0.685) 		0.0741
(0.607) 		0.0259
(0.379) 		0.00524
(0.147) 		0.00935
(0.221) 		0.0102
(0.224) 		0.00722
(0.177)
CSGALNACT2 5 (3%) 142 0.0493
(0.52) 		0.182
(0.848) 		0.0449
(0.52) 		0.0224
(0.366) 		0.00057
(0.0224) 		0.0111
(0.233) 		0.0336
(0.44) 		0.0161
(0.317) 		0.0245
(0.371) 		0.0418
(0.503)
CDC27 6 (4%) 141 0.0118
(0.241) 		0.442
(1.00) 		0.21
(0.893) 		0.184
(0.848) 		0.0583
(0.536) 		0.0575
(0.536) 		0.324
(0.987) 		0.139
(0.786) 		0.168
(0.848) 		0.282
(0.947)
SP8 6 (4%) 141 0.0354
(0.445) 		0.341
(0.987) 		0.0765
(0.608) 		0.0216
(0.366) 		0.228
(0.93) 		0.00626
(0.161) 		0.0487
(0.52) 		0.0217
(0.366) 		0.0243
(0.371) 		0.1
(0.664)
RBM3 3 (2%) 144 0.00629
(0.161) 		0.384
(0.987) 		1
(1.00) 		0.948
(1.00) 		0.112
(0.695) 		0.615
(1.00) 		0.607
(1.00) 		0.412
(1.00)
FAM18B2 26 (18%) 121 0.162
(0.837) 		0.36
(0.987) 		0.718
(1.00) 		0.532
(1.00) 		0.646
(1.00) 		0.497
(1.00) 		0.3
(0.964) 		0.447
(1.00) 		0.7
(1.00) 		0.67
(1.00)
FAM104B 7 (5%) 140 0.0827
(0.634) 		0.475
(1.00) 		0.248
(0.947) 		0.719
(1.00) 		0.0934
(0.656) 		0.263
(0.947) 		0.0965
(0.664) 		0.253
(0.947) 		0.539
(1.00) 		0.578
(1.00)
NRAS 7 (5%) 140 0.068
(0.59) 		0.297
(0.964) 		0.156
(0.82) 		0.0353
(0.445) 		0.0232
(0.371) 		0.144
(0.789) 		0.0988
(0.664) 		0.0168
(0.32) 		0.0713
(0.604) 		0.172
(0.848)
DDX11 8 (5%) 139 0.914
(1.00) 		0.685
(1.00) 		0.589
(1.00) 		0.143
(0.789) 		0.561
(1.00) 		0.362
(0.987) 		0.133
(0.777) 		0.29
(0.95) 		0.653
(1.00) 		0.284
(0.948)
MUC6 15 (10%) 132 0.956
(1.00) 		0.442
(1.00) 		0.59
(1.00) 		0.0716
(0.604) 		0.987
(1.00) 		0.965
(1.00) 		1
(1.00) 		0.733
(1.00) 		0.777
(1.00) 		0.732
(1.00)
PNPLA4 5 (3%) 142 0.665
(1.00) 		0.562
(1.00) 		0.441
(1.00) 		0.717
(1.00) 		0.499
(1.00) 		0.554
(1.00) 		0.378
(0.987) 		0.446
(1.00) 		0.32
(0.987) 		0.776
(1.00)
SERINC2 4 (3%) 143 1
(1.00) 		0.744
(1.00) 		0.163
(0.837) 		0.053
(0.524) 		0.775
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.586
(1.00) 		0.813
(1.00) 		0.273
(0.947)
RHPN2 6 (4%) 141 0.813
(1.00) 		0.799
(1.00) 		0.78
(1.00) 		1
(1.00) 		0.964
(1.00) 		0.923
(1.00) 		0.578
(1.00) 		1
(1.00) 		1
(1.00) 		0.88
(1.00)
RBM10 5 (3%) 142 0.428
(1.00) 		0.267
(0.947) 		0.879
(1.00) 		0.718
(1.00) 		0.207
(0.891) 		0.711
(1.00) 		0.631
(1.00) 		0.597
(1.00) 		0.606
(1.00) 		0.277
(0.947)
HSF4 6 (4%) 141 0.169
(0.848) 		0.107
(0.685) 		0.499
(1.00) 		1
(1.00) 		0.696
(1.00) 		0.141
(0.786) 		0.205
(0.891) 		0.368
(0.987) 		0.277
(0.947) 		0.594
(1.00)
MLLT3 4 (3%) 143 0.462
(1.00) 		0.744
(1.00) 		0.735
(1.00) 		0.283
(0.947) 		1
(1.00) 		0.585
(1.00) 		0.467
(1.00) 		0.718
(1.00)
ERC1 7 (5%) 140 0.366
(0.987) 		0.864
(1.00) 		0.909
(1.00) 		0.862
(1.00) 		0.866
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.677
(1.00)
MEF2A 3 (2%) 144 1
(1.00) 		0.758
(1.00) 		0.766
(1.00) 		0.328
(0.987) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.314
(0.987)
NAT10 4 (3%) 143 0.33
(0.987) 		0.822
(1.00) 		0.865
(1.00) 		0.595
(1.00) 		0.592
(1.00) 		0.259
(0.947) 		0.833
(1.00) 		1
(1.00) 		1
(1.00) 		0.651
(1.00)
SPIN2A 3 (2%) 144 0.6
(1.00) 		0.508
(1.00) 		0.504
(1.00) 		0.372
(0.987) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.783
(1.00)
DEK 5 (3%) 142 0.0633
(0.566) 		0.0197
(0.353) 		0.439
(1.00) 		0.276
(0.947) 		0.0842
(0.634) 		0.0181
(0.335) 		0.376
(0.987) 		0.319
(0.987) 		0.444
(1.00) 		0.0784
(0.609)
FANK1 4 (3%) 143 0.176
(0.848) 		0.743
(1.00) 		0.24
(0.943) 		0.6
(1.00) 		0.457
(1.00) 		0.708
(1.00) 		0.457
(1.00) 		0.282
(0.947) 		0.272
(0.947) 		0.434
(1.00)
ANKRD11 7 (5%) 140 0.851
(1.00) 		0.283
(0.947) 		0.593
(1.00) 		0.65
(1.00) 		0.0374
(0.46) 		0.851
(1.00) 		0.333
(0.987) 		0.287
(0.95) 		0.278
(0.947) 		0.665
(1.00)
C22ORF43 3 (2%) 144 0.0472
(0.52) 		0.507
(1.00) 		0.0512
(0.521) 		0.795
(1.00) 		0.849
(1.00) 		0.736
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.713
(1.00)
ATXN3 3 (2%) 144 0.717
(1.00) 		1
(1.00) 		0.212
(0.895) 		0.0996
(0.664) 		0.428
(1.00) 		0.181
(0.848) 		0.499
(1.00) 		0.0915
(0.656) 		0.0929
(0.656) 		0.333
(0.987)
TPTE2 5 (3%) 142 0.716
(1.00) 		0.523
(1.00) 		1
(1.00) 		1
(1.00) 		0.439
(1.00) 		0.633
(1.00) 		0.0492
(0.52) 		0.382
(0.987) 		0.442
(1.00) 		0.907
(1.00)
KRTAP10-10 5 (3%) 142 1
(1.00) 		0.457
(1.00) 		0.761
(1.00) 		0.535
(1.00) 		0.471
(1.00) 		0.872
(1.00) 		0.158
(0.827) 		0.596
(1.00) 		0.603
(1.00) 		0.177
(0.848)
ZNF680 3 (2%) 144 0.185
(0.848) 		0.671
(1.00) 		0.516
(1.00) 		0.232
(0.93) 		0.619
(1.00) 		0.857
(1.00) 		0.0586
(0.536) 		0.341
(0.987) 		0.331
(0.987) 		0.816
(1.00)
RAC1 4 (3%) 143 0.702
(1.00) 		0.903
(1.00) 		0.644
(1.00) 		1
(1.00) 		0.27
(0.947) 		0.638
(1.00) 		0.254
(0.947) 		0.481
(1.00) 		0.367
(0.987) 		0.177
(0.848)
NBPF10 7 (5%) 140 0.23
(0.93) 		0.789
(1.00) 		0.784
(1.00) 		1
(1.00) 		0.232
(0.93) 		0.233
(0.93) 		0.555
(1.00) 		0.417
(1.00) 		0.421
(1.00) 		0.281
(0.947)
FAM8A1 3 (2%) 144 0.444
(1.00) 		0.759
(1.00) 		0.0773
(0.608) 		0.517
(1.00) 		0.0579
(0.536) 		0.344
(0.987) 		0.333
(0.987) 		0.103
(0.677)
PSMD11 4 (3%) 143 0.0848
(0.634) 		0.0767
(0.608) 		0.296
(0.964) 		0.232
(0.93) 		0.458
(1.00) 		0.754
(1.00) 		0.558
(1.00) 		0.196
(0.863) 		0.365
(0.987) 		0.698
(1.00)
KRTAP1-1 3 (2%) 144 1
(1.00) 		0.444
(1.00) 		1
(1.00) 		0.474
(1.00) 		0.775
(1.00) 		0.617
(1.00) 		0.609
(1.00) 		0.413
(1.00)
OPLAH 4 (3%) 143 0.255
(0.947) 		0.353
(0.987) 		0.573
(1.00) 		0.797
(1.00) 		1
(1.00) 		0.314
(0.987) 		0.557
(1.00) 		0.28
(0.947) 		1
(1.00) 		0.858
(1.00)
FAM101B 4 (3%) 143 1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.627
(1.00) 		0.496
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
MUC2 16 (11%) 131 0.518
(1.00) 		0.917
(1.00) 		0.566
(1.00) 		0.43
(1.00) 		0.34
(0.987) 		0.984
(1.00) 		0.499
(1.00) 		0.943
(1.00) 		0.791
(1.00) 		0.513
(1.00)
HTT 3 (2%) 144 1
(1.00) 		0.383
(0.987) 		1
(1.00) 		0.681
(1.00) 		0.631
(1.00) 		0.614
(1.00) 		0.608
(1.00) 		0.939
(1.00)
EZH2 4 (3%) 143 0.884
(1.00) 		0.256
(0.947) 		0.563
(1.00) 		0.545
(1.00) 		0.557
(1.00) 		0.28
(0.947) 		0.274
(0.947) 		0.375
(0.987)
PABPC3 4 (3%) 143 0.886
(1.00) 		0.516
(1.00) 		0.236
(0.933) 		0.608
(1.00) 		0.195
(0.863) 		0.382
(0.987) 		0.576
(1.00) 		0.361
(0.987)
CUX1 5 (3%) 142 0.908
(1.00) 		1
(1.00) 		0.864
(1.00) 		0.596
(1.00) 		0.469
(1.00) 		0.964
(1.00) 		0.631
(1.00) 		0.854
(1.00) 		0.857
(1.00) 		0.858
(1.00)
DLC1 3 (2%) 144 0.445
(1.00) 		1
(1.00) 		0.641
(1.00) 		1
(1.00) 		1
(1.00) 		0.949
(1.00) 		0.63
(1.00) 		0.618
(1.00) 		0.609
(1.00) 		0.939
(1.00)
STAB1 7 (5%) 140 0.72
(1.00) 		0.141
(0.786) 		0.357
(0.987) 		1
(1.00) 		0.454
(1.00) 		0.5
(1.00) 		0.232
(0.93) 		0.196
(0.863) 		0.124
(0.729) 		0.618
(1.00)
NOTCH1 5 (3%) 142 0.72
(1.00) 		0.863
(1.00) 		0.219
(0.917) 		0.844
(1.00) 		0.114
(0.702) 		0.448
(1.00) 		0.377
(0.987) 		0.319
(0.987) 		0.209
(0.893) 		0.753
(1.00)
EPAS1 5 (3%) 142 0.614
(1.00) 		1
(1.00) 		0.831
(1.00) 		0.68
(1.00) 		0.484
(1.00) 		0.789
(1.00) 		0.631
(1.00) 		0.855
(1.00) 		0.86
(1.00) 		0.521
(1.00)
PIK3CD 4 (3%) 143 0.0477
(0.52) 		0.353
(0.987) 		0.185
(0.848) 		0.372
(0.987) 		0.141
(0.786) 		0.696
(1.00) 		0.69
(1.00) 		0.256
(0.947)
BCL11B 5 (3%) 142 0.0985
(0.664) 		0.602
(1.00) 		0.527
(1.00) 		0.535
(1.00) 		0.436
(1.00) 		0.936
(1.00) 		0.528
(1.00) 		0.383
(0.987) 		0.444
(1.00) 		0.719
(1.00)
KIAA0430 3 (2%) 144 0.442
(1.00) 		0.107
(0.685) 		0.688
(1.00) 		0.773
(1.00) 		0.631
(1.00) 		0.616
(1.00) 		0.606
(1.00) 		0.941
(1.00)
MTIF3 3 (2%) 144 1
(1.00) 		0.859
(1.00) 		1
(1.00) 		1
(1.00) 		0.848
(1.00) 		1
(1.00) 		0.378
(0.987) 		0.796
(1.00) 		0.796
(1.00) 		1
(1.00)
BTN2A2 3 (2%) 144 0.446
(1.00) 		0.756
(1.00) 		0.179
(0.848) 		0.812
(1.00) 		0.373
(0.987) 		0.796
(1.00) 		0.795
(1.00) 		0.646
(1.00)
C17ORF64 3 (2%) 144 0.843
(1.00) 		0.858
(1.00) 		0.85
(1.00) 		0.37
(0.987) 		1
(1.00) 		1
(1.00) 		0.453
(1.00) 		0.558
(1.00)
RUNX2 4 (3%) 143 0.329
(0.987) 		1
(1.00) 		0.864
(1.00) 		0.6
(1.00) 		1
(1.00) 		1
(1.00) 		0.83
(1.00) 		1
(1.00) 		1
(1.00) 		0.652
(1.00)
SSBP3 3 (2%) 144 0.843
(1.00) 		1
(1.00) 		0.385
(0.987) 		0.0591
(0.536) 		0.497
(1.00) 		0.0928
(0.656) 		0.0929
(0.656) 		0.0728
(0.605)
GSX2 4 (3%) 143 0.152
(0.811) 		0.468
(1.00) 		0.647
(1.00) 		0.0273
(0.379) 		0.0533
(0.524) 		0.243
(0.947) 		0.0656
(0.578) 		0.15
(0.811) 		0.811
(1.00) 		0.561
(1.00)
SP4 4 (3%) 143 0.153
(0.811) 		0.121
(0.724) 		0.171
(0.848) 		0.112
(0.695) 		0.316
(0.987) 		0.0275
(0.379) 		0.0276
(0.379) 		0.118
(0.713)
PCMTD1 5 (3%) 142 0.175
(0.848) 		0.118
(0.713) 		0.453
(1.00) 		0.536
(1.00) 		0.523
(1.00) 		0.444
(1.00) 		0.378
(0.987) 		0.318
(0.987) 		0.207
(0.891) 		0.551
(1.00)
ZNF814 5 (3%) 142 0.135
(0.781) 		0.429
(1.00) 		0.933
(1.00) 		0.841
(1.00) 		0.301
(0.964) 		0.258
(0.947) 		0.734
(1.00) 		1
(1.00) 		1
(1.00) 		0.452
(1.00)
TTC38 4 (3%) 143 0.288
(0.95) 		0.514
(1.00) 		0.915
(1.00) 		0.194
(0.863) 		0.435
(1.00) 		0.819
(1.00) 		0.195
(0.863) 		0.381
(0.987) 		0.579
(1.00) 		0.0454
(0.52)
'FAM18B2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.162 (Fisher's exact test), Q value = 0.84

Table S1.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
FAM18B2 MUTATED 5 9 11 1
FAM18B2 WILD-TYPE 42 23 43 13
'FAM18B2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.36 (Fisher's exact test), Q value = 0.99

Table S2.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
FAM18B2 MUTATED 5 2 8 11
FAM18B2 WILD-TYPE 38 18 26 39
'FAM18B2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S3.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
FAM18B2 MUTATED 7 2 3 9 3
FAM18B2 WILD-TYPE 37 6 7 27 15
'FAM18B2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.532 (Fisher's exact test), Q value = 1

Table S4.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
FAM18B2 MUTATED 9 7 8
FAM18B2 WILD-TYPE 41 17 34
'FAM18B2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S5.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
FAM18B2 MUTATED 3 7 5 5 2 4 0
FAM18B2 WILD-TYPE 30 22 28 17 6 17 1
'FAM18B2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S6.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
FAM18B2 MUTATED 4 6 3 6 2 4 1
FAM18B2 WILD-TYPE 38 20 9 18 6 19 11
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 0.96

Table S7.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
FAM18B2 MUTATED 6 10 10
FAM18B2 WILD-TYPE 44 46 31
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.447 (Fisher's exact test), Q value = 1

Table S8.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
FAM18B2 MUTATED 10 6 10
FAM18B2 WILD-TYPE 58 32 31
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S9.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
FAM18B2 MUTATED 10 7 9
FAM18B2 WILD-TYPE 57 29 35
'FAM18B2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.67 (Fisher's exact test), Q value = 1

Table S10.  Gene #1: 'FAM18B2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
FAM18B2 MUTATED 4 6 4 7 4 1
FAM18B2 WILD-TYPE 29 29 15 20 15 13
'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00444 (Fisher's exact test), Q value = 0.13

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
KIT MUTATED 15 5 3 3
KIT WILD-TYPE 32 27 51 11

Figure S1.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
KIT MUTATED 20 2 0 4
KIT WILD-TYPE 23 18 34 46

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

'KIT MUTATION STATUS' versus 'RPPA_CNMF'

P value = 3e-05 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
KIT MUTATED 18 3 0 1 0
KIT WILD-TYPE 26 5 10 35 18

Figure S3.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KIT MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
KIT MUTATED 21 1 0
KIT WILD-TYPE 29 23 42

Figure S4.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

Table S15.  Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
KIT MUTATED 23 0 0 0 2 1 0
KIT WILD-TYPE 10 29 33 22 6 20 1

Figure S5.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KIT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
KIT MUTATED 25 0 0 1 0 0 0
KIT WILD-TYPE 17 26 12 23 8 23 12

Figure S6.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

Table S17.  Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
KIT MUTATED 23 2 1
KIT WILD-TYPE 27 54 40

Figure S7.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KIT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
KIT MUTATED 25 0 1
KIT WILD-TYPE 43 38 40

Figure S8.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KIT MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
KIT MUTATED 25 0 1
KIT WILD-TYPE 42 36 43

Figure S9.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KIT MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

Table S20.  Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
KIT MUTATED 20 5 0 0 0 1
KIT WILD-TYPE 13 30 19 27 19 13

Figure S10.  Get High-res Image Gene #2: 'KIT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00135 (Fisher's exact test), Q value = 0.047

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
KRAS MUTATED 6 9 1 3
KRAS WILD-TYPE 41 23 53 11

Figure S11.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0103 (Fisher's exact test), Q value = 0.22

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
KRAS MUTATED 10 3 0 6
KRAS WILD-TYPE 33 17 34 44

Figure S12.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00392 (Fisher's exact test), Q value = 0.12

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
KRAS MUTATED 11 2 0 1 0
KRAS WILD-TYPE 33 6 10 35 18

Figure S13.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00033 (Fisher's exact test), Q value = 0.015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
KRAS MUTATED 13 0 1
KRAS WILD-TYPE 37 24 41

Figure S14.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00038 (Fisher's exact test), Q value = 0.016

Table S25.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
KRAS MUTATED 8 7 0 1 3 0 0
KRAS WILD-TYPE 25 22 33 21 5 21 1

Figure S15.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00185 (Fisher's exact test), Q value = 0.061

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
KRAS MUTATED 12 6 0 1 0 0 0
KRAS WILD-TYPE 30 20 12 23 8 23 12

Figure S16.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00066

Table S27.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
KRAS MUTATED 16 2 1
KRAS WILD-TYPE 34 54 40

Figure S17.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 3e-05 (Fisher's exact test), Q value = 0.0015

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
KRAS MUTATED 18 0 1
KRAS WILD-TYPE 50 38 40

Figure S18.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.0012

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
KRAS MUTATED 18 0 1
KRAS WILD-TYPE 49 36 43

Figure S19.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00062 (Fisher's exact test), Q value = 0.023

Table S30.  Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
KRAS MUTATED 8 10 0 1 0 0
KRAS WILD-TYPE 25 25 19 26 19 14

Figure S20.  Get High-res Image Gene #3: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'FAM104B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0827 (Fisher's exact test), Q value = 0.63

Table S31.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
FAM104B MUTATED 3 3 0 1
FAM104B WILD-TYPE 44 29 54 13
'FAM104B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.475 (Fisher's exact test), Q value = 1

Table S32.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
FAM104B MUTATED 4 0 1 2
FAM104B WILD-TYPE 39 20 33 48
'FAM104B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 0.95

Table S33.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
FAM104B MUTATED 3 1 0 0 1
FAM104B WILD-TYPE 41 7 10 36 17
'FAM104B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S34.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
FAM104B MUTATED 3 0 2
FAM104B WILD-TYPE 47 24 40
'FAM104B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0934 (Fisher's exact test), Q value = 0.66

Table S35.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
FAM104B MUTATED 5 0 2 0 0 0 0
FAM104B WILD-TYPE 28 29 31 22 8 21 1
'FAM104B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.263 (Fisher's exact test), Q value = 0.95

Table S36.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
FAM104B MUTATED 5 0 1 0 0 1 0
FAM104B WILD-TYPE 37 26 11 24 8 22 12
'FAM104B MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0965 (Fisher's exact test), Q value = 0.66

Table S37.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
FAM104B MUTATED 5 2 0
FAM104B WILD-TYPE 45 54 41
'FAM104B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.253 (Fisher's exact test), Q value = 0.95

Table S38.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
FAM104B MUTATED 5 2 0
FAM104B WILD-TYPE 63 36 41
'FAM104B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S39.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
FAM104B MUTATED 5 1 1
FAM104B WILD-TYPE 62 35 43
'FAM104B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S40.  Gene #4: 'FAM104B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
FAM104B MUTATED 2 3 0 0 1 1
FAM104B WILD-TYPE 31 32 19 27 18 13
'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0493 (Fisher's exact test), Q value = 0.52

Table S41.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
CSGALNACT2 MUTATED 0 0 5 0
CSGALNACT2 WILD-TYPE 47 32 49 14

Figure S21.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S42.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
CSGALNACT2 MUTATED 0 0 1 4
CSGALNACT2 WILD-TYPE 43 20 33 46
'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0449 (Fisher's exact test), Q value = 0.52

Table S43.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
CSGALNACT2 MUTATED 0 0 0 5 0
CSGALNACT2 WILD-TYPE 44 8 10 31 18

Figure S22.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0224 (Fisher's exact test), Q value = 0.37

Table S44.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
CSGALNACT2 MUTATED 0 3 2
CSGALNACT2 WILD-TYPE 50 21 40

Figure S23.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00057 (Fisher's exact test), Q value = 0.022

Table S45.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
CSGALNACT2 MUTATED 0 0 0 0 0 5 0
CSGALNACT2 WILD-TYPE 33 29 33 22 8 16 1

Figure S24.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0111 (Fisher's exact test), Q value = 0.23

Table S46.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
CSGALNACT2 MUTATED 0 0 2 3 0 0 0
CSGALNACT2 WILD-TYPE 42 26 10 21 8 23 12

Figure S25.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0336 (Fisher's exact test), Q value = 0.44

Table S47.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
CSGALNACT2 MUTATED 0 1 4
CSGALNACT2 WILD-TYPE 50 55 37

Figure S26.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0161 (Fisher's exact test), Q value = 0.32

Table S48.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
CSGALNACT2 MUTATED 0 1 4
CSGALNACT2 WILD-TYPE 68 37 37

Figure S27.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0245 (Fisher's exact test), Q value = 0.37

Table S49.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
CSGALNACT2 MUTATED 0 1 4
CSGALNACT2 WILD-TYPE 67 35 40

Figure S28.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'CSGALNACT2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0418 (Fisher's exact test), Q value = 0.5

Table S50.  Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
CSGALNACT2 MUTATED 0 0 1 2 0 2
CSGALNACT2 WILD-TYPE 33 35 18 25 19 12

Figure S29.  Get High-res Image Gene #5: 'CSGALNACT2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.068 (Fisher's exact test), Q value = 0.59

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
NRAS MUTATED 4 3 0 0
NRAS WILD-TYPE 43 29 54 14
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.297 (Fisher's exact test), Q value = 0.96

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
NRAS MUTATED 4 1 0 2
NRAS WILD-TYPE 39 19 34 48
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.156 (Fisher's exact test), Q value = 0.82

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
NRAS MUTATED 4 1 0 0 0
NRAS WILD-TYPE 40 7 10 36 18
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0353 (Fisher's exact test), Q value = 0.44

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
NRAS MUTATED 5 0 0
NRAS WILD-TYPE 45 24 42

Figure S30.  Get High-res Image Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0232 (Fisher's exact test), Q value = 0.37

Table S55.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
NRAS MUTATED 6 1 0 0 0 0 0
NRAS WILD-TYPE 27 28 33 22 8 21 1

Figure S31.  Get High-res Image Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.144 (Fisher's exact test), Q value = 0.79

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
NRAS MUTATED 6 1 0 0 0 0 0
NRAS WILD-TYPE 36 25 12 24 8 23 12
'NRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0988 (Fisher's exact test), Q value = 0.66

Table S57.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
NRAS MUTATED 5 2 0
NRAS WILD-TYPE 45 54 41
'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0168 (Fisher's exact test), Q value = 0.32

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
NRAS MUTATED 7 0 0
NRAS WILD-TYPE 61 38 41

Figure S32.  Get High-res Image Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0713 (Fisher's exact test), Q value = 0.6

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
NRAS MUTATED 6 1 0
NRAS WILD-TYPE 61 35 44
'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S60.  Gene #6: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
NRAS MUTATED 3 4 0 0 0 0
NRAS WILD-TYPE 30 31 19 27 19 14
'DDX11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.914 (Fisher's exact test), Q value = 1

Table S61.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
DDX11 MUTATED 3 1 3 1
DDX11 WILD-TYPE 44 31 51 13
'DDX11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.685 (Fisher's exact test), Q value = 1

Table S62.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
DDX11 MUTATED 2 0 3 3
DDX11 WILD-TYPE 41 20 31 47
'DDX11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S63.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
DDX11 MUTATED 2 1 0 2 2
DDX11 WILD-TYPE 42 7 10 34 16
'DDX11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.79

Table S64.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
DDX11 MUTATED 2 0 5
DDX11 WILD-TYPE 48 24 37
'DDX11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S65.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
DDX11 MUTATED 1 2 4 0 0 1 0
DDX11 WILD-TYPE 32 27 29 22 8 20 1
'DDX11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.362 (Fisher's exact test), Q value = 0.99

Table S66.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
DDX11 MUTATED 1 2 1 0 1 2 1
DDX11 WILD-TYPE 41 24 11 24 7 21 11
'DDX11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.133 (Fisher's exact test), Q value = 0.78

Table S67.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
DDX11 MUTATED 1 6 1
DDX11 WILD-TYPE 49 50 40
'DDX11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.29 (Fisher's exact test), Q value = 0.95

Table S68.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
DDX11 MUTATED 3 4 1
DDX11 WILD-TYPE 65 34 40
'DDX11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.653 (Fisher's exact test), Q value = 1

Table S69.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
DDX11 MUTATED 3 3 2
DDX11 WILD-TYPE 64 33 42
'DDX11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.284 (Fisher's exact test), Q value = 0.95

Table S70.  Gene #7: 'DDX11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
DDX11 MUTATED 0 3 2 1 2 0
DDX11 WILD-TYPE 33 32 17 26 17 14
'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.956 (Fisher's exact test), Q value = 1

Table S71.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
MUC6 MUTATED 6 3 5 1
MUC6 WILD-TYPE 41 29 49 13
'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S72.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
MUC6 MUTATED 5 0 4 6
MUC6 WILD-TYPE 38 20 30 44
'MUC6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.59 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
MUC6 MUTATED 3 1 0 4 3
MUC6 WILD-TYPE 41 7 10 32 15
'MUC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0716 (Fisher's exact test), Q value = 0.6

Table S74.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
MUC6 MUTATED 4 0 7
MUC6 WILD-TYPE 46 24 35
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.987 (Fisher's exact test), Q value = 1

Table S75.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
MUC6 MUTATED 3 3 3 2 1 3 0
MUC6 WILD-TYPE 30 26 30 20 7 18 1
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.965 (Fisher's exact test), Q value = 1

Table S76.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
MUC6 MUTATED 4 2 1 2 1 3 2
MUC6 WILD-TYPE 38 24 11 22 7 20 10
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S77.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
MUC6 MUTATED 5 6 4
MUC6 WILD-TYPE 45 50 37
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.733 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
MUC6 MUTATED 6 5 4
MUC6 WILD-TYPE 62 33 37
'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.777 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
MUC6 MUTATED 6 5 4
MUC6 WILD-TYPE 61 31 40
'MUC6 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.732 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
MUC6 MUTATED 3 3 3 4 2 0
MUC6 WILD-TYPE 30 32 16 23 17 14
'PNPLA4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
PNPLA4 MUTATED 3 1 1 0
PNPLA4 WILD-TYPE 44 31 53 14
'PNPLA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.562 (Fisher's exact test), Q value = 1

Table S82.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
PNPLA4 MUTATED 3 0 1 1
PNPLA4 WILD-TYPE 40 20 33 49
'PNPLA4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.441 (Fisher's exact test), Q value = 1

Table S83.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
PNPLA4 MUTATED 3 1 0 1 0
PNPLA4 WILD-TYPE 41 7 10 35 18
'PNPLA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S84.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
PNPLA4 MUTATED 3 0 2
PNPLA4 WILD-TYPE 47 24 40
'PNPLA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
PNPLA4 MUTATED 3 0 1 0 0 1 0
PNPLA4 WILD-TYPE 30 29 32 22 8 20 1
'PNPLA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.554 (Fisher's exact test), Q value = 1

Table S86.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
PNPLA4 MUTATED 3 0 1 0 0 1 0
PNPLA4 WILD-TYPE 39 26 11 24 8 22 12
'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.99

Table S87.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
PNPLA4 MUTATED 3 2 0
PNPLA4 WILD-TYPE 47 54 41
'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S88.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
PNPLA4 MUTATED 3 2 0
PNPLA4 WILD-TYPE 65 36 41
'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.32 (Fisher's exact test), Q value = 0.99

Table S89.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
PNPLA4 MUTATED 3 2 0
PNPLA4 WILD-TYPE 64 34 44
'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S90.  Gene #9: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
PNPLA4 MUTATED 2 1 1 0 1 0
PNPLA4 WILD-TYPE 31 34 18 27 18 14
'SERINC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S91.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
SERINC2 MUTATED 1 1 2 0
SERINC2 WILD-TYPE 46 31 52 14
'SERINC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
SERINC2 MUTATED 1 0 2 1
SERINC2 WILD-TYPE 42 20 32 49
'SERINC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.163 (Fisher's exact test), Q value = 0.84

Table S93.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
SERINC2 MUTATED 0 0 1 2 0
SERINC2 WILD-TYPE 44 8 9 34 18
'SERINC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.053 (Fisher's exact test), Q value = 0.52

Table S94.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
SERINC2 MUTATED 0 0 3
SERINC2 WILD-TYPE 50 24 39
'SERINC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S95.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
SERINC2 MUTATED 1 0 2 1 0 0 0
SERINC2 WILD-TYPE 32 29 31 21 8 21 1
'SERINC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S96.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
SERINC2 MUTATED 1 0 1 1 0 1 0
SERINC2 WILD-TYPE 41 26 11 23 8 22 12
'SERINC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S97.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
SERINC2 MUTATED 1 2 1
SERINC2 WILD-TYPE 49 54 40
'SERINC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S98.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
SERINC2 MUTATED 1 2 1
SERINC2 WILD-TYPE 67 36 40
'SERINC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
SERINC2 MUTATED 1 1 2
SERINC2 WILD-TYPE 66 35 42
'SERINC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.273 (Fisher's exact test), Q value = 0.95

Table S100.  Gene #10: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
SERINC2 MUTATED 1 0 2 1 0 0
SERINC2 WILD-TYPE 32 35 17 26 19 14
'RHPN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.813 (Fisher's exact test), Q value = 1

Table S101.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
RHPN2 MUTATED 2 1 2 1
RHPN2 WILD-TYPE 45 31 52 13
'RHPN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S102.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
RHPN2 MUTATED 1 1 1 3
RHPN2 WILD-TYPE 42 19 33 47
'RHPN2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S103.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
RHPN2 MUTATED 3 0 1 1 1
RHPN2 WILD-TYPE 41 8 9 35 17
'RHPN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S104.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
RHPN2 MUTATED 3 1 2
RHPN2 WILD-TYPE 47 23 40
'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S105.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
RHPN2 MUTATED 1 2 1 1 0 1 0
RHPN2 WILD-TYPE 32 27 32 21 8 20 1
'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S106.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
RHPN2 MUTATED 1 2 0 1 0 1 1
RHPN2 WILD-TYPE 41 24 12 23 8 22 11
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S107.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
RHPN2 MUTATED 3 1 2
RHPN2 WILD-TYPE 47 55 39
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S108.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
RHPN2 MUTATED 3 1 2
RHPN2 WILD-TYPE 65 37 39
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S109.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
RHPN2 MUTATED 3 1 2
RHPN2 WILD-TYPE 64 35 42
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.88 (Fisher's exact test), Q value = 1

Table S110.  Gene #11: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
RHPN2 MUTATED 1 2 0 2 1 0
RHPN2 WILD-TYPE 32 33 19 25 18 14
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 1

Table S111.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
RBM10 MUTATED 1 2 1 1
RBM10 WILD-TYPE 46 30 53 13
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.267 (Fisher's exact test), Q value = 0.95

Table S112.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
RBM10 MUTATED 1 2 0 2
RBM10 WILD-TYPE 42 18 34 48
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
RBM10 MUTATED 3 0 0 2 0
RBM10 WILD-TYPE 41 8 10 34 18
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S114.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
RBM10 MUTATED 3 0 2
RBM10 WILD-TYPE 47 24 40
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.89

Table S115.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
RBM10 MUTATED 0 3 0 1 0 1 0
RBM10 WILD-TYPE 33 26 33 21 8 20 1
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.711 (Fisher's exact test), Q value = 1

Table S116.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
RBM10 MUTATED 1 2 0 1 0 0 1
RBM10 WILD-TYPE 41 24 12 23 8 23 11
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S117.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
RBM10 MUTATED 2 1 2
RBM10 WILD-TYPE 48 55 39
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
RBM10 MUTATED 3 0 2
RBM10 WILD-TYPE 65 38 39
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S119.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
RBM10 MUTATED 3 0 2
RBM10 WILD-TYPE 64 36 42
'RBM10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.277 (Fisher's exact test), Q value = 0.95

Table S120.  Gene #12: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
RBM10 MUTATED 0 3 0 2 0 0
RBM10 WILD-TYPE 33 32 19 25 19 14
'HSF4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.85

Table S121.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
HSF4 MUTATED 4 0 1 1
HSF4 WILD-TYPE 43 32 53 13
'HSF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.69

Table S122.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
HSF4 MUTATED 4 1 1 0
HSF4 WILD-TYPE 39 19 33 50
'HSF4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S123.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
HSF4 MUTATED 2 1 1 1 1
HSF4 WILD-TYPE 42 7 9 35 17
'HSF4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S124.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
HSF4 MUTATED 3 1 2
HSF4 WILD-TYPE 47 23 40
'HSF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S125.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
HSF4 MUTATED 2 1 1 0 1 1 0
HSF4 WILD-TYPE 31 28 32 22 7 20 1
'HSF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.141 (Fisher's exact test), Q value = 0.79

Table S126.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
HSF4 MUTATED 4 0 1 0 1 0 0
HSF4 WILD-TYPE 38 26 11 24 7 23 12
'HSF4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.205 (Fisher's exact test), Q value = 0.89

Table S127.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
HSF4 MUTATED 4 2 0
HSF4 WILD-TYPE 46 54 41
'HSF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.368 (Fisher's exact test), Q value = 0.99

Table S128.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
HSF4 MUTATED 4 2 0
HSF4 WILD-TYPE 64 36 41
'HSF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 0.95

Table S129.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
HSF4 MUTATED 4 2 0
HSF4 WILD-TYPE 63 34 44
'HSF4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.594 (Fisher's exact test), Q value = 1

Table S130.  Gene #13: 'HSF4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
HSF4 MUTATED 3 1 1 0 1 0
HSF4 WILD-TYPE 30 34 18 27 18 14
'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0118 (Fisher's exact test), Q value = 0.24

Table S131.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
CDC27 MUTATED 1 3 0 2
CDC27 WILD-TYPE 46 29 54 12

Figure S33.  Get High-res Image Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S132.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
CDC27 MUTATED 2 2 1 1
CDC27 WILD-TYPE 41 18 33 49
'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.21 (Fisher's exact test), Q value = 0.89

Table S133.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
CDC27 MUTATED 4 0 1 0 0
CDC27 WILD-TYPE 40 8 9 36 18
'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S134.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
CDC27 MUTATED 4 1 0
CDC27 WILD-TYPE 46 23 42
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0583 (Fisher's exact test), Q value = 0.54

Table S135.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
CDC27 MUTATED 1 4 0 0 1 0 0
CDC27 WILD-TYPE 32 25 33 22 7 21 1
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0575 (Fisher's exact test), Q value = 0.54

Table S136.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
CDC27 MUTATED 1 4 0 0 1 0 0
CDC27 WILD-TYPE 41 22 12 24 7 23 12
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 0.99

Table S137.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
CDC27 MUTATED 3 3 0
CDC27 WILD-TYPE 47 53 41
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.139 (Fisher's exact test), Q value = 0.79

Table S138.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
CDC27 MUTATED 5 1 0
CDC27 WILD-TYPE 63 37 41
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.168 (Fisher's exact test), Q value = 0.85

Table S139.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
CDC27 MUTATED 5 1 0
CDC27 WILD-TYPE 62 35 44
'CDC27 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.95

Table S140.  Gene #14: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
CDC27 MUTATED 1 4 0 0 1 0
CDC27 WILD-TYPE 32 31 19 27 18 14
'MLLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
MLLT3 MUTATED 3 0 1 0
MLLT3 WILD-TYPE 44 32 53 14
'MLLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.744 (Fisher's exact test), Q value = 1

Table S142.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
MLLT3 MUTATED 1 0 2 1
MLLT3 WILD-TYPE 42 20 32 49
'MLLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S143.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
MLLT3 MUTATED 1 0 2 0 0 1 0
MLLT3 WILD-TYPE 32 29 31 22 8 20 1
'MLLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 0.95

Table S144.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
MLLT3 MUTATED 1 0 0 0 1 1 1
MLLT3 WILD-TYPE 41 26 12 24 7 22 11
'MLLT3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S145.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
MLLT3 MUTATED 1 2 1
MLLT3 WILD-TYPE 49 54 40
'MLLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.585 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
MLLT3 MUTATED 1 2 1
MLLT3 WILD-TYPE 67 36 40
'MLLT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.467 (Fisher's exact test), Q value = 1

Table S147.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
MLLT3 MUTATED 1 2 1
MLLT3 WILD-TYPE 66 34 43
'MLLT3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.718 (Fisher's exact test), Q value = 1

Table S148.  Gene #15: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
MLLT3 MUTATED 1 0 1 1 1 0
MLLT3 WILD-TYPE 32 35 18 26 18 14
'ERC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.366 (Fisher's exact test), Q value = 0.99

Table S149.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
ERC1 MUTATED 2 1 2 2
ERC1 WILD-TYPE 45 31 52 12
'ERC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S150.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
ERC1 MUTATED 2 0 2 3
ERC1 WILD-TYPE 41 20 32 47
'ERC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.909 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
ERC1 MUTATED 2 0 1 2 1
ERC1 WILD-TYPE 42 8 9 34 17
'ERC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.862 (Fisher's exact test), Q value = 1

Table S152.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
ERC1 MUTATED 2 1 3
ERC1 WILD-TYPE 48 23 39
'ERC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S153.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
ERC1 MUTATED 2 1 1 1 1 1 0
ERC1 WILD-TYPE 31 28 32 21 7 20 1
'ERC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
ERC1 MUTATED 3 0 0 1 1 1 1
ERC1 WILD-TYPE 39 26 12 23 7 22 11
'ERC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S155.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
ERC1 MUTATED 2 3 2
ERC1 WILD-TYPE 48 53 39
'ERC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S156.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
ERC1 MUTATED 3 2 2
ERC1 WILD-TYPE 65 36 39
'ERC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S157.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
ERC1 MUTATED 3 2 2
ERC1 WILD-TYPE 64 34 42
'ERC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S158.  Gene #16: 'ERC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
ERC1 MUTATED 1 2 0 2 2 0
ERC1 WILD-TYPE 32 33 19 25 17 14
'MEF2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S159.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
MEF2A MUTATED 1 1 1 0
MEF2A WILD-TYPE 46 31 53 14
'MEF2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S160.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
MEF2A MUTATED 2 0 0 1
MEF2A WILD-TYPE 41 20 34 49
'MEF2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.766 (Fisher's exact test), Q value = 1

Table S161.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
MEF2A MUTATED 0 1 1 0 0 1 0
MEF2A WILD-TYPE 33 28 32 22 8 20 1
'MEF2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.328 (Fisher's exact test), Q value = 0.99

Table S162.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
MEF2A MUTATED 0 1 1 0 0 1 0
MEF2A WILD-TYPE 42 25 11 24 8 22 12
'MEF2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S163.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
MEF2A MUTATED 1 1 1
MEF2A WILD-TYPE 49 55 40
'MEF2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S164.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
MEF2A MUTATED 1 1 1
MEF2A WILD-TYPE 67 37 40
'MEF2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S165.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
MEF2A MUTATED 1 1 1
MEF2A WILD-TYPE 66 35 43
'MEF2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 0.99

Table S166.  Gene #17: 'MEF2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
MEF2A MUTATED 0 1 0 0 1 1
MEF2A WILD-TYPE 33 34 19 27 18 13
'SP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0354 (Fisher's exact test), Q value = 0.44

Table S167.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
SP8 MUTATED 0 0 5 1
SP8 WILD-TYPE 47 32 49 13

Figure S34.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.99

Table S168.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
SP8 MUTATED 0 1 2 3
SP8 WILD-TYPE 43 19 32 47
'SP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0765 (Fisher's exact test), Q value = 0.61

Table S169.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
SP8 MUTATED 0 0 1 4 0
SP8 WILD-TYPE 44 8 9 32 18
'SP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0216 (Fisher's exact test), Q value = 0.37

Table S170.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
SP8 MUTATED 0 3 2
SP8 WILD-TYPE 50 21 40

Figure S35.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.228 (Fisher's exact test), Q value = 0.93

Table S171.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
SP8 MUTATED 0 0 2 2 0 2 0
SP8 WILD-TYPE 33 29 31 20 8 19 1
'SP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00626 (Fisher's exact test), Q value = 0.16

Table S172.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
SP8 MUTATED 0 0 1 4 1 0 0
SP8 WILD-TYPE 42 26 11 20 7 23 12

Figure S36.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0487 (Fisher's exact test), Q value = 0.52

Table S173.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
SP8 MUTATED 0 2 4
SP8 WILD-TYPE 50 54 37

Figure S37.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0217 (Fisher's exact test), Q value = 0.37

Table S174.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
SP8 MUTATED 0 2 4
SP8 WILD-TYPE 68 36 37

Figure S38.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0243 (Fisher's exact test), Q value = 0.37

Table S175.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
SP8 MUTATED 0 2 4
SP8 WILD-TYPE 67 34 40

Figure S39.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.1 (Fisher's exact test), Q value = 0.66

Table S176.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
SP8 MUTATED 0 0 1 3 1 1
SP8 WILD-TYPE 33 35 18 24 18 13
'NAT10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.33 (Fisher's exact test), Q value = 0.99

Table S177.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
NAT10 MUTATED 0 2 2 0
NAT10 WILD-TYPE 47 30 52 14
'NAT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.822 (Fisher's exact test), Q value = 1

Table S178.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
NAT10 MUTATED 1 1 1 1
NAT10 WILD-TYPE 42 19 33 49
'NAT10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S179.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
NAT10 MUTATED 1 0 0 1 1
NAT10 WILD-TYPE 43 8 10 35 17
'NAT10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.595 (Fisher's exact test), Q value = 1

Table S180.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
NAT10 MUTATED 1 0 2
NAT10 WILD-TYPE 49 24 40
'NAT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.592 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
NAT10 MUTATED 0 2 1 0 0 1 0
NAT10 WILD-TYPE 33 27 32 22 8 20 1
'NAT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.259 (Fisher's exact test), Q value = 0.95

Table S182.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
NAT10 MUTATED 0 2 0 0 0 1 1
NAT10 WILD-TYPE 42 24 12 24 8 22 11
'NAT10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S183.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
NAT10 MUTATED 2 1 1
NAT10 WILD-TYPE 48 55 40
'NAT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S184.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
NAT10 MUTATED 2 1 1
NAT10 WILD-TYPE 66 37 40
'NAT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S185.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
NAT10 MUTATED 2 1 1
NAT10 WILD-TYPE 65 35 43
'NAT10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.651 (Fisher's exact test), Q value = 1

Table S186.  Gene #19: 'NAT10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
NAT10 MUTATED 0 2 1 1 0 0
NAT10 WILD-TYPE 33 33 18 26 19 14
'SPIN2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S187.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
SPIN2A MUTATED 0 1 2 0
SPIN2A WILD-TYPE 47 31 52 14
'SPIN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.508 (Fisher's exact test), Q value = 1

Table S188.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
SPIN2A MUTATED 0 1 1 1
SPIN2A WILD-TYPE 43 19 33 49
'SPIN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.504 (Fisher's exact test), Q value = 1

Table S189.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
SPIN2A MUTATED 0 1 0 1 0 1 0
SPIN2A WILD-TYPE 33 28 33 21 8 20 1
'SPIN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.99

Table S190.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
SPIN2A MUTATED 0 1 1 1 0 0 0
SPIN2A WILD-TYPE 42 25 11 23 8 23 12
'SPIN2A MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S191.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
SPIN2A MUTATED 1 1 1
SPIN2A WILD-TYPE 49 55 40
'SPIN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S192.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
SPIN2A MUTATED 1 1 1
SPIN2A WILD-TYPE 67 37 40
'SPIN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S193.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
SPIN2A MUTATED 1 1 1
SPIN2A WILD-TYPE 66 35 43
'SPIN2A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S194.  Gene #20: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
SPIN2A MUTATED 0 1 1 1 0 0
SPIN2A WILD-TYPE 33 34 18 26 19 14
'DEK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0633 (Fisher's exact test), Q value = 0.57

Table S195.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
DEK MUTATED 0 3 1 1
DEK WILD-TYPE 47 29 53 13
'DEK MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0197 (Fisher's exact test), Q value = 0.35

Table S196.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
DEK MUTATED 0 3 1 1
DEK WILD-TYPE 43 17 33 49

Figure S40.  Get High-res Image Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'DEK MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S197.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
DEK MUTATED 3 1 0 1 0
DEK WILD-TYPE 41 7 10 35 18
'DEK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.276 (Fisher's exact test), Q value = 0.95

Table S198.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
DEK MUTATED 4 0 1
DEK WILD-TYPE 46 24 41
'DEK MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0842 (Fisher's exact test), Q value = 0.63

Table S199.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
DEK MUTATED 0 4 1 0 0 0 0
DEK WILD-TYPE 33 25 32 22 8 21 1
'DEK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0181 (Fisher's exact test), Q value = 0.33

Table S200.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
DEK MUTATED 0 4 1 0 0 0 0
DEK WILD-TYPE 42 22 11 24 8 23 12

Figure S41.  Get High-res Image Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'DEK MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.376 (Fisher's exact test), Q value = 0.99

Table S201.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
DEK MUTATED 3 2 0
DEK WILD-TYPE 47 54 41
'DEK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.99

Table S202.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
DEK MUTATED 4 1 0
DEK WILD-TYPE 64 37 41
'DEK MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S203.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
DEK MUTATED 4 0 1
DEK WILD-TYPE 63 36 43
'DEK MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0784 (Fisher's exact test), Q value = 0.61

Table S204.  Gene #21: 'DEK MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
DEK MUTATED 0 4 1 0 0 0
DEK WILD-TYPE 33 31 18 27 19 14
'FANK1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S205.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
FANK1 MUTATED 0 2 1 1
FANK1 WILD-TYPE 47 30 53 13
'FANK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.743 (Fisher's exact test), Q value = 1

Table S206.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
FANK1 MUTATED 1 0 2 1
FANK1 WILD-TYPE 42 20 32 49
'FANK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 0.94

Table S207.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
FANK1 MUTATED 1 0 0 0 2
FANK1 WILD-TYPE 43 8 10 36 16
'FANK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S208.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
FANK1 MUTATED 1 0 2
FANK1 WILD-TYPE 49 24 40
'FANK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S209.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
FANK1 MUTATED 0 2 2 0 0 0 0
FANK1 WILD-TYPE 33 27 31 22 8 21 1
'FANK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.708 (Fisher's exact test), Q value = 1

Table S210.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
FANK1 MUTATED 1 1 0 0 0 2 0
FANK1 WILD-TYPE 41 25 12 24 8 21 12
'FANK1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S211.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
FANK1 MUTATED 1 3 0
FANK1 WILD-TYPE 49 53 41
'FANK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.282 (Fisher's exact test), Q value = 0.95

Table S212.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
FANK1 MUTATED 2 2 0
FANK1 WILD-TYPE 66 36 41
'FANK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 0.95

Table S213.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
FANK1 MUTATED 2 2 0
FANK1 WILD-TYPE 65 34 44
'FANK1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.434 (Fisher's exact test), Q value = 1

Table S214.  Gene #22: 'FANK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
FANK1 MUTATED 0 2 1 0 1 0
FANK1 WILD-TYPE 33 33 18 27 18 14
'ANKRD11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S215.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
ANKRD11 MUTATED 3 2 2 0
ANKRD11 WILD-TYPE 44 30 52 14
'ANKRD11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.283 (Fisher's exact test), Q value = 0.95

Table S216.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
ANKRD11 MUTATED 3 2 0 2
ANKRD11 WILD-TYPE 40 18 34 48
'ANKRD11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S217.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
ANKRD11 MUTATED 3 1 0 2 0
ANKRD11 WILD-TYPE 41 7 10 34 18
'ANKRD11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S218.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
ANKRD11 MUTATED 4 1 1
ANKRD11 WILD-TYPE 46 23 41
'ANKRD11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0374 (Fisher's exact test), Q value = 0.46

Table S219.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
ANKRD11 MUTATED 2 2 0 2 0 0 1
ANKRD11 WILD-TYPE 31 27 33 20 8 21 0

Figure S42.  Get High-res Image Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'ANKRD11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S220.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
ANKRD11 MUTATED 3 2 0 1 0 0 1
ANKRD11 WILD-TYPE 39 24 12 23 8 23 11
'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.99

Table S221.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
ANKRD11 MUTATED 4 1 2
ANKRD11 WILD-TYPE 46 55 39
'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.287 (Fisher's exact test), Q value = 0.95

Table S222.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
ANKRD11 MUTATED 5 0 2
ANKRD11 WILD-TYPE 63 38 39
'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.278 (Fisher's exact test), Q value = 0.95

Table S223.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
ANKRD11 MUTATED 5 0 2
ANKRD11 WILD-TYPE 62 36 42
'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S224.  Gene #23: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
ANKRD11 MUTATED 3 2 0 2 0 0
ANKRD11 WILD-TYPE 30 33 19 25 19 14
'C22ORF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0472 (Fisher's exact test), Q value = 0.52

Table S225.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
C22ORF43 MUTATED 0 2 0 1
C22ORF43 WILD-TYPE 47 30 54 13

Figure S43.  Get High-res Image Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'C22ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 1

Table S226.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
C22ORF43 MUTATED 0 1 1 1
C22ORF43 WILD-TYPE 43 19 33 49
'C22ORF43 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0512 (Fisher's exact test), Q value = 0.52

Table S227.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
C22ORF43 MUTATED 1 0 2 0 0
C22ORF43 WILD-TYPE 43 8 8 36 18
'C22ORF43 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S228.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 49 23 41
'C22ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.849 (Fisher's exact test), Q value = 1

Table S229.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
C22ORF43 MUTATED 0 1 1 1 0 0 0
C22ORF43 WILD-TYPE 33 28 32 21 8 21 1
'C22ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.736 (Fisher's exact test), Q value = 1

Table S230.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
C22ORF43 MUTATED 0 1 0 1 0 1 0
C22ORF43 WILD-TYPE 42 25 12 23 8 22 12
'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S231.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 49 55 40
'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S232.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 67 37 40
'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S233.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 66 35 43
'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S234.  Gene #24: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
C22ORF43 MUTATED 1 0 0 1 1 0
C22ORF43 WILD-TYPE 32 35 19 26 18 14
'ATXN3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S235.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
ATXN3 MUTATED 2 0 1 0
ATXN3 WILD-TYPE 45 32 53 14
'ATXN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S236.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
ATXN3 MUTATED 1 0 1 1
ATXN3 WILD-TYPE 42 20 33 49
'ATXN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.212 (Fisher's exact test), Q value = 0.9

Table S237.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
ATXN3 MUTATED 0 0 1 1 1
ATXN3 WILD-TYPE 44 8 9 35 17
'ATXN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0996 (Fisher's exact test), Q value = 0.66

Table S238.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 50 22 41
'ATXN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.428 (Fisher's exact test), Q value = 1

Table S239.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
ATXN3 MUTATED 0 0 2 1 0 0 0
ATXN3 WILD-TYPE 33 29 31 21 8 21 1
'ATXN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.181 (Fisher's exact test), Q value = 0.85

Table S240.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
ATXN3 MUTATED 0 0 0 1 1 1 0
ATXN3 WILD-TYPE 42 26 12 23 7 22 12
'ATXN3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S241.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 50 54 40
'ATXN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0915 (Fisher's exact test), Q value = 0.66

Table S242.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 68 36 40
'ATXN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0929 (Fisher's exact test), Q value = 0.66

Table S243.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 67 34 43
'ATXN3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.333 (Fisher's exact test), Q value = 0.99

Table S244.  Gene #25: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
ATXN3 MUTATED 0 0 1 1 1 0
ATXN3 WILD-TYPE 33 35 18 26 18 14
'TPTE2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S245.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
TPTE2 MUTATED 2 2 1 0
TPTE2 WILD-TYPE 45 30 53 14
'TPTE2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S246.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
TPTE2 MUTATED 2 0 0 3
TPTE2 WILD-TYPE 41 20 34 47
'TPTE2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S247.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
TPTE2 MUTATED 2 0 0 1 0
TPTE2 WILD-TYPE 42 8 10 35 18
'TPTE2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S248.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
TPTE2 MUTATED 2 0 1
TPTE2 WILD-TYPE 48 24 41
'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.439 (Fisher's exact test), Q value = 1

Table S249.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
TPTE2 MUTATED 3 1 0 1 0 0 0
TPTE2 WILD-TYPE 30 28 33 21 8 21 1
'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.633 (Fisher's exact test), Q value = 1

Table S250.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
TPTE2 MUTATED 3 1 0 0 0 0 1
TPTE2 WILD-TYPE 39 25 12 24 8 23 11
'TPTE2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0492 (Fisher's exact test), Q value = 0.52

Table S251.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
TPTE2 MUTATED 4 0 1
TPTE2 WILD-TYPE 46 56 40

Figure S44.  Get High-res Image Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'TPTE2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.99

Table S252.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
TPTE2 MUTATED 4 0 1
TPTE2 WILD-TYPE 64 38 40
'TPTE2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S253.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
TPTE2 MUTATED 4 0 1
TPTE2 WILD-TYPE 63 36 43
'TPTE2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S254.  Gene #26: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
TPTE2 MUTATED 2 2 0 1 0 0
TPTE2 WILD-TYPE 31 33 19 26 19 14
'KRTAP10-10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S255.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
KRTAP10-10 MUTATED 2 1 2 0
KRTAP10-10 WILD-TYPE 45 31 52 14
'KRTAP10-10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.457 (Fisher's exact test), Q value = 1

Table S256.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
KRTAP10-10 MUTATED 3 0 0 2
KRTAP10-10 WILD-TYPE 40 20 34 48
'KRTAP10-10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.761 (Fisher's exact test), Q value = 1

Table S257.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
KRTAP10-10 MUTATED 3 0 0 1 0
KRTAP10-10 WILD-TYPE 41 8 10 35 18
'KRTAP10-10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S258.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
KRTAP10-10 MUTATED 3 0 1
KRTAP10-10 WILD-TYPE 47 24 41
'KRTAP10-10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S259.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
KRTAP10-10 MUTATED 2 1 0 2 0 0 0
KRTAP10-10 WILD-TYPE 31 28 33 20 8 21 1
'KRTAP10-10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.872 (Fisher's exact test), Q value = 1

Table S260.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
KRTAP10-10 MUTATED 2 1 0 1 0 0 1
KRTAP10-10 WILD-TYPE 40 25 12 23 8 23 11
'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.158 (Fisher's exact test), Q value = 0.83

Table S261.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
KRTAP10-10 MUTATED 3 0 2
KRTAP10-10 WILD-TYPE 47 56 39
'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S262.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
KRTAP10-10 MUTATED 3 0 2
KRTAP10-10 WILD-TYPE 65 38 39
'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.603 (Fisher's exact test), Q value = 1

Table S263.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
KRTAP10-10 MUTATED 3 0 2
KRTAP10-10 WILD-TYPE 64 36 42
'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.85

Table S264.  Gene #27: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
KRTAP10-10 MUTATED 2 1 0 0 0 2
KRTAP10-10 WILD-TYPE 31 34 19 27 19 12
'ZNF680 MUTATION STATUS' versus 'CN_CNMF'

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

Table S265.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
ZNF680 MUTATED 1 1 0 1
ZNF680 WILD-TYPE 46 31 54 13
'ZNF680 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.671 (Fisher's exact test), Q value = 1

Table S266.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
ZNF680 MUTATED 1 1 0 1
ZNF680 WILD-TYPE 42 19 34 49
'ZNF680 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S267.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
ZNF680 MUTATED 3 0 0 0 0
ZNF680 WILD-TYPE 41 8 10 36 18
'ZNF680 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.93

Table S268.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
ZNF680 MUTATED 3 0 0
ZNF680 WILD-TYPE 47 24 42
'ZNF680 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S269.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
ZNF680 MUTATED 2 1 0 0 0 0 0
ZNF680 WILD-TYPE 31 28 33 22 8 21 1
'ZNF680 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S270.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
ZNF680 MUTATED 2 1 0 0 0 0 0
ZNF680 WILD-TYPE 40 25 12 24 8 23 12
'ZNF680 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0586 (Fisher's exact test), Q value = 0.54

Table S271.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
ZNF680 MUTATED 3 0 0
ZNF680 WILD-TYPE 47 56 41
'ZNF680 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.341 (Fisher's exact test), Q value = 0.99

Table S272.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
ZNF680 MUTATED 3 0 0
ZNF680 WILD-TYPE 65 38 41
'ZNF680 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.331 (Fisher's exact test), Q value = 0.99

Table S273.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
ZNF680 MUTATED 3 0 0
ZNF680 WILD-TYPE 64 36 44
'ZNF680 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S274.  Gene #28: 'ZNF680 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
ZNF680 MUTATED 2 1 0 0 0 0
ZNF680 WILD-TYPE 31 34 19 27 19 14
'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.702 (Fisher's exact test), Q value = 1

Table S275.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
RAC1 MUTATED 1 2 1 0
RAC1 WILD-TYPE 46 30 53 14
'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S276.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
RAC1 MUTATED 2 0 1 1
RAC1 WILD-TYPE 41 20 33 49
'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S277.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
RAC1 MUTATED 2 0 0 0 1
RAC1 WILD-TYPE 42 8 10 36 17
'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S278.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
RAC1 MUTATED 2 0 1
RAC1 WILD-TYPE 48 24 41
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.27 (Fisher's exact test), Q value = 0.95

Table S279.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
RAC1 MUTATED 2 0 1 0 1 0 0
RAC1 WILD-TYPE 31 29 32 22 7 21 1
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S280.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
RAC1 MUTATED 3 0 0 0 0 1 0
RAC1 WILD-TYPE 39 26 12 24 8 22 12
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.254 (Fisher's exact test), Q value = 0.95

Table S281.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
RAC1 MUTATED 3 1 0
RAC1 WILD-TYPE 47 55 41
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S282.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
RAC1 MUTATED 3 1 0
RAC1 WILD-TYPE 65 37 41
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.367 (Fisher's exact test), Q value = 0.99

Table S283.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
RAC1 MUTATED 3 1 0
RAC1 WILD-TYPE 64 35 44
'RAC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.177 (Fisher's exact test), Q value = 0.85

Table S284.  Gene #29: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
RAC1 MUTATED 3 0 0 0 1 0
RAC1 WILD-TYPE 30 35 19 27 18 14
'NBPF10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.23 (Fisher's exact test), Q value = 0.93

Table S285.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
NBPF10 MUTATED 5 1 1 0
NBPF10 WILD-TYPE 42 31 53 14
'NBPF10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S286.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
NBPF10 MUTATED 3 0 2 2
NBPF10 WILD-TYPE 40 20 32 48
'NBPF10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.784 (Fisher's exact test), Q value = 1

Table S287.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
NBPF10 MUTATED 2 0 1 1 1
NBPF10 WILD-TYPE 42 8 9 35 17
'NBPF10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S288.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
NBPF10 MUTATED 2 1 2
NBPF10 WILD-TYPE 48 23 40
'NBPF10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.93

Table S289.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
NBPF10 MUTATED 1 1 2 1 2 0 0
NBPF10 WILD-TYPE 32 28 31 21 6 21 1
'NBPF10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.233 (Fisher's exact test), Q value = 0.93

Table S290.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
NBPF10 MUTATED 1 1 1 1 2 1 0
NBPF10 WILD-TYPE 41 25 11 23 6 22 12
'NBPF10 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S291.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
NBPF10 MUTATED 1 4 2
NBPF10 WILD-TYPE 49 52 39
'NBPF10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.417 (Fisher's exact test), Q value = 1

Table S292.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
NBPF10 MUTATED 2 3 2
NBPF10 WILD-TYPE 66 35 39
'NBPF10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S293.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
NBPF10 MUTATED 2 3 2
NBPF10 WILD-TYPE 65 33 42
'NBPF10 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.95

Table S294.  Gene #30: 'NBPF10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
NBPF10 MUTATED 1 1 0 1 3 1
NBPF10 WILD-TYPE 32 34 19 26 16 13
'FAM8A1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S295.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
FAM8A1 MUTATED 2 1 0 0
FAM8A1 WILD-TYPE 45 31 54 14
'FAM8A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.759 (Fisher's exact test), Q value = 1

Table S296.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
FAM8A1 MUTATED 2 0 0 1
FAM8A1 WILD-TYPE 41 20 34 49
'FAM8A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0773 (Fisher's exact test), Q value = 0.61

Table S297.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
FAM8A1 MUTATED 2 0 0 0 1 0 0
FAM8A1 WILD-TYPE 31 29 33 22 7 21 1
'FAM8A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S298.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
FAM8A1 MUTATED 3 0 0 0 0 0 0
FAM8A1 WILD-TYPE 39 26 12 24 8 23 12
'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0579 (Fisher's exact test), Q value = 0.54

Table S299.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
FAM8A1 MUTATED 3 0 0
FAM8A1 WILD-TYPE 47 56 41
'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.344 (Fisher's exact test), Q value = 0.99

Table S300.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
FAM8A1 MUTATED 3 0 0
FAM8A1 WILD-TYPE 65 38 41
'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.333 (Fisher's exact test), Q value = 0.99

Table S301.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
FAM8A1 MUTATED 3 0 0
FAM8A1 WILD-TYPE 64 36 44
'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.68

Table S302.  Gene #31: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
FAM8A1 MUTATED 3 0 0 0 0 0
FAM8A1 WILD-TYPE 30 35 19 27 19 14
'PSMD11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0848 (Fisher's exact test), Q value = 0.63

Table S303.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
PSMD11 MUTATED 1 3 0 0
PSMD11 WILD-TYPE 46 29 54 14
'PSMD11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0767 (Fisher's exact test), Q value = 0.61

Table S304.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
PSMD11 MUTATED 3 1 0 0
PSMD11 WILD-TYPE 40 19 34 50
'PSMD11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.296 (Fisher's exact test), Q value = 0.96

Table S305.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
PSMD11 MUTATED 2 1 0 0 0
PSMD11 WILD-TYPE 42 7 10 36 18
'PSMD11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.232 (Fisher's exact test), Q value = 0.93

Table S306.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
PSMD11 MUTATED 3 0 0
PSMD11 WILD-TYPE 47 24 42
'PSMD11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 1

Table S307.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
PSMD11 MUTATED 2 2 0 0 0 0 0
PSMD11 WILD-TYPE 31 27 33 22 8 21 1
'PSMD11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S308.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
PSMD11 MUTATED 2 2 0 0 0 0 0
PSMD11 WILD-TYPE 40 24 12 24 8 23 12
'PSMD11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S309.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
PSMD11 MUTATED 2 2 0
PSMD11 WILD-TYPE 48 54 41
'PSMD11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.86

Table S310.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
PSMD11 MUTATED 4 0 0
PSMD11 WILD-TYPE 64 38 41
'PSMD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.365 (Fisher's exact test), Q value = 0.99

Table S311.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
PSMD11 MUTATED 3 1 0
PSMD11 WILD-TYPE 64 35 44
'PSMD11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S312.  Gene #32: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
PSMD11 MUTATED 2 2 0 0 0 0
PSMD11 WILD-TYPE 31 33 19 27 19 14
'KRTAP1-1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S313.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
KRTAP1-1 MUTATED 1 1 1 0
KRTAP1-1 WILD-TYPE 46 31 53 14
'KRTAP1-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S314.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
KRTAP1-1 MUTATED 2 0 1 0
KRTAP1-1 WILD-TYPE 41 20 33 50
'KRTAP1-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S315.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
KRTAP1-1 MUTATED 1 1 1 0 0 0 0
KRTAP1-1 WILD-TYPE 32 28 32 22 8 21 1
'KRTAP1-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.474 (Fisher's exact test), Q value = 1

Table S316.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
KRTAP1-1 MUTATED 2 0 1 0 0 0 0
KRTAP1-1 WILD-TYPE 40 26 11 24 8 23 12
'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S317.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
KRTAP1-1 MUTATED 1 2 0
KRTAP1-1 WILD-TYPE 49 54 41
'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S318.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
KRTAP1-1 MUTATED 2 1 0
KRTAP1-1 WILD-TYPE 66 37 41
'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S319.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
KRTAP1-1 MUTATED 2 1 0
KRTAP1-1 WILD-TYPE 65 35 44
'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.413 (Fisher's exact test), Q value = 1

Table S320.  Gene #33: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
KRTAP1-1 MUTATED 0 2 1 0 0 0
KRTAP1-1 WILD-TYPE 33 33 18 27 19 14
'OPLAH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.255 (Fisher's exact test), Q value = 0.95

Table S321.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
OPLAH MUTATED 2 2 0 0
OPLAH WILD-TYPE 45 30 54 14
'OPLAH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.99

Table S322.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
OPLAH MUTATED 3 0 0 1
OPLAH WILD-TYPE 40 20 34 49
'OPLAH MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S323.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
OPLAH MUTATED 1 0 1 1 0
OPLAH WILD-TYPE 43 8 9 35 18
'OPLAH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S324.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
OPLAH MUTATED 1 1 1
OPLAH WILD-TYPE 49 23 41
'OPLAH MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S325.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
OPLAH MUTATED 1 1 1 1 0 0 0
OPLAH WILD-TYPE 32 28 32 21 8 21 1
'OPLAH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.314 (Fisher's exact test), Q value = 0.99

Table S326.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
OPLAH MUTATED 1 1 1 0 1 0 0
OPLAH WILD-TYPE 41 25 11 24 7 23 12
'OPLAH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S327.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
OPLAH MUTATED 2 2 0
OPLAH WILD-TYPE 48 54 41
'OPLAH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.95

Table S328.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
OPLAH MUTATED 2 2 0
OPLAH WILD-TYPE 66 36 41
'OPLAH MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S329.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
OPLAH MUTATED 2 1 1
OPLAH WILD-TYPE 65 35 43
'OPLAH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S330.  Gene #34: 'OPLAH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
OPLAH MUTATED 1 1 1 0 1 0
OPLAH WILD-TYPE 32 34 18 27 18 14
'FAM101B MUTATION STATUS' versus 'CN_CNMF'

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

Table S331.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
FAM101B MUTATED 1 1 2 0
FAM101B WILD-TYPE 46 31 52 14
'FAM101B MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S332.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
FAM101B MUTATED 1 0 1 2
FAM101B WILD-TYPE 42 20 33 48
'FAM101B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S333.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
FAM101B MUTATED 2 0 0 1 0
FAM101B WILD-TYPE 42 8 10 35 18
'FAM101B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S334.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
FAM101B MUTATED 2 0 1
FAM101B WILD-TYPE 48 24 41
'FAM101B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S335.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
FAM101B MUTATED 0 2 1 1 0 0 0
FAM101B WILD-TYPE 33 27 32 21 8 21 1
'FAM101B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.496 (Fisher's exact test), Q value = 1

Table S336.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
FAM101B MUTATED 0 2 0 1 0 1 0
FAM101B WILD-TYPE 42 24 12 23 8 22 12
'FAM101B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S337.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
FAM101B MUTATED 1 2 1
FAM101B WILD-TYPE 49 54 40
'FAM101B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S338.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
FAM101B MUTATED 2 1 1
FAM101B WILD-TYPE 66 37 40
'FAM101B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S339.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
FAM101B MUTATED 2 1 1
FAM101B WILD-TYPE 65 35 43
'FAM101B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S340.  Gene #35: 'FAM101B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
FAM101B MUTATED 1 1 1 1 0 0
FAM101B WILD-TYPE 32 34 18 26 19 14
'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S341.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
MUC2 MUTATED 4 4 5 3
MUC2 WILD-TYPE 43 28 49 11
'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S342.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
MUC2 MUTATED 4 2 3 7
MUC2 WILD-TYPE 39 18 31 43
'MUC2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S343.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
MUC2 MUTATED 4 0 0 6 1
MUC2 WILD-TYPE 40 8 10 30 17
'MUC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.43 (Fisher's exact test), Q value = 1

Table S344.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
MUC2 MUTATED 4 4 3
MUC2 WILD-TYPE 46 20 39
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.34 (Fisher's exact test), Q value = 0.99

Table S345.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
MUC2 MUTATED 2 3 3 3 1 3 1
MUC2 WILD-TYPE 31 26 30 19 7 18 0
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S346.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
MUC2 MUTATED 4 3 1 3 1 2 2
MUC2 WILD-TYPE 38 23 11 21 7 21 10
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.499 (Fisher's exact test), Q value = 1

Table S347.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
MUC2 MUTATED 7 4 5
MUC2 WILD-TYPE 43 52 36
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.943 (Fisher's exact test), Q value = 1

Table S348.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
MUC2 MUTATED 7 4 5
MUC2 WILD-TYPE 61 34 36
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.791 (Fisher's exact test), Q value = 1

Table S349.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
MUC2 MUTATED 7 3 6
MUC2 WILD-TYPE 60 33 38
'MUC2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S350.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
MUC2 MUTATED 4 3 1 5 3 0
MUC2 WILD-TYPE 29 32 18 22 16 14
'HTT MUTATION STATUS' versus 'CN_CNMF'

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

Table S351.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
HTT MUTATED 1 1 1 0
HTT WILD-TYPE 46 31 53 14
'HTT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.383 (Fisher's exact test), Q value = 0.99

Table S352.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
HTT MUTATED 1 1 1 0
HTT WILD-TYPE 42 19 33 50
'HTT MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S353.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
HTT MUTATED 1 1 1 0 0 0 0
HTT WILD-TYPE 32 28 32 22 8 21 1
'HTT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S354.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
HTT MUTATED 1 1 1 0 0 0 0
HTT WILD-TYPE 41 25 11 24 8 23 12
'HTT MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S355.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
HTT MUTATED 2 1 0
HTT WILD-TYPE 48 55 41
'HTT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S356.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
HTT MUTATED 2 1 0
HTT WILD-TYPE 66 37 41
'HTT MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S357.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
HTT MUTATED 2 1 0
HTT WILD-TYPE 65 35 44
'HTT MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S358.  Gene #37: 'HTT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
HTT MUTATED 1 1 1 0 0 0
HTT WILD-TYPE 32 34 18 27 19 14
'EZH2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S359.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
EZH2 MUTATED 2 1 1 0
EZH2 WILD-TYPE 45 31 53 14
'EZH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.256 (Fisher's exact test), Q value = 0.95

Table S360.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
EZH2 MUTATED 2 0 2 0
EZH2 WILD-TYPE 41 20 32 50
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S361.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
EZH2 MUTATED 2 0 2 0 0 0 0
EZH2 WILD-TYPE 31 29 31 22 8 21 1
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S362.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
EZH2 MUTATED 2 0 0 0 0 2 0
EZH2 WILD-TYPE 40 26 12 24 8 21 12
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.557 (Fisher's exact test), Q value = 1

Table S363.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
EZH2 MUTATED 2 2 0
EZH2 WILD-TYPE 48 54 41
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.28 (Fisher's exact test), Q value = 0.95

Table S364.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
EZH2 MUTATED 2 2 0
EZH2 WILD-TYPE 66 36 41
'EZH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.274 (Fisher's exact test), Q value = 0.95

Table S365.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
EZH2 MUTATED 2 2 0
EZH2 WILD-TYPE 65 34 44
'EZH2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.375 (Fisher's exact test), Q value = 0.99

Table S366.  Gene #38: 'EZH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
EZH2 MUTATED 2 0 1 0 1 0
EZH2 WILD-TYPE 31 35 18 27 18 14
'PABPC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S367.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
PABPC3 MUTATED 2 1 1 0
PABPC3 WILD-TYPE 45 31 53 14
'PABPC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S368.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
PABPC3 MUTATED 1 0 0 3
PABPC3 WILD-TYPE 42 20 34 47
'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.236 (Fisher's exact test), Q value = 0.93

Table S369.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
PABPC3 MUTATED 1 0 0 1 1 1 0
PABPC3 WILD-TYPE 32 29 33 21 7 20 1
'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S370.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
PABPC3 MUTATED 2 0 0 1 0 0 1
PABPC3 WILD-TYPE 40 26 12 23 8 23 11
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.86

Table S371.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
PABPC3 MUTATED 2 0 2
PABPC3 WILD-TYPE 48 56 39
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 0.99

Table S372.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
PABPC3 MUTATED 2 0 2
PABPC3 WILD-TYPE 66 38 39
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S373.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
PABPC3 MUTATED 2 0 2
PABPC3 WILD-TYPE 65 36 42
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.361 (Fisher's exact test), Q value = 0.99

Table S374.  Gene #39: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
PABPC3 MUTATED 2 0 0 2 0 0
PABPC3 WILD-TYPE 31 35 19 25 19 14
'CUX1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.908 (Fisher's exact test), Q value = 1

Table S375.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
CUX1 MUTATED 1 1 3 0
CUX1 WILD-TYPE 46 31 51 14
'CUX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S376.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
CUX1 MUTATED 2 0 1 2
CUX1 WILD-TYPE 41 20 33 48
'CUX1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S377.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
CUX1 MUTATED 1 0 0 1 1
CUX1 WILD-TYPE 43 8 10 35 17
'CUX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S378.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
CUX1 MUTATED 1 0 2
CUX1 WILD-TYPE 49 24 40
'CUX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.469 (Fisher's exact test), Q value = 1

Table S379.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
CUX1 MUTATED 0 1 1 1 1 1 0
CUX1 WILD-TYPE 33 28 32 21 7 20 1
'CUX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S380.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
CUX1 MUTATED 1 1 0 1 0 1 1
CUX1 WILD-TYPE 41 25 12 23 8 22 11
'CUX1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S381.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
CUX1 MUTATED 2 1 2
CUX1 WILD-TYPE 48 55 39
'CUX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S382.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
CUX1 MUTATED 2 1 2
CUX1 WILD-TYPE 66 37 39
'CUX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.857 (Fisher's exact test), Q value = 1

Table S383.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
CUX1 MUTATED 2 1 2
CUX1 WILD-TYPE 65 35 42
'CUX1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S384.  Gene #40: 'CUX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
CUX1 MUTATED 1 1 1 2 0 0
CUX1 WILD-TYPE 32 34 18 25 19 14
'DLC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.445 (Fisher's exact test), Q value = 1

Table S385.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
DLC1 MUTATED 2 1 0 0
DLC1 WILD-TYPE 45 31 54 14
'DLC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S386.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
DLC1 MUTATED 1 0 1 1
DLC1 WILD-TYPE 42 20 33 49
'DLC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.641 (Fisher's exact test), Q value = 1

Table S387.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
DLC1 MUTATED 2 0 0 0 1
DLC1 WILD-TYPE 42 8 10 36 17
'DLC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S388.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
DLC1 MUTATED 2 0 1
DLC1 WILD-TYPE 48 24 41
'DLC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S389.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
DLC1 MUTATED 1 1 1 0 0 0 0
DLC1 WILD-TYPE 32 28 32 22 8 21 1
'DLC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S390.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
DLC1 MUTATED 1 1 0 0 0 1 0
DLC1 WILD-TYPE 41 25 12 24 8 22 12
'DLC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S391.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
DLC1 MUTATED 2 1 0
DLC1 WILD-TYPE 48 55 41
'DLC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S392.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
DLC1 MUTATED 2 1 0
DLC1 WILD-TYPE 66 37 41
'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S393.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
DLC1 MUTATED 2 1 0
DLC1 WILD-TYPE 65 35 44
'DLC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S394.  Gene #41: 'DLC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
DLC1 MUTATED 1 1 0 0 1 0
DLC1 WILD-TYPE 32 34 19 27 18 14
'STAB1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S395.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
STAB1 MUTATED 3 1 2 1
STAB1 WILD-TYPE 44 31 52 13
'STAB1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.79

Table S396.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
STAB1 MUTATED 3 1 3 0
STAB1 WILD-TYPE 40 19 31 50
'STAB1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.357 (Fisher's exact test), Q value = 0.99

Table S397.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
STAB1 MUTATED 2 0 1 0 1
STAB1 WILD-TYPE 42 8 9 36 17
'STAB1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S398.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
STAB1 MUTATED 2 1 1
STAB1 WILD-TYPE 48 23 41
'STAB1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.454 (Fisher's exact test), Q value = 1

Table S399.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
STAB1 MUTATED 2 1 3 0 1 0 0
STAB1 WILD-TYPE 31 28 30 22 7 21 1
'STAB1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S400.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
STAB1 MUTATED 3 1 0 0 0 3 0
STAB1 WILD-TYPE 39 25 12 24 8 20 12
'STAB1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 0.93

Table S401.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
STAB1 MUTATED 3 4 0
STAB1 WILD-TYPE 47 52 41
'STAB1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.196 (Fisher's exact test), Q value = 0.86

Table S402.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
STAB1 MUTATED 4 3 0
STAB1 WILD-TYPE 64 35 41
'STAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.124 (Fisher's exact test), Q value = 0.73

Table S403.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
STAB1 MUTATED 4 3 0
STAB1 WILD-TYPE 63 33 44
'STAB1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S404.  Gene #42: 'STAB1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
STAB1 MUTATED 2 2 2 0 1 0
STAB1 WILD-TYPE 31 33 17 27 18 14
'NOTCH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S405.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
NOTCH1 MUTATED 2 2 1 0
NOTCH1 WILD-TYPE 45 30 53 14
'NOTCH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S406.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
NOTCH1 MUTATED 2 1 1 1
NOTCH1 WILD-TYPE 41 19 33 49
'NOTCH1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.219 (Fisher's exact test), Q value = 0.92

Table S407.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
NOTCH1 MUTATED 2 1 1 0 1
NOTCH1 WILD-TYPE 42 7 9 36 17
'NOTCH1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S408.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
NOTCH1 MUTATED 3 1 1
NOTCH1 WILD-TYPE 47 23 41
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.7

Table S409.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
NOTCH1 MUTATED 0 3 1 0 1 0 0
NOTCH1 WILD-TYPE 33 26 32 22 7 21 1
'NOTCH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.448 (Fisher's exact test), Q value = 1

Table S410.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
NOTCH1 MUTATED 1 3 0 0 0 1 0
NOTCH1 WILD-TYPE 41 23 12 24 8 22 12
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 0.99

Table S411.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
NOTCH1 MUTATED 3 2 0
NOTCH1 WILD-TYPE 47 54 41
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 0.99

Table S412.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
NOTCH1 MUTATED 4 1 0
NOTCH1 WILD-TYPE 64 37 41
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.209 (Fisher's exact test), Q value = 0.89

Table S413.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
NOTCH1 MUTATED 4 1 0
NOTCH1 WILD-TYPE 63 35 44
'NOTCH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S414.  Gene #43: 'NOTCH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
NOTCH1 MUTATED 2 2 1 0 0 0
NOTCH1 WILD-TYPE 31 33 18 27 19 14
'AHDC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.783 (Fisher's exact test), Q value = 1

Table S415.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
AHDC1 MUTATED 2 0 2 0
AHDC1 WILD-TYPE 45 32 52 14
'AHDC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0509 (Fisher's exact test), Q value = 0.52

Table S416.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
AHDC1 MUTATED 0 0 0 4
AHDC1 WILD-TYPE 43 20 34 46
'AHDC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0333 (Fisher's exact test), Q value = 0.44

Table S417.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
AHDC1 MUTATED 0 0 2 2 0
AHDC1 WILD-TYPE 44 8 8 34 18

Figure S45.  Get High-res Image Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'AHDC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.69

Table S418.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
AHDC1 MUTATED 0 2 2
AHDC1 WILD-TYPE 50 22 40
'AHDC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0741 (Fisher's exact test), Q value = 0.61

Table S419.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
AHDC1 MUTATED 0 0 0 2 0 2 0
AHDC1 WILD-TYPE 33 29 33 20 8 19 1
'AHDC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0259 (Fisher's exact test), Q value = 0.38

Table S420.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
AHDC1 MUTATED 0 0 0 2 0 0 2
AHDC1 WILD-TYPE 42 26 12 22 8 23 10

Figure S46.  Get High-res Image Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00524 (Fisher's exact test), Q value = 0.15

Table S421.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
AHDC1 MUTATED 0 0 4
AHDC1 WILD-TYPE 50 56 37

Figure S47.  Get High-res Image Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00935 (Fisher's exact test), Q value = 0.22

Table S422.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
AHDC1 MUTATED 0 0 4
AHDC1 WILD-TYPE 68 38 37

Figure S48.  Get High-res Image Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0102 (Fisher's exact test), Q value = 0.22

Table S423.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
AHDC1 MUTATED 0 0 4
AHDC1 WILD-TYPE 67 36 40

Figure S49.  Get High-res Image Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00722 (Fisher's exact test), Q value = 0.18

Table S424.  Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
AHDC1 MUTATED 0 0 0 4 0 0
AHDC1 WILD-TYPE 33 35 19 23 19 14

Figure S50.  Get High-res Image Gene #44: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S425.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
EPAS1 MUTATED 2 0 3 0
EPAS1 WILD-TYPE 45 32 51 14
'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S426.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
EPAS1 MUTATED 2 0 1 2
EPAS1 WILD-TYPE 41 20 33 48
'EPAS1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S427.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
EPAS1 MUTATED 1 0 0 2 1
EPAS1 WILD-TYPE 43 8 10 34 17
'EPAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.68 (Fisher's exact test), Q value = 1

Table S428.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
EPAS1 MUTATED 1 1 2
EPAS1 WILD-TYPE 49 23 40
'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.484 (Fisher's exact test), Q value = 1

Table S429.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
EPAS1 MUTATED 2 0 1 0 0 2 0
EPAS1 WILD-TYPE 31 29 32 22 8 19 1
'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.789 (Fisher's exact test), Q value = 1

Table S430.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
EPAS1 MUTATED 2 0 0 1 0 1 1
EPAS1 WILD-TYPE 40 26 12 23 8 22 11
'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S431.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
EPAS1 MUTATED 2 1 2
EPAS1 WILD-TYPE 48 55 39
'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S432.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
EPAS1 MUTATED 2 1 2
EPAS1 WILD-TYPE 66 37 39
'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.86 (Fisher's exact test), Q value = 1

Table S433.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
EPAS1 MUTATED 2 1 2
EPAS1 WILD-TYPE 65 35 42
'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S434.  Gene #45: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
EPAS1 MUTATED 2 0 1 1 0 1
EPAS1 WILD-TYPE 31 35 18 26 19 13
'PIK3CD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0477 (Fisher's exact test), Q value = 0.52

Table S435.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
PIK3CD MUTATED 4 0 0 0
PIK3CD WILD-TYPE 43 32 54 14

Figure S51.  Get High-res Image Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PIK3CD MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 0.99

Table S436.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
PIK3CD MUTATED 3 0 0 1
PIK3CD WILD-TYPE 40 20 34 49
'PIK3CD MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S437.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
PIK3CD MUTATED 3 0 0 0 0 1 0
PIK3CD WILD-TYPE 30 29 33 22 8 20 1
'PIK3CD MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.372 (Fisher's exact test), Q value = 0.99

Table S438.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
PIK3CD MUTATED 3 0 0 0 0 0 1
PIK3CD WILD-TYPE 39 26 12 24 8 23 11
'PIK3CD MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.141 (Fisher's exact test), Q value = 0.79

Table S439.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
PIK3CD MUTATED 3 0 1
PIK3CD WILD-TYPE 47 56 40
'PIK3CD MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S440.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
PIK3CD MUTATED 3 0 1
PIK3CD WILD-TYPE 65 38 40
'PIK3CD MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S441.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
PIK3CD MUTATED 3 0 1
PIK3CD WILD-TYPE 64 36 43
'PIK3CD MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.256 (Fisher's exact test), Q value = 0.95

Table S442.  Gene #46: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
PIK3CD MUTATED 3 0 0 1 0 0
PIK3CD WILD-TYPE 30 35 19 26 19 14
'BCL11B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0985 (Fisher's exact test), Q value = 0.66

Table S443.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
BCL11B MUTATED 2 3 0 0
BCL11B WILD-TYPE 45 29 54 14
'BCL11B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S444.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
BCL11B MUTATED 2 1 0 2
BCL11B WILD-TYPE 41 19 34 48
'BCL11B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.527 (Fisher's exact test), Q value = 1

Table S445.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
BCL11B MUTATED 2 1 0 1 0
BCL11B WILD-TYPE 42 7 10 35 18
'BCL11B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S446.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
BCL11B MUTATED 3 0 1
BCL11B WILD-TYPE 47 24 41
'BCL11B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.436 (Fisher's exact test), Q value = 1

Table S447.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
BCL11B MUTATED 3 1 0 1 0 0 0
BCL11B WILD-TYPE 30 28 33 21 8 21 1
'BCL11B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S448.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
BCL11B MUTATED 3 1 0 1 0 0 0
BCL11B WILD-TYPE 39 25 12 23 8 23 12
'BCL11B MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S449.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
BCL11B MUTATED 3 1 1
BCL11B WILD-TYPE 47 55 40
'BCL11B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.383 (Fisher's exact test), Q value = 0.99

Table S450.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
BCL11B MUTATED 4 0 1
BCL11B WILD-TYPE 64 38 40
'BCL11B MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S451.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
BCL11B MUTATED 4 0 1
BCL11B WILD-TYPE 63 36 43
'BCL11B MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.719 (Fisher's exact test), Q value = 1

Table S452.  Gene #47: 'BCL11B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
BCL11B MUTATED 1 3 0 1 0 0
BCL11B WILD-TYPE 32 32 19 26 19 14
'KIAA0430 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.442 (Fisher's exact test), Q value = 1

Table S453.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
KIAA0430 MUTATED 2 1 0 0
KIAA0430 WILD-TYPE 45 31 54 14
'KIAA0430 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.107 (Fisher's exact test), Q value = 0.69

Table S454.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
KIAA0430 MUTATED 3 0 0 0
KIAA0430 WILD-TYPE 40 20 34 50
'KIAA0430 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S455.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
KIAA0430 MUTATED 2 0 1 0 0 0 0
KIAA0430 WILD-TYPE 31 29 32 22 8 21 1
'KIAA0430 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S456.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
KIAA0430 MUTATED 2 0 0 0 0 1 0
KIAA0430 WILD-TYPE 40 26 12 24 8 22 12
'KIAA0430 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.631 (Fisher's exact test), Q value = 1

Table S457.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
KIAA0430 MUTATED 2 1 0
KIAA0430 WILD-TYPE 48 55 41
'KIAA0430 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S458.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
KIAA0430 MUTATED 2 1 0
KIAA0430 WILD-TYPE 66 37 41
'KIAA0430 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S459.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
KIAA0430 MUTATED 2 1 0
KIAA0430 WILD-TYPE 65 35 44
'KIAA0430 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.941 (Fisher's exact test), Q value = 1

Table S460.  Gene #48: 'KIAA0430 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
KIAA0430 MUTATED 1 1 0 0 1 0
KIAA0430 WILD-TYPE 32 34 19 27 18 14
'MTIF3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S461.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
MTIF3 MUTATED 1 1 1 0
MTIF3 WILD-TYPE 46 31 53 14
'MTIF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S462.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
MTIF3 MUTATED 1 0 0 2
MTIF3 WILD-TYPE 42 20 34 48
'MTIF3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S463.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
MTIF3 MUTATED 2 0 0 1 0
MTIF3 WILD-TYPE 42 8 10 35 18
'MTIF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S464.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
MTIF3 MUTATED 2 0 1
MTIF3 WILD-TYPE 48 24 41
'MTIF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S465.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
MTIF3 MUTATED 1 1 0 1 0 0 0
MTIF3 WILD-TYPE 32 28 33 21 8 21 1
'MTIF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S466.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
MTIF3 MUTATED 1 1 0 1 0 0 0
MTIF3 WILD-TYPE 41 25 12 23 8 23 12
'MTIF3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.99

Table S467.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
MTIF3 MUTATED 2 0 1
MTIF3 WILD-TYPE 48 56 40
'MTIF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S468.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
MTIF3 MUTATED 2 0 1
MTIF3 WILD-TYPE 66 38 40
'MTIF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S469.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
MTIF3 MUTATED 2 0 1
MTIF3 WILD-TYPE 65 36 43
'MTIF3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S470.  Gene #49: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
MTIF3 MUTATED 1 1 0 1 0 0
MTIF3 WILD-TYPE 32 34 19 26 19 14
'BTN2A2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.446 (Fisher's exact test), Q value = 1

Table S471.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
BTN2A2 MUTATED 2 1 0 0
BTN2A2 WILD-TYPE 45 31 54 14
'BTN2A2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S472.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
BTN2A2 MUTATED 2 0 0 1
BTN2A2 WILD-TYPE 41 20 34 49
'BTN2A2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.179 (Fisher's exact test), Q value = 0.85

Table S473.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
BTN2A2 MUTATED 1 0 0 1 1 0 0
BTN2A2 WILD-TYPE 32 29 33 21 7 21 1
'BTN2A2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.812 (Fisher's exact test), Q value = 1

Table S474.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
BTN2A2 MUTATED 2 0 0 1 0 0 0
BTN2A2 WILD-TYPE 40 26 12 23 8 23 12
'BTN2A2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 0.99

Table S475.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
BTN2A2 MUTATED 2 0 1
BTN2A2 WILD-TYPE 48 56 40
'BTN2A2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S476.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
BTN2A2 MUTATED 2 0 1
BTN2A2 WILD-TYPE 66 38 40
'BTN2A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.795 (Fisher's exact test), Q value = 1

Table S477.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
BTN2A2 MUTATED 2 0 1
BTN2A2 WILD-TYPE 65 36 43
'BTN2A2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.646 (Fisher's exact test), Q value = 1

Table S478.  Gene #50: 'BTN2A2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
BTN2A2 MUTATED 1 1 0 0 0 1
BTN2A2 WILD-TYPE 32 34 19 27 19 13
'C17ORF64 MUTATION STATUS' versus 'CN_CNMF'

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

Table S479.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
C17ORF64 MUTATED 1 0 2 0
C17ORF64 WILD-TYPE 46 32 52 14
'C17ORF64 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S480.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
C17ORF64 MUTATED 1 0 0 2
C17ORF64 WILD-TYPE 42 20 34 48
'C17ORF64 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S481.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
C17ORF64 MUTATED 0 1 1 1 0 0 0
C17ORF64 WILD-TYPE 33 28 32 21 8 21 1
'C17ORF64 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.37 (Fisher's exact test), Q value = 0.99

Table S482.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
C17ORF64 MUTATED 0 1 1 1 0 0 0
C17ORF64 WILD-TYPE 42 25 11 23 8 23 12
'C17ORF64 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S483.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
C17ORF64 MUTATED 1 1 1
C17ORF64 WILD-TYPE 49 55 40
'C17ORF64 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S484.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
C17ORF64 MUTATED 1 1 1
C17ORF64 WILD-TYPE 67 37 40
'C17ORF64 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S485.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
C17ORF64 MUTATED 1 0 2
C17ORF64 WILD-TYPE 66 36 42
'C17ORF64 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.558 (Fisher's exact test), Q value = 1

Table S486.  Gene #51: 'C17ORF64 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
C17ORF64 MUTATED 0 1 0 1 0 1
C17ORF64 WILD-TYPE 33 34 19 26 19 13
'RUNX2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.329 (Fisher's exact test), Q value = 0.99

Table S487.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
RUNX2 MUTATED 0 2 2 0
RUNX2 WILD-TYPE 47 30 52 14
'RUNX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S488.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
RUNX2 MUTATED 1 0 1 2
RUNX2 WILD-TYPE 42 20 33 48
'RUNX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.864 (Fisher's exact test), Q value = 1

Table S489.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
RUNX2 MUTATED 1 0 0 1 1
RUNX2 WILD-TYPE 43 8 10 35 17
'RUNX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S490.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
RUNX2 MUTATED 1 0 2
RUNX2 WILD-TYPE 49 24 40
'RUNX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S491.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
RUNX2 MUTATED 1 1 1 1 0 0 0
RUNX2 WILD-TYPE 32 28 32 21 8 21 1
'RUNX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S492.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
RUNX2 MUTATED 1 1 0 1 0 1 0
RUNX2 WILD-TYPE 41 25 12 23 8 22 12
'RUNX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S493.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
RUNX2 MUTATED 2 1 1
RUNX2 WILD-TYPE 48 55 40
'RUNX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S494.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
RUNX2 MUTATED 2 1 1
RUNX2 WILD-TYPE 66 37 40
'RUNX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S495.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
RUNX2 MUTATED 2 1 1
RUNX2 WILD-TYPE 65 35 43
'RUNX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S496.  Gene #52: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
RUNX2 MUTATED 0 2 1 1 0 0
RUNX2 WILD-TYPE 33 33 18 26 19 14
'SSBP3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S497.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
SSBP3 MUTATED 1 0 2 0
SSBP3 WILD-TYPE 46 32 52 14
'SSBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S498.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
SSBP3 MUTATED 1 0 1 1
SSBP3 WILD-TYPE 42 20 33 49
'SSBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.385 (Fisher's exact test), Q value = 0.99

Table S499.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
SSBP3 MUTATED 0 0 2 0 0 1 0
SSBP3 WILD-TYPE 33 29 31 22 8 20 1
'SSBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0591 (Fisher's exact test), Q value = 0.54

Table S500.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
SSBP3 MUTATED 0 0 0 0 1 1 1
SSBP3 WILD-TYPE 42 26 12 24 7 22 11
'SSBP3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.497 (Fisher's exact test), Q value = 1

Table S501.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
SSBP3 MUTATED 0 2 1
SSBP3 WILD-TYPE 50 54 40
'SSBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0928 (Fisher's exact test), Q value = 0.66

Table S502.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
SSBP3 MUTATED 0 2 1
SSBP3 WILD-TYPE 68 36 40
'SSBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0929 (Fisher's exact test), Q value = 0.66

Table S503.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
SSBP3 MUTATED 0 2 1
SSBP3 WILD-TYPE 67 34 43
'SSBP3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0728 (Fisher's exact test), Q value = 0.6

Table S504.  Gene #53: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
SSBP3 MUTATED 0 0 0 1 2 0
SSBP3 WILD-TYPE 33 35 19 26 17 14
'GSX2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.152 (Fisher's exact test), Q value = 0.81

Table S505.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
GSX2 MUTATED 0 0 3 1
GSX2 WILD-TYPE 47 32 51 13
'GSX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.468 (Fisher's exact test), Q value = 1

Table S506.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
GSX2 MUTATED 0 1 1 2
GSX2 WILD-TYPE 43 19 33 48
'GSX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.647 (Fisher's exact test), Q value = 1

Table S507.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
GSX2 MUTATED 1 0 0 3 0
GSX2 WILD-TYPE 43 8 10 33 18
'GSX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.38

Table S508.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
GSX2 MUTATED 1 3 0
GSX2 WILD-TYPE 49 21 42

Figure S52.  Get High-res Image Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'GSX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0533 (Fisher's exact test), Q value = 0.52

Table S509.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
GSX2 MUTATED 0 1 0 0 0 3 0
GSX2 WILD-TYPE 33 28 33 22 8 18 1
'GSX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 0.95

Table S510.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
GSX2 MUTATED 0 1 1 2 0 0 0
GSX2 WILD-TYPE 42 25 11 22 8 23 12
'GSX2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0656 (Fisher's exact test), Q value = 0.58

Table S511.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
GSX2 MUTATED 1 0 3
GSX2 WILD-TYPE 49 56 38
'GSX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.15 (Fisher's exact test), Q value = 0.81

Table S512.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
GSX2 MUTATED 1 0 3
GSX2 WILD-TYPE 67 38 38
'GSX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S513.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
GSX2 MUTATED 1 1 2
GSX2 WILD-TYPE 66 35 42
'GSX2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.561 (Fisher's exact test), Q value = 1

Table S514.  Gene #54: 'GSX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
GSX2 MUTATED 0 1 1 1 0 1
GSX2 WILD-TYPE 33 34 18 26 19 13
'SP4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.153 (Fisher's exact test), Q value = 0.81

Table S515.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
SP4 MUTATED 0 0 3 1
SP4 WILD-TYPE 47 32 51 13
'SP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.121 (Fisher's exact test), Q value = 0.72

Table S516.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
SP4 MUTATED 0 0 3 1
SP4 WILD-TYPE 43 20 31 49
'SP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.171 (Fisher's exact test), Q value = 0.85

Table S517.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
SP4 MUTATED 0 0 2 0 0 2 0
SP4 WILD-TYPE 33 29 31 22 8 19 1
'SP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.69

Table S518.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
SP4 MUTATED 0 0 1 1 1 1 0
SP4 WILD-TYPE 42 26 11 23 7 22 12
'SP4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.316 (Fisher's exact test), Q value = 0.99

Table S519.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
SP4 MUTATED 0 3 1
SP4 WILD-TYPE 50 53 40
'SP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0275 (Fisher's exact test), Q value = 0.38

Table S520.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
SP4 MUTATED 0 3 1
SP4 WILD-TYPE 68 35 40

Figure S53.  Get High-res Image Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0276 (Fisher's exact test), Q value = 0.38

Table S521.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
SP4 MUTATED 0 3 1
SP4 WILD-TYPE 67 33 43

Figure S54.  Get High-res Image Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.118 (Fisher's exact test), Q value = 0.71

Table S522.  Gene #55: 'SP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
SP4 MUTATED 0 0 2 1 1 0
SP4 WILD-TYPE 33 35 17 26 18 14
'PCMTD1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S523.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
PCMTD1 MUTATED 2 2 0 1
PCMTD1 WILD-TYPE 45 30 54 13
'PCMTD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.118 (Fisher's exact test), Q value = 0.71

Table S524.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
PCMTD1 MUTATED 2 2 1 0
PCMTD1 WILD-TYPE 41 18 33 50
'PCMTD1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.453 (Fisher's exact test), Q value = 1

Table S525.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
PCMTD1 MUTATED 3 0 0 0 1
PCMTD1 WILD-TYPE 41 8 10 36 17
'PCMTD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S526.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
PCMTD1 MUTATED 3 0 1
PCMTD1 WILD-TYPE 47 24 41
'PCMTD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S527.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
PCMTD1 MUTATED 1 3 1 0 0 0 0
PCMTD1 WILD-TYPE 32 26 32 22 8 21 1
'PCMTD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.444 (Fisher's exact test), Q value = 1

Table S528.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
PCMTD1 MUTATED 1 3 0 0 0 1 0
PCMTD1 WILD-TYPE 41 23 12 24 8 22 12
'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 0.99

Table S529.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
PCMTD1 MUTATED 3 2 0
PCMTD1 WILD-TYPE 47 54 41
'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.318 (Fisher's exact test), Q value = 0.99

Table S530.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
PCMTD1 MUTATED 4 1 0
PCMTD1 WILD-TYPE 64 37 41
'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.207 (Fisher's exact test), Q value = 0.89

Table S531.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
PCMTD1 MUTATED 4 1 0
PCMTD1 WILD-TYPE 63 35 44
'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.551 (Fisher's exact test), Q value = 1

Table S532.  Gene #56: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
PCMTD1 MUTATED 1 3 0 0 1 0
PCMTD1 WILD-TYPE 32 32 19 27 18 14
'RBM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00629 (Fisher's exact test), Q value = 0.16

Table S533.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
RBM3 MUTATED 0 1 0 2
RBM3 WILD-TYPE 47 31 54 12

Figure S55.  Get High-res Image Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'RBM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 0.99

Table S534.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
RBM3 MUTATED 1 1 1 0
RBM3 WILD-TYPE 42 19 33 50
'RBM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S535.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
RBM3 MUTATED 1 1 1 0 0 0 0
RBM3 WILD-TYPE 32 28 32 22 8 21 1
'RBM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.948 (Fisher's exact test), Q value = 1

Table S536.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
RBM3 MUTATED 1 1 0 0 0 1 0
RBM3 WILD-TYPE 41 25 12 24 8 22 12
'RBM3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.112 (Fisher's exact test), Q value = 0.69

Table S537.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
RBM3 MUTATED 0 3 0
RBM3 WILD-TYPE 50 53 41
'RBM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S538.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
RBM3 MUTATED 2 1 0
RBM3 WILD-TYPE 66 37 41
'RBM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S539.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
RBM3 MUTATED 2 1 0
RBM3 WILD-TYPE 65 35 44
'RBM3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.412 (Fisher's exact test), Q value = 1

Table S540.  Gene #57: 'RBM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
RBM3 MUTATED 0 2 0 0 1 0
RBM3 WILD-TYPE 33 33 19 27 18 14
'ZNF814 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.135 (Fisher's exact test), Q value = 0.78

Table S541.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
ZNF814 MUTATED 0 3 2 0
ZNF814 WILD-TYPE 47 29 52 14
'ZNF814 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 1

Table S542.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
ZNF814 MUTATED 1 2 1 1
ZNF814 WILD-TYPE 42 18 33 49
'ZNF814 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S543.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
ZNF814 MUTATED 3 0 0 1 1
ZNF814 WILD-TYPE 41 8 10 35 17
'ZNF814 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S544.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
ZNF814 MUTATED 3 1 1
ZNF814 WILD-TYPE 47 23 41
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.301 (Fisher's exact test), Q value = 0.96

Table S545.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
ZNF814 MUTATED 0 3 1 0 0 1 0
ZNF814 WILD-TYPE 33 26 32 22 8 20 1
'ZNF814 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.258 (Fisher's exact test), Q value = 0.95

Table S546.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
ZNF814 MUTATED 0 3 0 1 0 1 0
ZNF814 WILD-TYPE 42 23 12 23 8 22 12
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S547.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
ZNF814 MUTATED 1 3 1
ZNF814 WILD-TYPE 49 53 40
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S548.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
ZNF814 MUTATED 3 1 1
ZNF814 WILD-TYPE 65 37 40
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S549.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
ZNF814 MUTATED 3 1 1
ZNF814 WILD-TYPE 64 35 43
'ZNF814 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.452 (Fisher's exact test), Q value = 1

Table S550.  Gene #58: 'ZNF814 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
ZNF814 MUTATED 0 3 1 1 0 0
ZNF814 WILD-TYPE 33 32 18 26 19 14
'TTC38 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.288 (Fisher's exact test), Q value = 0.95

Table S551.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 32 54 14
TTC38 MUTATED 0 1 2 1
TTC38 WILD-TYPE 47 31 52 13
'TTC38 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S552.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 43 20 34 50
TTC38 MUTATED 1 0 0 3
TTC38 WILD-TYPE 42 20 34 47
'TTC38 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S553.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5
ALL 44 8 10 36 18
TTC38 MUTATED 2 0 0 2 0
TTC38 WILD-TYPE 42 8 10 34 18
'TTC38 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.194 (Fisher's exact test), Q value = 0.86

Table S554.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 24 42
TTC38 MUTATED 2 2 0
TTC38 WILD-TYPE 48 22 42
'TTC38 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.435 (Fisher's exact test), Q value = 1

Table S555.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 33 29 33 22 8 21 1
TTC38 MUTATED 1 1 0 0 0 2 0
TTC38 WILD-TYPE 32 28 33 22 8 19 1
'TTC38 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S556.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6 CLUS_7
ALL 42 26 12 24 8 23 12
TTC38 MUTATED 1 1 0 2 0 0 0
TTC38 WILD-TYPE 41 25 12 22 8 23 12
'TTC38 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.195 (Fisher's exact test), Q value = 0.86

Table S557.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 50 56 41
TTC38 MUTATED 2 0 2
TTC38 WILD-TYPE 48 56 39
'TTC38 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 0.99

Table S558.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
TTC38 MUTATED 2 0 2
TTC38 WILD-TYPE 66 38 39
'TTC38 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S559.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
TTC38 MUTATED 2 0 2
TTC38 WILD-TYPE 65 36 42
'TTC38 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0454 (Fisher's exact test), Q value = 0.52

Table S560.  Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4 CLUS_5 CLUS_6
ALL 33 35 19 27 19 14
TTC38 MUTATED 0 2 0 0 0 2
TTC38 WILD-TYPE 33 33 19 27 19 12

Figure S56.  Get High-res Image Gene #59: 'TTC38 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

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/TGCT-TP/22570895/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/22541961/TGCT-TP.transferedmergedcluster.txt

  • Number of patients = 147

  • Number of significantly mutated genes = 59

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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