Correlation between gene mutation status and molecular subtypes
Testicular Germ Cell Tumors (Primary solid tumor)
02 April 2015  |  analyses__2015_04_02
Maintainer Information
Citation Information
doi:10.7908/C1S46R2V
Maintained by TCGA GDAC Team (Broad Institute/MD Anderson Cancer Center/Harvard Medical School)
Cite as Broad Institute TCGA Genome Data Analysis Center (2015): Correlation between gene mutation status and molecular subtypes. Broad Institute of MIT and Harvard. doi:10.7908/C1S46R2V
Overview
Introduction

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

Summary

Testing the association between mutation status of 63 genes and 10 molecular subtypes across 147 patients, 42 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 'CN_CNMF',  'RPPA_CNMF',  'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL', and 'MIRSEQ_CHIERARCHICAL'.

  • NRAS mutation correlated to 'MRNASEQ_CNMF',  'MIRSEQ_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

  • SP8 mutation correlated to 'MRNASEQ_CNMF' and 'MRNASEQ_CHIERARCHICAL'.

  • SPTAN1 mutation correlated to 'MRNASEQ_CNMF',  'MRNASEQ_CHIERARCHICAL',  'MIRSEQ_CNMF',  'MIRSEQ_CHIERARCHICAL',  'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

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

Results
Overview of the results

Table 1.  Get Full Table Overview of the association between mutation status of 63 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, 42 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 0.0017
(0.063) 		0.00012
(0.0054) 		1e-05
(0.000573) 		1e-05
(0.000573) 		1e-05
(0.000573) 		1e-05
(0.000573) 		1e-05
(0.000573) 		1e-05
(0.000573) 		1e-05
(0.000573) 		1e-05
(0.000573)
KRAS 19 (13%) 128 0.00631
(0.166) 		0.00032
(0.0126) 		0.00308
(0.102) 		0.00019
(0.00798) 		1e-05
(0.000573) 		0.00181
(0.0633) 		2e-05
(0.000969) 		1e-05
(0.000573) 		1e-05
(0.000573) 		2e-05
(0.000969)
SPTAN1 4 (3%) 143 0.0384
(0.397) 		0.323
(1.00) 		0.00444
(0.133) 		0.0095
(0.194) 		0.00486
(0.136) 		0.00939
(0.194) 		0.0106
(0.202) 		0.0146
(0.236)
AHDC1 4 (3%) 143 0.56
(1.00) 		0.00792
(0.192) 		0.0619
(0.527) 		0.108
(0.689) 		0.00412
(0.13) 		0.0268
(0.315) 		0.00496
(0.136) 		0.00955
(0.194) 		0.0102
(0.202) 		0.0143
(0.236)
CSGALNACT2 5 (3%) 142 0.013
(0.227) 		0.194
(0.925) 		0.00875
(0.194) 		0.0229
(0.304) 		0.00865
(0.194) 		0.0115
(0.213) 		0.0309
(0.341) 		0.0162
(0.249) 		0.0247
(0.305) 		0.0779
(0.613)
NRAS 7 (5%) 140 0.0504
(0.475) 		0.0798
(0.621) 		0.0973
(0.652) 		0.275
(1.00) 		0.0166
(0.249) 		0.145
(0.814) 		0.013
(0.227) 		0.0179
(0.258) 		0.0691
(0.558) 		0.0133
(0.227)
SP8 6 (4%) 141 0.0897
(0.643) 		0.517
(1.00) 		0.0308
(0.341) 		0.0237
(0.304) 		0.0157
(0.247) 		0.00676
(0.17) 		0.0481
(0.475) 		0.0214
(0.293) 		0.0241
(0.304) 		0.0839
(0.633)
ANKLE1 12 (8%) 135 0.154
(0.828) 		0.287
(1.00) 		0.869
(1.00) 		0.363
(1.00) 		0.637
(1.00) 		0.876
(1.00) 		1
(1.00) 		0.74
(1.00) 		0.739
(1.00) 		0.421
(1.00)
FAM104B 7 (5%) 140 0.377
(1.00) 		0.502
(1.00) 		0.382
(1.00) 		0.617
(1.00) 		0.353
(1.00) 		0.264
(1.00) 		0.0973
(0.652) 		0.25
(1.00) 		0.54
(1.00) 		0.545
(1.00)
DDX11 8 (5%) 139 1
(1.00) 		0.279
(1.00) 		0.279
(1.00) 		0.145
(0.814) 		0.408
(1.00) 		0.363
(1.00) 		0.132
(0.791) 		0.291
(1.00) 		0.652
(1.00) 		0.101
(0.67)
PNPLA4 5 (3%) 142 0.521
(1.00) 		1
(1.00) 		0.378
(1.00) 		0.616
(1.00) 		0.522
(1.00) 		0.553
(1.00) 		0.374
(1.00) 		0.449
(1.00) 		0.318
(1.00) 		0.476
(1.00)
SERINC2 4 (3%) 143 0.462
(1.00) 		0.834
(1.00) 		0.139
(0.807) 		0.103
(0.67) 		0.811
(1.00) 		0.738
(1.00) 		1
(1.00) 		0.585
(1.00) 		0.812
(1.00) 		0.843
(1.00)
RBM10 5 (3%) 142 0.621
(1.00) 		0.277
(1.00) 		0.92
(1.00) 		0.724
(1.00) 		0.45
(1.00) 		0.709
(1.00) 		0.634
(1.00) 		0.598
(1.00) 		0.604
(1.00) 		0.555
(1.00)
DEK 5 (3%) 142 0.0359
(0.384) 		0.865
(1.00) 		0.622
(1.00) 		0.275
(1.00) 		0.381
(1.00) 		0.0184
(0.258) 		0.376
(1.00) 		0.319
(1.00) 		0.441
(1.00) 		0.157
(0.84)
ERC1 7 (5%) 140 0.886
(1.00) 		0.796
(1.00) 		0.607
(1.00) 		0.865
(1.00) 		1
(1.00) 		0.561
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.954
(1.00)
HSF4 6 (4%) 141 0.247
(1.00) 		0.217
(0.978) 		0.392
(1.00) 		1
(1.00) 		0.423
(1.00) 		0.142
(0.814) 		0.202
(0.934) 		0.369
(1.00) 		0.276
(1.00) 		0.284
(1.00)
MUC6 15 (10%) 132 0.695
(1.00) 		0.622
(1.00) 		0.351
(1.00) 		0.0894
(0.643) 		0.834
(1.00) 		0.966
(1.00) 		1
(1.00) 		0.735
(1.00) 		0.775
(1.00) 		0.917
(1.00)
FANK1 4 (3%) 143 0.386
(1.00) 		0.835
(1.00) 		0.176
(0.909) 		0.601
(1.00) 		0.378
(1.00) 		0.709
(1.00) 		0.455
(1.00) 		0.278
(1.00) 		0.271
(1.00) 		0.191
(0.925)
MLLT3 4 (3%) 143 0.559
(1.00) 		0.833
(1.00) 		0.81
(1.00) 		0.283
(1.00) 		1
(1.00) 		0.587
(1.00) 		0.464
(1.00) 		0.842
(1.00)
RHPN2 6 (4%) 141 0.878
(1.00) 		0.247
(1.00) 		1
(1.00) 		1
(1.00) 		0.88
(1.00) 		0.921
(1.00) 		0.577
(1.00) 		1
(1.00) 		1
(1.00) 		0.853
(1.00)
KRTAP1-1 3 (2%) 144 1
(1.00) 		0.774
(1.00) 		0.794
(1.00) 		0.475
(1.00) 		0.779
(1.00) 		0.614
(1.00) 		0.61
(1.00) 		0.704
(1.00)
ANKRD11 7 (5%) 140 0.887
(1.00) 		0.0817
(0.628) 		0.777
(1.00) 		0.571
(1.00) 		0.257
(1.00) 		0.851
(1.00) 		0.335
(1.00) 		0.286
(1.00) 		0.277
(1.00) 		0.379
(1.00)
SPIN2A 3 (2%) 144 0.631
(1.00) 		1
(1.00) 		1
(1.00) 		0.373
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.892
(1.00)
ATXN3 3 (2%) 144 0.779
(1.00) 		0.3
(1.00) 		0.217
(0.978) 		0.0547
(0.5) 		0.154
(0.828) 		0.18
(0.916) 		0.489
(1.00) 		0.0932
(0.643) 		0.0931
(0.643) 		0.502
(1.00)
MEF2A 3 (2%) 144 1
(1.00) 		1
(1.00) 		1
(1.00) 		0.33
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.892
(1.00)
SSBP3 3 (2%) 144 0.778
(1.00) 		0.298
(1.00) 		0.154
(0.828) 		0.0582
(0.509) 		0.489
(1.00) 		0.0939
(0.643) 		0.0927
(0.643) 		0.503
(1.00)
KRTAP10-10 5 (3%) 142 1
(1.00) 		0.626
(1.00) 		0.731
(1.00) 		0.535
(1.00) 		0.451
(1.00) 		0.87
(1.00) 		0.185
(0.925) 		0.598
(1.00) 		0.602
(1.00) 		0.617
(1.00)
BCL11B 5 (3%) 142 0.519
(1.00) 		0.277
(1.00) 		0.653
(1.00) 		0.534
(1.00) 		0.323
(1.00) 		0.936
(1.00) 		0.527
(1.00) 		0.382
(1.00) 		0.441
(1.00) 		0.423
(1.00)
FAM101B 4 (3%) 143 1
(1.00) 		0.69
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		0.501
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
PSMD11 4 (3%) 143 0.0678
(0.555) 		0.0368
(0.386) 		0.44
(1.00) 		0.229
(1.00) 		0.193
(0.925) 		0.753
(1.00) 		0.315
(1.00) 		0.195
(0.925) 		0.367
(1.00) 		0.134
(0.798)
FAM8A1 3 (2%) 144 0.497
(1.00) 		0.108
(0.689) 		0.248
(1.00) 		0.518
(1.00) 		0.0597
(0.516) 		0.342
(1.00) 		0.332
(1.00) 		0.0241
(0.304)
CRB2 6 (4%) 141 0.579
(1.00) 		0.594
(1.00) 		0.778
(1.00) 		0.574
(1.00) 		0.661
(1.00) 		0.439
(1.00) 		0.449
(1.00) 		0.659
(1.00) 		0.659
(1.00) 		0.0648
(0.545)
OPLAH 4 (3%) 143 0.824
(1.00) 		0.549
(1.00) 		0.528
(1.00) 		1
(1.00) 		1
(1.00) 		0.309
(1.00) 		0.56
(1.00) 		0.278
(1.00) 		1
(1.00) 		0.539
(1.00)
C22ORF43 3 (2%) 144 0.373
(1.00) 		1
(1.00) 		0.0563
(0.506) 		1
(1.00) 		1
(1.00) 		0.735
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
GAS2L2 3 (2%) 144 1
(1.00) 		0.201
(0.934) 		0.855
(1.00) 		0.601
(1.00) 		1
(1.00) 		0.421
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00) 		1
(1.00)
CDC27 6 (4%) 141 0.0335
(0.364) 		0.775
(1.00) 		0.189
(0.925) 		0.179
(0.916) 		0.169
(0.89) 		0.0574
(0.509) 		0.33
(1.00) 		0.138
(0.807) 		0.169
(0.89) 		0.0488
(0.475)
MUC2 16 (11%) 131 0.4
(1.00) 		0.945
(1.00) 		0.262
(1.00) 		0.425
(1.00) 		0.518
(1.00) 		0.985
(1.00) 		0.501
(1.00) 		0.944
(1.00) 		0.792
(1.00) 		0.793
(1.00)
TPTE2 5 (3%) 142 0.622
(1.00) 		0.232
(1.00) 		1
(1.00) 		1
(1.00) 		0.318
(1.00) 		0.636
(1.00) 		0.0505
(0.475) 		0.381
(1.00) 		0.443
(1.00) 		0.422
(1.00)
NAT10 4 (3%) 143 0.387
(1.00) 		1
(1.00) 		0.855
(1.00) 		0.602
(1.00) 		1
(1.00) 		0.254
(1.00) 		0.832
(1.00) 		1
(1.00) 		1
(1.00) 		0.493
(1.00)
INTS4 3 (2%) 144 1
(1.00) 		1
(1.00) 		0.796
(1.00) 		0.95
(1.00) 		0.629
(1.00) 		0.614
(1.00) 		0.608
(1.00) 		0.707
(1.00)
TTC38 4 (3%) 143 0.384
(1.00) 		0.114
(0.709) 		0.891
(1.00) 		0.197
(0.926) 		0.287
(1.00) 		0.817
(1.00) 		0.193
(0.925) 		0.381
(1.00) 		0.578
(1.00) 		0.255
(1.00)
RBM3 3 (2%) 144 0.374
(1.00) 		0.774
(1.00) 		0.796
(1.00) 		0.95
(1.00) 		0.115
(0.709) 		0.618
(1.00) 		0.605
(1.00) 		0.131
(0.791)
TCHH 5 (3%) 142 0.518
(1.00) 		0.131
(0.791) 		0.0734
(0.585) 		0.533
(1.00) 		0.379
(1.00) 		0.909
(1.00) 		0.372
(1.00) 		0.322
(1.00) 		0.209
(0.954) 		0.331
(1.00)
ZC3H11A 3 (2%) 144 0.0526
(0.488) 		0.774
(1.00) 		0.618
(1.00) 		0.471
(1.00) 		0.373
(1.00) 		0.796
(1.00) 		0.794
(1.00) 		0.397
(1.00)
RAC1 4 (3%) 143 0.384
(1.00) 		0.388
(1.00) 		0.62
(1.00) 		1
(1.00) 		0.59
(1.00) 		0.634
(1.00) 		0.316
(1.00) 		0.481
(1.00) 		0.366
(1.00) 		0.0849
(0.633)
MTIF3 3 (2%) 144 1
(1.00) 		0.402
(1.00) 		1
(1.00) 		1
(1.00) 		0.621
(1.00) 		1
(1.00) 		0.373
(1.00) 		0.797
(1.00) 		0.793
(1.00) 		0.797
(1.00)
MFF 3 (2%) 144 1
(1.00) 		0.774
(1.00) 		0.617
(1.00) 		1
(1.00) 		0.797
(1.00) 		0.949
(1.00) 		0.631
(1.00) 		0.617
(1.00) 		0.608
(1.00) 		0.704
(1.00)
PABPC3 4 (3%) 143 1
(1.00) 		0.464
(1.00) 		0.284
(1.00) 		0.609
(1.00) 		0.192
(0.925) 		0.38
(1.00) 		0.576
(1.00) 		0.305
(1.00)
CUX1 5 (3%) 142 0.731
(1.00) 		0.863
(1.00) 		0.856
(1.00) 		0.602
(1.00) 		0.722
(1.00) 		0.962
(1.00) 		0.635
(1.00) 		0.855
(1.00) 		0.858
(1.00) 		0.72
(1.00)
PCMTD1 5 (3%) 142 0.0915
(0.643) 		0.625
(1.00) 		0.462
(1.00) 		0.535
(1.00) 		0.382
(1.00) 		0.447
(1.00) 		0.373
(1.00) 		0.317
(1.00) 		0.208
(0.954) 		0.33
(1.00)
EZH2 4 (3%) 143 0.826
(1.00) 		0.548
(1.00) 		0.379
(1.00) 		0.544
(1.00) 		0.56
(1.00) 		0.278
(1.00) 		0.275
(1.00) 		0.279
(1.00)
HTT 3 (2%) 144 1
(1.00) 		0.774
(1.00) 		0.795
(1.00) 		0.682
(1.00) 		0.628
(1.00) 		0.618
(1.00) 		0.606
(1.00) 		0.705
(1.00)
GSX2 4 (3%) 143 0.31
(1.00) 		0.324
(1.00) 		0.324
(1.00) 		0.0273
(0.315) 		0.698
(1.00) 		0.243
(1.00) 		0.0666
(0.552) 		0.151
(0.828) 		0.813
(1.00) 		0.788
(1.00)
RFC3 3 (2%) 144 1
(1.00) 		0.52
(1.00) 		0.528
(1.00) 		0.599
(1.00) 		0.451
(1.00) 		0.329
(1.00) 		0.779
(1.00) 		0.244
(1.00) 		1
(1.00) 		0.252
(1.00)
CHD4 4 (3%) 143 1
(1.00) 		0.69
(1.00) 		1
(1.00) 		0.831
(1.00) 		1
(1.00) 		0.409
(1.00) 		1
(1.00) 		1
(1.00) 		0.576
(1.00) 		1
(1.00)
RUNX2 4 (3%) 143 1
(1.00) 		0.686
(1.00) 		0.856
(1.00) 		0.601
(1.00) 		1
(1.00) 		1
(1.00) 		0.832
(1.00) 		1
(1.00) 		1
(1.00) 		0.495
(1.00)
SP4 4 (3%) 143 0.306
(1.00) 		0.0184
(0.258) 		0.0503
(0.475) 		0.112
(0.703) 		0.252
(1.00) 		0.0274
(0.315) 		0.0275
(0.315) 		0.173
(0.9)
DIAPH1 3 (2%) 144 1
(1.00) 		0.644
(1.00) 		0.62
(1.00) 		0.813
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.796
(1.00) 		0.797
(1.00)
PLEC 10 (7%) 137 0.0498
(0.475) 		0.272
(1.00) 		0.379
(1.00) 		0.148
(0.826) 		0.639
(1.00) 		0.195
(0.925) 		0.425
(1.00) 		0.698
(1.00) 		0.336
(1.00) 		0.0854
(0.633)
NHS 3 (2%) 144 0.78
(1.00) 		0.773
(1.00) 		0.318
(1.00) 		1
(1.00) 		0.794
(1.00) 		0.772
(1.00) 		0.627
(1.00) 		0.618
(1.00) 		0.608
(1.00) 		0.705
(1.00)
PIK3CD 4 (3%) 143 0.24
(1.00) 		0.265
(1.00) 		0.483
(1.00) 		0.369
(1.00) 		0.14
(0.807) 		0.699
(1.00) 		0.69
(1.00) 		0.102
(0.67)
EPAS1 5 (3%) 142 0.446
(1.00) 		0.866
(1.00) 		0.808
(1.00) 		0.83
(1.00) 		0.724
(1.00) 		0.788
(1.00) 		0.633
(1.00) 		0.853
(1.00) 		0.858
(1.00) 		0.719
(1.00)
DLC1 3 (2%) 144 0.276
(1.00) 		1
(1.00) 		0.623
(1.00) 		1
(1.00) 		0.796
(1.00) 		0.95
(1.00) 		0.629
(1.00) 		0.616
(1.00) 		0.608
(1.00) 		0.702
(1.00)
'KIT MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0017 (Fisher's exact test), Q value = 0.063

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
KIT MUTATED 14 9 3
KIT WILD-TYPE 33 33 55

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

'KIT MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00012 (Fisher's exact test), Q value = 0.0054

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
KIT MUTATED 19 2 5
KIT WILD-TYPE 35 46 40

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

'KIT MUTATION STATUS' versus 'RPPA_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
KIT MUTATED 19 2 1 0
KIT WILD-TYPE 28 12 33 21

Figure S3.  Get High-res Image Gene #1: '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 = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
KIT MUTATED 20 1 1
KIT WILD-TYPE 29 23 42

Figure S4.  Get High-res Image Gene #1: '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 = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
KIT MUTATED 25 0 1
KIT WILD-TYPE 43 40 38

Figure S5.  Get High-res Image Gene #1: '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 = 0.00057

Table S6.  Gene #1: '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 #1: '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 = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
KIT MUTATED 23 2 1
KIT WILD-TYPE 28 54 39

Figure S7.  Get High-res Image Gene #1: '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 = 0.00057

Table S8.  Gene #1: '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 #1: '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 = 0.00057

Table S9.  Gene #1: '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 #1: '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 = 0.00057

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
KIT MUTATED 21 4 0 1
KIT WILD-TYPE 15 28 38 40

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

'KRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.00631 (Fisher's exact test), Q value = 0.17

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
KRAS MUTATED 7 10 2
KRAS WILD-TYPE 40 32 56

Figure S11.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'KRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00032 (Fisher's exact test), Q value = 0.013

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
KRAS MUTATED 13 0 6
KRAS WILD-TYPE 41 48 39

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

'KRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00308 (Fisher's exact test), Q value = 0.1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
KRAS MUTATED 12 1 1 0
KRAS WILD-TYPE 35 13 33 21

Figure S13.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'KRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00019 (Fisher's exact test), Q value = 0.008

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
KRAS MUTATED 13 0 1
KRAS WILD-TYPE 36 24 42

Figure S14.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
KRAS MUTATED 18 0 1
KRAS WILD-TYPE 50 40 38

Figure S15.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00181 (Fisher's exact test), Q value = 0.063

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

'KRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 2e-05 (Fisher's exact test), Q value = 0.00097

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
KRAS MUTATED 16 2 1
KRAS WILD-TYPE 35 54 39

Figure S17.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'KRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

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

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

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

'KRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 2e-05 (Fisher's exact test), Q value = 0.00097

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
KRAS MUTATED 9 9 0 1
KRAS WILD-TYPE 27 23 38 40

Figure S20.  Get High-res Image Gene #2: 'KRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'ANKLE1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.83

Table S21.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
ANKLE1 MUTATED 1 5 6
ANKLE1 WILD-TYPE 46 37 52
'ANKLE1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S22.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
ANKLE1 MUTATED 4 2 6
ANKLE1 WILD-TYPE 50 46 39
'ANKLE1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.869 (Fisher's exact test), Q value = 1

Table S23.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
ANKLE1 MUTATED 4 0 3 1
ANKLE1 WILD-TYPE 43 14 31 20
'ANKLE1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S24.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
ANKLE1 MUTATED 4 0 4
ANKLE1 WILD-TYPE 45 24 39
'ANKLE1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S25.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
ANKLE1 MUTATED 7 2 3
ANKLE1 WILD-TYPE 61 38 36
'ANKLE1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.876 (Fisher's exact test), Q value = 1

Table S26.  Gene #3: 'ANKLE1 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
ANKLE1 MUTATED 3 4 1 2 0 1 1
ANKLE1 WILD-TYPE 39 22 11 22 8 22 11
'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S27.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
ANKLE1 MUTATED 4 5 3
ANKLE1 WILD-TYPE 47 51 37
'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S28.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
ANKLE1 MUTATED 7 2 3
ANKLE1 WILD-TYPE 61 36 38
'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.739 (Fisher's exact test), Q value = 1

Table S29.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
ANKLE1 MUTATED 7 2 3
ANKLE1 WILD-TYPE 60 34 41
'ANKLE1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S30.  Gene #3: 'ANKLE1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
ANKLE1 MUTATED 2 5 2 3
ANKLE1 WILD-TYPE 34 27 36 38
'FAM104B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.377 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
FAM104B MUTATED 3 3 1
FAM104B WILD-TYPE 44 39 57
'FAM104B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.502 (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
ALL 54 48 45
FAM104B MUTATED 4 1 2
FAM104B WILD-TYPE 50 47 43
'FAM104B MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
FAM104B MUTATED 3 1 0 1
FAM104B WILD-TYPE 44 13 34 20
'FAM104B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.617 (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 49 24 43
FAM104B MUTATED 2 0 3
FAM104B WILD-TYPE 47 24 40
'FAM104B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.353 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
FAM104B MUTATED 5 2 0
FAM104B WILD-TYPE 63 38 39
'FAM104B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.264 (Fisher's exact test), Q value = 1

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 = 0.0973 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
FAM104B MUTATED 5 2 0
FAM104B WILD-TYPE 46 54 40
'FAM104B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.25 (Fisher's exact test), Q value = 1

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 = 0.54 (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 = 0.545 (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
ALL 36 32 38 41
FAM104B MUTATED 2 3 1 1
FAM104B WILD-TYPE 34 29 37 40
'CSGALNACT2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.013 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
CSGALNACT2 MUTATED 0 0 5
CSGALNACT2 WILD-TYPE 47 42 53

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 = 0.194 (Fisher's exact test), Q value = 0.92

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
CSGALNACT2 MUTATED 0 3 2
CSGALNACT2 WILD-TYPE 54 45 43
'CSGALNACT2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00875 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
CSGALNACT2 MUTATED 0 0 5 0
CSGALNACT2 WILD-TYPE 47 14 29 21

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 = 0.0229 (Fisher's exact test), Q value = 0.3

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
CSGALNACT2 MUTATED 0 3 2
CSGALNACT2 WILD-TYPE 49 21 41

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 = 0.00865 (Fisher's exact test), Q value = 0.19

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
CSGALNACT2 MUTATED 0 1 4
CSGALNACT2 WILD-TYPE 68 39 35

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 = 0.0115 (Fisher's exact test), Q value = 0.21

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 = 0.0309 (Fisher's exact test), Q value = 0.34

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
CSGALNACT2 MUTATED 0 1 4
CSGALNACT2 WILD-TYPE 51 55 36

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 = 0.0162 (Fisher's exact test), Q value = 0.25

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 = 0.0247 (Fisher's exact test), Q value = 0.3

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 = 0.0779 (Fisher's exact test), Q value = 0.61

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
CSGALNACT2 MUTATED 0 0 1 4
CSGALNACT2 WILD-TYPE 36 32 37 37
'DDX11 MUTATION STATUS' versus 'CN_CNMF'

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

Table S51.  Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
DDX11 MUTATED 3 2 3
DDX11 WILD-TYPE 44 40 55
'DDX11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S52.  Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
DDX11 MUTATED 1 4 3
DDX11 WILD-TYPE 53 44 42
'DDX11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.279 (Fisher's exact test), Q value = 1

Table S53.  Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
DDX11 MUTATED 2 1 1 3
DDX11 WILD-TYPE 45 13 33 18
'DDX11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.81

Table S54.  Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
DDX11 MUTATED 2 0 5
DDX11 WILD-TYPE 47 24 38
'DDX11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.408 (Fisher's exact test), Q value = 1

Table S55.  Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
DDX11 MUTATED 3 4 1
DDX11 WILD-TYPE 65 36 38
'DDX11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.363 (Fisher's exact test), Q value = 1

Table S56.  Gene #6: '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 = 0.132 (Fisher's exact test), Q value = 0.79

Table S57.  Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
DDX11 MUTATED 1 6 1
DDX11 WILD-TYPE 50 50 39
'DDX11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.291 (Fisher's exact test), Q value = 1

Table S58.  Gene #6: '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 = 0.652 (Fisher's exact test), Q value = 1

Table S59.  Gene #6: '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 = 0.101 (Fisher's exact test), Q value = 0.67

Table S60.  Gene #6: 'DDX11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
DDX11 MUTATED 0 3 4 1
DDX11 WILD-TYPE 36 29 34 40
'NRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0504 (Fisher's exact test), Q value = 0.48

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
NRAS MUTATED 4 3 0
NRAS WILD-TYPE 43 39 58
'NRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0798 (Fisher's exact test), Q value = 0.62

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
NRAS MUTATED 5 0 2
NRAS WILD-TYPE 49 48 43
'NRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0973 (Fisher's exact test), Q value = 0.65

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
NRAS MUTATED 5 0 0 0
NRAS WILD-TYPE 42 14 34 21
'NRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
NRAS MUTATED 4 0 1
NRAS WILD-TYPE 45 24 42
'NRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0166 (Fisher's exact test), Q value = 0.25

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
NRAS MUTATED 7 0 0
NRAS WILD-TYPE 61 40 39

Figure S29.  Get High-res Image Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.145 (Fisher's exact test), Q value = 0.81

Table S66.  Gene #7: '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 = 0.013 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
NRAS MUTATED 6 1 0
NRAS WILD-TYPE 45 55 40

Figure S30.  Get High-res Image Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0179 (Fisher's exact test), Q value = 0.26

Table S68.  Gene #7: '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 S31.  Get High-res Image Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0691 (Fisher's exact test), Q value = 0.56

Table S69.  Gene #7: '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 = 0.0133 (Fisher's exact test), Q value = 0.23

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
NRAS MUTATED 4 3 0 0
NRAS WILD-TYPE 32 29 38 41

Figure S32.  Get High-res Image Gene #7: 'NRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'PNPLA4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S71.  Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
PNPLA4 MUTATED 3 1 1
PNPLA4 WILD-TYPE 44 41 57
'PNPLA4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S72.  Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
PNPLA4 MUTATED 2 2 1
PNPLA4 WILD-TYPE 52 46 44
'PNPLA4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S73.  Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
PNPLA4 MUTATED 3 1 0 1
PNPLA4 WILD-TYPE 44 13 34 20
'PNPLA4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S74.  Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
PNPLA4 MUTATED 2 0 3
PNPLA4 WILD-TYPE 47 24 40
'PNPLA4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S75.  Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
PNPLA4 MUTATED 3 2 0
PNPLA4 WILD-TYPE 65 38 39
'PNPLA4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S76.  Gene #8: '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 = 0.374 (Fisher's exact test), Q value = 1

Table S77.  Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
PNPLA4 MUTATED 3 2 0
PNPLA4 WILD-TYPE 48 54 40
'PNPLA4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S78.  Gene #8: '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 = 0.318 (Fisher's exact test), Q value = 1

Table S79.  Gene #8: '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 = 0.476 (Fisher's exact test), Q value = 1

Table S80.  Gene #8: 'PNPLA4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
PNPLA4 MUTATED 2 1 2 0
PNPLA4 WILD-TYPE 34 31 36 41
'SERINC2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S81.  Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
SERINC2 MUTATED 1 0 3
SERINC2 WILD-TYPE 46 42 55
'SERINC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S82.  Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
SERINC2 MUTATED 1 2 1
SERINC2 WILD-TYPE 53 46 44
'SERINC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.139 (Fisher's exact test), Q value = 0.81

Table S83.  Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
SERINC2 MUTATED 0 1 2 0
SERINC2 WILD-TYPE 47 13 32 21
'SERINC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.103 (Fisher's exact test), Q value = 0.67

Table S84.  Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
SERINC2 MUTATED 0 0 3
SERINC2 WILD-TYPE 49 24 40
'SERINC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.811 (Fisher's exact test), Q value = 1

Table S85.  Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
SERINC2 MUTATED 1 2 1
SERINC2 WILD-TYPE 67 38 38
'SERINC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S86.  Gene #9: '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 S87.  Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
SERINC2 MUTATED 1 2 1
SERINC2 WILD-TYPE 50 54 39
'SERINC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S88.  Gene #9: '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 = 0.812 (Fisher's exact test), Q value = 1

Table S89.  Gene #9: '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 = 0.843 (Fisher's exact test), Q value = 1

Table S90.  Gene #9: 'SERINC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
SERINC2 MUTATED 1 0 2 1
SERINC2 WILD-TYPE 35 32 36 40
'RBM10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S91.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
RBM10 MUTATED 2 2 1
RBM10 WILD-TYPE 45 40 57
'RBM10 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S92.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
RBM10 MUTATED 3 0 2
RBM10 WILD-TYPE 51 48 43
'RBM10 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.92 (Fisher's exact test), Q value = 1

Table S93.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
RBM10 MUTATED 3 0 1 1
RBM10 WILD-TYPE 44 14 33 20
'RBM10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S94.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
RBM10 MUTATED 3 0 2
RBM10 WILD-TYPE 46 24 41
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.45 (Fisher's exact test), Q value = 1

Table S95.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
RBM10 MUTATED 3 0 2
RBM10 WILD-TYPE 65 40 37
'RBM10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S96.  Gene #10: '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 = 0.634 (Fisher's exact test), Q value = 1

Table S97.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
RBM10 MUTATED 2 1 2
RBM10 WILD-TYPE 49 55 38
'RBM10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S98.  Gene #10: '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 = 0.604 (Fisher's exact test), Q value = 1

Table S99.  Gene #10: '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 = 0.555 (Fisher's exact test), Q value = 1

Table S100.  Gene #10: 'RBM10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
RBM10 MUTATED 1 2 0 2
RBM10 WILD-TYPE 35 30 38 39
'DEK MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0359 (Fisher's exact test), Q value = 0.38

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
DEK MUTATED 0 4 1
DEK WILD-TYPE 47 38 57

Figure S33.  Get High-res Image Gene #11: 'DEK MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'DEK MUTATION STATUS' versus 'METHLYATION_CNMF'

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

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
DEK MUTATED 2 1 2
DEK WILD-TYPE 52 47 43
'DEK MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
DEK MUTATED 3 1 1 0
DEK WILD-TYPE 44 13 33 21
'DEK MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.275 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
DEK MUTATED 4 0 1
DEK WILD-TYPE 45 24 42
'DEK MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.381 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
DEK MUTATED 4 1 0
DEK WILD-TYPE 64 39 39
'DEK MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0184 (Fisher's exact test), Q value = 0.26

Table S106.  Gene #11: '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 S34.  Get High-res Image Gene #11: '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 = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
DEK MUTATED 3 2 0
DEK WILD-TYPE 48 54 40
'DEK MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.319 (Fisher's exact test), Q value = 1

Table S108.  Gene #11: '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 = 0.441 (Fisher's exact test), Q value = 1

Table S109.  Gene #11: '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 = 0.157 (Fisher's exact test), Q value = 0.84

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

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
DEK MUTATED 1 3 1 0
DEK WILD-TYPE 35 29 37 41
'ERC1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S111.  Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
ERC1 MUTATED 3 2 2
ERC1 WILD-TYPE 44 40 56
'ERC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S112.  Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
ERC1 MUTATED 2 2 3
ERC1 WILD-TYPE 52 46 42
'ERC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.607 (Fisher's exact test), Q value = 1

Table S113.  Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
ERC1 MUTATED 2 1 1 2
ERC1 WILD-TYPE 45 13 33 19
'ERC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S114.  Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
ERC1 MUTATED 2 1 3
ERC1 WILD-TYPE 47 23 40
'ERC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S115.  Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
ERC1 MUTATED 3 2 2
ERC1 WILD-TYPE 65 38 37
'ERC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S116.  Gene #12: '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 S117.  Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
ERC1 MUTATED 2 3 2
ERC1 WILD-TYPE 49 53 38
'ERC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S118.  Gene #12: '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 S119.  Gene #12: '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 = 0.954 (Fisher's exact test), Q value = 1

Table S120.  Gene #12: 'ERC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
ERC1 MUTATED 1 2 2 2
ERC1 WILD-TYPE 35 30 36 39
'HSF4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 1

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
HSF4 MUTATED 4 1 1
HSF4 WILD-TYPE 43 41 57
'HSF4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.98

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
HSF4 MUTATED 4 2 0
HSF4 WILD-TYPE 50 46 45
'HSF4 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.392 (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
ALL 47 14 34 21
HSF4 MUTATED 2 2 1 1
HSF4 WILD-TYPE 45 12 33 20
'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 49 24 43
HSF4 MUTATED 3 1 2
HSF4 WILD-TYPE 46 23 41
'HSF4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.423 (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
ALL 68 40 39
HSF4 MUTATED 4 2 0
HSF4 WILD-TYPE 64 38 39
'HSF4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.142 (Fisher's exact test), Q value = 0.81

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 = 0.202 (Fisher's exact test), Q value = 0.93

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

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
HSF4 MUTATED 4 2 0
HSF4 WILD-TYPE 47 54 40
'HSF4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 1

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 = 0.276 (Fisher's exact test), Q value = 1

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 = 0.284 (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
ALL 36 32 38 41
HSF4 MUTATED 3 1 2 0
HSF4 WILD-TYPE 33 31 36 41
'MUC6 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.695 (Fisher's exact test), Q value = 1

Table S131.  Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
MUC6 MUTATED 6 3 6
MUC6 WILD-TYPE 41 39 52
'MUC6 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S132.  Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
MUC6 MUTATED 4 5 6
MUC6 WILD-TYPE 50 43 39
'MUC6 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.351 (Fisher's exact test), Q value = 1

Table S133.  Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
MUC6 MUTATED 4 0 3 4
MUC6 WILD-TYPE 43 14 31 17
'MUC6 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0894 (Fisher's exact test), Q value = 0.64

Table S134.  Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
MUC6 MUTATED 4 0 7
MUC6 WILD-TYPE 45 24 36
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S135.  Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
MUC6 MUTATED 6 5 4
MUC6 WILD-TYPE 62 35 35
'MUC6 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.966 (Fisher's exact test), Q value = 1

Table S136.  Gene #14: '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 S137.  Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
MUC6 MUTATED 5 6 4
MUC6 WILD-TYPE 46 50 36
'MUC6 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S138.  Gene #14: '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 = 0.775 (Fisher's exact test), Q value = 1

Table S139.  Gene #14: '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 = 0.917 (Fisher's exact test), Q value = 1

Table S140.  Gene #14: 'MUC6 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
MUC6 MUTATED 3 3 5 4
MUC6 WILD-TYPE 33 29 33 37
'FANK1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.386 (Fisher's exact test), Q value = 1

Table S141.  Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
FANK1 MUTATED 0 2 2
FANK1 WILD-TYPE 47 40 56
'FANK1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S142.  Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
FANK1 MUTATED 1 2 1
FANK1 WILD-TYPE 53 46 44
'FANK1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.176 (Fisher's exact test), Q value = 0.91

Table S143.  Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
FANK1 MUTATED 1 0 0 2
FANK1 WILD-TYPE 46 14 34 19
'FANK1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S144.  Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
FANK1 MUTATED 1 0 2
FANK1 WILD-TYPE 48 24 41
'FANK1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.378 (Fisher's exact test), Q value = 1

Table S145.  Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
FANK1 MUTATED 2 2 0
FANK1 WILD-TYPE 66 38 39
'FANK1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.709 (Fisher's exact test), Q value = 1

Table S146.  Gene #15: '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 = 0.455 (Fisher's exact test), Q value = 1

Table S147.  Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
FANK1 MUTATED 1 3 0
FANK1 WILD-TYPE 50 53 40
'FANK1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S148.  Gene #15: '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 = 0.271 (Fisher's exact test), Q value = 1

Table S149.  Gene #15: '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 = 0.191 (Fisher's exact test), Q value = 0.92

Table S150.  Gene #15: 'FANK1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
FANK1 MUTATED 0 2 2 0
FANK1 WILD-TYPE 36 30 36 41
'MLLT3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.559 (Fisher's exact test), Q value = 1

Table S151.  Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
MLLT3 MUTATED 2 0 2
MLLT3 WILD-TYPE 45 42 56
'MLLT3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S152.  Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
MLLT3 MUTATED 1 2 1
MLLT3 WILD-TYPE 53 46 44
'MLLT3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.81 (Fisher's exact test), Q value = 1

Table S153.  Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
MLLT3 MUTATED 1 2 1
MLLT3 WILD-TYPE 67 38 38
'MLLT3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.283 (Fisher's exact test), Q value = 1

Table S154.  Gene #16: '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 S155.  Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
MLLT3 MUTATED 1 2 1
MLLT3 WILD-TYPE 50 54 39
'MLLT3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S156.  Gene #16: '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 = 0.464 (Fisher's exact test), Q value = 1

Table S157.  Gene #16: '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 = 0.842 (Fisher's exact test), Q value = 1

Table S158.  Gene #16: 'MLLT3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
MLLT3 MUTATED 1 0 2 1
MLLT3 WILD-TYPE 35 32 36 40
'RHPN2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.878 (Fisher's exact test), Q value = 1

Table S159.  Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
RHPN2 MUTATED 2 1 3
RHPN2 WILD-TYPE 45 41 55
'RHPN2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.247 (Fisher's exact test), Q value = 1

Table S160.  Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
RHPN2 MUTATED 1 1 4
RHPN2 WILD-TYPE 53 47 41
'RHPN2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S161.  Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
RHPN2 MUTATED 3 0 2 1
RHPN2 WILD-TYPE 44 14 32 20
'RHPN2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S162.  Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
RHPN2 MUTATED 3 1 2
RHPN2 WILD-TYPE 46 23 41
'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S163.  Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
RHPN2 MUTATED 3 1 2
RHPN2 WILD-TYPE 65 39 37
'RHPN2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.921 (Fisher's exact test), Q value = 1

Table S164.  Gene #17: '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 = 0.577 (Fisher's exact test), Q value = 1

Table S165.  Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
RHPN2 MUTATED 3 1 2
RHPN2 WILD-TYPE 48 55 38
'RHPN2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S166.  Gene #17: '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 S167.  Gene #17: '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 = 0.853 (Fisher's exact test), Q value = 1

Table S168.  Gene #17: 'RHPN2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
RHPN2 MUTATED 1 2 1 2
RHPN2 WILD-TYPE 35 30 37 39
'SP8 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0897 (Fisher's exact test), Q value = 0.64

Table S169.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
SP8 MUTATED 0 1 5
SP8 WILD-TYPE 47 41 53
'SP8 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S170.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
SP8 MUTATED 1 3 2
SP8 WILD-TYPE 53 45 43
'SP8 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0308 (Fisher's exact test), Q value = 0.34

Table S171.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
SP8 MUTATED 0 1 4 0
SP8 WILD-TYPE 47 13 30 21

Figure S35.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'SP8 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0237 (Fisher's exact test), Q value = 0.3

Table S172.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
SP8 MUTATED 0 3 2
SP8 WILD-TYPE 49 21 41

Figure S36.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0157 (Fisher's exact test), Q value = 0.25

Table S173.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
SP8 MUTATED 0 2 4
SP8 WILD-TYPE 68 38 35

Figure S37.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SP8 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00676 (Fisher's exact test), Q value = 0.17

Table S174.  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 S38.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.0481 (Fisher's exact test), Q value = 0.48

Table S175.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
SP8 MUTATED 0 2 4
SP8 WILD-TYPE 51 54 36

Figure S39.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SP8 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0214 (Fisher's exact test), Q value = 0.29

Table S176.  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 S40.  Get High-res Image Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SP8 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0241 (Fisher's exact test), Q value = 0.3

Table S177.  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 S41.  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 = 0.0839 (Fisher's exact test), Q value = 0.63

Table S178.  Gene #18: 'SP8 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
SP8 MUTATED 0 0 2 4
SP8 WILD-TYPE 36 32 36 37
'KRTAP1-1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S179.  Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
KRTAP1-1 MUTATED 1 1 1
KRTAP1-1 WILD-TYPE 46 41 57
'KRTAP1-1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S180.  Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
KRTAP1-1 MUTATED 2 1 0
KRTAP1-1 WILD-TYPE 52 47 45
'KRTAP1-1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S181.  Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
KRTAP1-1 MUTATED 2 1 0
KRTAP1-1 WILD-TYPE 66 39 39
'KRTAP1-1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S182.  Gene #19: '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 = 0.779 (Fisher's exact test), Q value = 1

Table S183.  Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
KRTAP1-1 MUTATED 1 2 0
KRTAP1-1 WILD-TYPE 50 54 40
'KRTAP1-1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S184.  Gene #19: '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 = 0.61 (Fisher's exact test), Q value = 1

Table S185.  Gene #19: '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 = 0.704 (Fisher's exact test), Q value = 1

Table S186.  Gene #19: 'KRTAP1-1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
KRTAP1-1 MUTATED 1 1 1 0
KRTAP1-1 WILD-TYPE 35 31 37 41
'ANKRD11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S187.  Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
ANKRD11 MUTATED 3 2 2
ANKRD11 WILD-TYPE 44 40 56
'ANKRD11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0817 (Fisher's exact test), Q value = 0.63

Table S188.  Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
ANKRD11 MUTATED 5 0 2
ANKRD11 WILD-TYPE 49 48 43
'ANKRD11 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S189.  Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
ANKRD11 MUTATED 3 1 2 0
ANKRD11 WILD-TYPE 44 13 32 21
'ANKRD11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.571 (Fisher's exact test), Q value = 1

Table S190.  Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
ANKRD11 MUTATED 4 1 1
ANKRD11 WILD-TYPE 45 23 42
'ANKRD11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.257 (Fisher's exact test), Q value = 1

Table S191.  Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
ANKRD11 MUTATED 5 0 2
ANKRD11 WILD-TYPE 63 40 37
'ANKRD11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S192.  Gene #20: '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 = 0.335 (Fisher's exact test), Q value = 1

Table S193.  Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
ANKRD11 MUTATED 4 1 2
ANKRD11 WILD-TYPE 47 55 38
'ANKRD11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.286 (Fisher's exact test), Q value = 1

Table S194.  Gene #20: '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 = 0.277 (Fisher's exact test), Q value = 1

Table S195.  Gene #20: '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 = 0.379 (Fisher's exact test), Q value = 1

Table S196.  Gene #20: 'ANKRD11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
ANKRD11 MUTATED 3 2 0 2
ANKRD11 WILD-TYPE 33 30 38 39
'SPIN2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S197.  Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
SPIN2A MUTATED 0 1 2
SPIN2A WILD-TYPE 47 41 56
'SPIN2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S198.  Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
SPIN2A MUTATED 1 1 1
SPIN2A WILD-TYPE 53 47 44
'SPIN2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S199.  Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
SPIN2A MUTATED 1 1 1
SPIN2A WILD-TYPE 67 39 38
'SPIN2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S200.  Gene #21: '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 S201.  Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
SPIN2A MUTATED 1 1 1
SPIN2A WILD-TYPE 50 55 39
'SPIN2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S202.  Gene #21: '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 S203.  Gene #21: '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 = 0.892 (Fisher's exact test), Q value = 1

Table S204.  Gene #21: 'SPIN2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
SPIN2A MUTATED 0 1 1 1
SPIN2A WILD-TYPE 36 31 37 40
'ATXN3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S205.  Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
ATXN3 MUTATED 1 0 2
ATXN3 WILD-TYPE 46 42 56
'ATXN3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.3 (Fisher's exact test), Q value = 1

Table S206.  Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 54 46 44
'ATXN3 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.217 (Fisher's exact test), Q value = 0.98

Table S207.  Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
ATXN3 MUTATED 0 1 1 1
ATXN3 WILD-TYPE 47 13 33 20
'ATXN3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0547 (Fisher's exact test), Q value = 0.5

Table S208.  Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 49 22 42
'ATXN3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.83

Table S209.  Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 68 38 38
'ATXN3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.18 (Fisher's exact test), Q value = 0.92

Table S210.  Gene #22: '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 = 0.489 (Fisher's exact test), Q value = 1

Table S211.  Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
ATXN3 MUTATED 0 2 1
ATXN3 WILD-TYPE 51 54 39
'ATXN3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0932 (Fisher's exact test), Q value = 0.64

Table S212.  Gene #22: '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 = 0.0931 (Fisher's exact test), Q value = 0.64

Table S213.  Gene #22: '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 = 0.502 (Fisher's exact test), Q value = 1

Table S214.  Gene #22: 'ATXN3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
ATXN3 MUTATED 0 0 2 1
ATXN3 WILD-TYPE 36 32 36 40
'MEF2A MUTATION STATUS' versus 'CN_CNMF'

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

Table S215.  Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
MEF2A MUTATED 1 1 1
MEF2A WILD-TYPE 46 41 57
'MEF2A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S216.  Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
MEF2A MUTATED 1 1 1
MEF2A WILD-TYPE 53 47 44
'MEF2A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S217.  Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
MEF2A MUTATED 1 1 1
MEF2A WILD-TYPE 67 39 38
'MEF2A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.33 (Fisher's exact test), Q value = 1

Table S218.  Gene #23: '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 S219.  Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
MEF2A MUTATED 1 1 1
MEF2A WILD-TYPE 50 55 39
'MEF2A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S220.  Gene #23: '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 S221.  Gene #23: '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 = 0.892 (Fisher's exact test), Q value = 1

Table S222.  Gene #23: 'MEF2A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
MEF2A MUTATED 0 1 1 1
MEF2A WILD-TYPE 36 31 37 40
'SSBP3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S223.  Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
SSBP3 MUTATED 1 0 2
SSBP3 WILD-TYPE 46 42 56
'SSBP3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.298 (Fisher's exact test), Q value = 1

Table S224.  Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
SSBP3 MUTATED 0 2 1
SSBP3 WILD-TYPE 54 46 44
'SSBP3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.154 (Fisher's exact test), Q value = 0.83

Table S225.  Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
SSBP3 MUTATED 0 2 1
SSBP3 WILD-TYPE 68 38 38
'SSBP3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0582 (Fisher's exact test), Q value = 0.51

Table S226.  Gene #24: '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 = 0.489 (Fisher's exact test), Q value = 1

Table S227.  Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
SSBP3 MUTATED 0 2 1
SSBP3 WILD-TYPE 51 54 39
'SSBP3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0939 (Fisher's exact test), Q value = 0.64

Table S228.  Gene #24: '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 = 0.0927 (Fisher's exact test), Q value = 0.64

Table S229.  Gene #24: '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 = 0.503 (Fisher's exact test), Q value = 1

Table S230.  Gene #24: 'SSBP3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
SSBP3 MUTATED 0 0 2 1
SSBP3 WILD-TYPE 36 32 36 40
'KRTAP10-10 MUTATION STATUS' versus 'CN_CNMF'

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

Table S231.  Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
KRTAP10-10 MUTATED 2 1 2
KRTAP10-10 WILD-TYPE 45 41 56
'KRTAP10-10 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S232.  Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
KRTAP10-10 MUTATED 3 1 1
KRTAP10-10 WILD-TYPE 51 47 44
'KRTAP10-10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S233.  Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
KRTAP10-10 MUTATED 3 0 1 0
KRTAP10-10 WILD-TYPE 44 14 33 21
'KRTAP10-10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S234.  Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
KRTAP10-10 MUTATED 3 0 1
KRTAP10-10 WILD-TYPE 46 24 42
'KRTAP10-10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S235.  Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
KRTAP10-10 MUTATED 3 0 2
KRTAP10-10 WILD-TYPE 65 40 37
'KRTAP10-10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S236.  Gene #25: '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 = 0.185 (Fisher's exact test), Q value = 0.92

Table S237.  Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
KRTAP10-10 MUTATED 3 0 2
KRTAP10-10 WILD-TYPE 48 56 38
'KRTAP10-10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S238.  Gene #25: '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 = 0.602 (Fisher's exact test), Q value = 1

Table S239.  Gene #25: '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 = 0.617 (Fisher's exact test), Q value = 1

Table S240.  Gene #25: 'KRTAP10-10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
KRTAP10-10 MUTATED 2 1 0 2
KRTAP10-10 WILD-TYPE 34 31 38 39
'BCL11B MUTATION STATUS' versus 'CN_CNMF'

P value = 0.519 (Fisher's exact test), Q value = 1

Table S241.  Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
BCL11B MUTATED 3 1 1
BCL11B WILD-TYPE 44 41 57
'BCL11B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.277 (Fisher's exact test), Q value = 1

Table S242.  Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
BCL11B MUTATED 3 0 2
BCL11B WILD-TYPE 51 48 43
'BCL11B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S243.  Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
BCL11B MUTATED 2 1 1 0
BCL11B WILD-TYPE 45 13 33 21
'BCL11B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.534 (Fisher's exact test), Q value = 1

Table S244.  Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
BCL11B MUTATED 3 0 1
BCL11B WILD-TYPE 46 24 42
'BCL11B MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S245.  Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
BCL11B MUTATED 4 0 1
BCL11B WILD-TYPE 64 40 38
'BCL11B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S246.  Gene #26: '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 = 0.527 (Fisher's exact test), Q value = 1

Table S247.  Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
BCL11B MUTATED 3 1 1
BCL11B WILD-TYPE 48 55 39
'BCL11B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S248.  Gene #26: '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 = 0.441 (Fisher's exact test), Q value = 1

Table S249.  Gene #26: '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 = 0.423 (Fisher's exact test), Q value = 1

Table S250.  Gene #26: 'BCL11B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
BCL11B MUTATED 2 2 0 1
BCL11B WILD-TYPE 34 30 38 40
'FAM101B MUTATION STATUS' versus 'CN_CNMF'

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

Table S251.  Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
FAM101B MUTATED 1 1 2
FAM101B WILD-TYPE 46 41 56
'FAM101B MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S252.  Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
FAM101B MUTATED 1 1 2
FAM101B WILD-TYPE 53 47 43
'FAM101B MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S253.  Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
FAM101B MUTATED 2 0 1 0
FAM101B WILD-TYPE 45 14 33 21
'FAM101B MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S254.  Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
FAM101B MUTATED 2 0 1
FAM101B WILD-TYPE 47 24 42
'FAM101B MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S255.  Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
FAM101B MUTATED 2 1 1
FAM101B WILD-TYPE 66 39 38
'FAM101B MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S256.  Gene #27: '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 S257.  Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
FAM101B MUTATED 1 2 1
FAM101B WILD-TYPE 50 54 39
'FAM101B MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S258.  Gene #27: '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 S259.  Gene #27: '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 S260.  Gene #27: 'FAM101B MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
FAM101B MUTATED 1 1 1 1
FAM101B WILD-TYPE 35 31 37 40
'PSMD11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0678 (Fisher's exact test), Q value = 0.55

Table S261.  Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
PSMD11 MUTATED 1 3 0
PSMD11 WILD-TYPE 46 39 58
'PSMD11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0368 (Fisher's exact test), Q value = 0.39

Table S262.  Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
PSMD11 MUTATED 4 0 0
PSMD11 WILD-TYPE 50 48 45

Figure S42.  Get High-res Image Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'PSMD11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.44 (Fisher's exact test), Q value = 1

Table S263.  Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
PSMD11 MUTATED 3 0 0 0
PSMD11 WILD-TYPE 44 14 34 21
'PSMD11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.229 (Fisher's exact test), Q value = 1

Table S264.  Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
PSMD11 MUTATED 3 0 0
PSMD11 WILD-TYPE 46 24 43
'PSMD11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.193 (Fisher's exact test), Q value = 0.92

Table S265.  Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
PSMD11 MUTATED 4 0 0
PSMD11 WILD-TYPE 64 40 39
'PSMD11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.753 (Fisher's exact test), Q value = 1

Table S266.  Gene #28: '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 = 0.315 (Fisher's exact test), Q value = 1

Table S267.  Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
PSMD11 MUTATED 3 1 0
PSMD11 WILD-TYPE 48 55 40
'PSMD11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.92

Table S268.  Gene #28: '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 = 0.367 (Fisher's exact test), Q value = 1

Table S269.  Gene #28: '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 = 0.134 (Fisher's exact test), Q value = 0.8

Table S270.  Gene #28: 'PSMD11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
PSMD11 MUTATED 2 2 0 0
PSMD11 WILD-TYPE 34 30 38 41
'FAM8A1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S271.  Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
FAM8A1 MUTATED 2 0 1
FAM8A1 WILD-TYPE 45 42 57
'FAM8A1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.108 (Fisher's exact test), Q value = 0.69

Table S272.  Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
FAM8A1 MUTATED 3 0 0
FAM8A1 WILD-TYPE 51 48 45
'FAM8A1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.248 (Fisher's exact test), Q value = 1

Table S273.  Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
FAM8A1 MUTATED 3 0 0
FAM8A1 WILD-TYPE 65 40 39
'FAM8A1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S274.  Gene #29: '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 = 0.0597 (Fisher's exact test), Q value = 0.52

Table S275.  Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
FAM8A1 MUTATED 3 0 0
FAM8A1 WILD-TYPE 48 56 40
'FAM8A1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.342 (Fisher's exact test), Q value = 1

Table S276.  Gene #29: '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 = 0.332 (Fisher's exact test), Q value = 1

Table S277.  Gene #29: '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 = 0.0241 (Fisher's exact test), Q value = 0.3

Table S278.  Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
FAM8A1 MUTATED 3 0 0 0
FAM8A1 WILD-TYPE 33 32 38 41

Figure S43.  Get High-res Image Gene #29: 'FAM8A1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'SPTAN1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0384 (Fisher's exact test), Q value = 0.4

Table S279.  Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
SPTAN1 MUTATED 0 0 4
SPTAN1 WILD-TYPE 47 42 54

Figure S44.  Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'SPTAN1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.323 (Fisher's exact test), Q value = 1

Table S280.  Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
SPTAN1 MUTATED 0 2 2
SPTAN1 WILD-TYPE 54 46 43
'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S281.  Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
SPTAN1 MUTATED 0 0 4
SPTAN1 WILD-TYPE 68 40 35

Figure S45.  Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0095 (Fisher's exact test), Q value = 0.19

Table S282.  Gene #30: 'SPTAN1 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
SPTAN1 MUTATED 0 0 0 4 0 0 0
SPTAN1 WILD-TYPE 42 26 12 20 8 23 12

Figure S46.  Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00486 (Fisher's exact test), Q value = 0.14

Table S283.  Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
SPTAN1 MUTATED 0 0 4
SPTAN1 WILD-TYPE 51 56 36

Figure S47.  Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00939 (Fisher's exact test), Q value = 0.19

Table S284.  Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
SPTAN1 MUTATED 0 0 4
SPTAN1 WILD-TYPE 68 38 37

Figure S48.  Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0106 (Fisher's exact test), Q value = 0.2

Table S285.  Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
SPTAN1 MUTATED 0 0 4
SPTAN1 WILD-TYPE 67 36 40

Figure S49.  Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SPTAN1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0146 (Fisher's exact test), Q value = 0.24

Table S286.  Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
SPTAN1 MUTATED 0 0 0 4
SPTAN1 WILD-TYPE 36 32 38 37

Figure S50.  Get High-res Image Gene #30: 'SPTAN1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'CRB2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.579 (Fisher's exact test), Q value = 1

Table S287.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
CRB2 MUTATED 1 3 2
CRB2 WILD-TYPE 46 39 56
'CRB2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S288.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
CRB2 MUTATED 2 1 3
CRB2 WILD-TYPE 52 47 42
'CRB2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.778 (Fisher's exact test), Q value = 1

Table S289.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
CRB2 MUTATED 4 0 1 1
CRB2 WILD-TYPE 43 14 33 20
'CRB2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S290.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
CRB2 MUTATED 4 1 1
CRB2 WILD-TYPE 45 23 42
'CRB2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S291.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
CRB2 MUTATED 4 1 1
CRB2 WILD-TYPE 64 39 38
'CRB2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S292.  Gene #31: 'CRB2 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
CRB2 MUTATED 1 3 1 1 0 0 0
CRB2 WILD-TYPE 41 23 11 23 8 23 12
'CRB2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.449 (Fisher's exact test), Q value = 1

Table S293.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
CRB2 MUTATED 1 4 1
CRB2 WILD-TYPE 50 52 39
'CRB2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S294.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
CRB2 MUTATED 4 1 1
CRB2 WILD-TYPE 64 37 40
'CRB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.659 (Fisher's exact test), Q value = 1

Table S295.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
CRB2 MUTATED 4 1 1
CRB2 WILD-TYPE 63 35 43
'CRB2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0648 (Fisher's exact test), Q value = 0.54

Table S296.  Gene #31: 'CRB2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
CRB2 MUTATED 0 4 1 1
CRB2 WILD-TYPE 36 28 37 40
'OPLAH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.824 (Fisher's exact test), Q value = 1

Table S297.  Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
OPLAH MUTATED 2 1 1
OPLAH WILD-TYPE 45 41 57
'OPLAH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.549 (Fisher's exact test), Q value = 1

Table S298.  Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
OPLAH MUTATED 2 2 0
OPLAH WILD-TYPE 52 46 45
'OPLAH MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S299.  Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
OPLAH MUTATED 1 1 1 0
OPLAH WILD-TYPE 46 13 33 21
'OPLAH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S300.  Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
OPLAH MUTATED 1 1 1
OPLAH WILD-TYPE 48 23 42
'OPLAH MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S301.  Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
OPLAH MUTATED 2 1 1
OPLAH WILD-TYPE 66 39 38
'OPLAH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.309 (Fisher's exact test), Q value = 1

Table S302.  Gene #32: '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 = 0.56 (Fisher's exact test), Q value = 1

Table S303.  Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
OPLAH MUTATED 2 2 0
OPLAH WILD-TYPE 49 54 40
'OPLAH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S304.  Gene #32: '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 S305.  Gene #32: '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 = 0.539 (Fisher's exact test), Q value = 1

Table S306.  Gene #32: 'OPLAH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
OPLAH MUTATED 1 1 2 0
OPLAH WILD-TYPE 35 31 36 41
'C22ORF43 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S307.  Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
C22ORF43 MUTATED 0 2 1
C22ORF43 WILD-TYPE 47 40 57
'C22ORF43 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S308.  Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 53 47 44
'C22ORF43 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0563 (Fisher's exact test), Q value = 0.51

Table S309.  Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
C22ORF43 MUTATED 1 2 0 0
C22ORF43 WILD-TYPE 46 12 34 21
'C22ORF43 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S310.  Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 48 23 42
'C22ORF43 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S311.  Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 67 39 38
'C22ORF43 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S312.  Gene #33: '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 S313.  Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
C22ORF43 MUTATED 1 1 1
C22ORF43 WILD-TYPE 50 55 39
'C22ORF43 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S314.  Gene #33: '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 S315.  Gene #33: '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 = 1 (Fisher's exact test), Q value = 1

Table S316.  Gene #33: 'C22ORF43 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
C22ORF43 MUTATED 1 0 1 1
C22ORF43 WILD-TYPE 35 32 37 40
'GAS2L2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S317.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
GAS2L2 MUTATED 1 1 1
GAS2L2 WILD-TYPE 46 41 57
'GAS2L2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.201 (Fisher's exact test), Q value = 0.93

Table S318.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
GAS2L2 MUTATED 0 1 2
GAS2L2 WILD-TYPE 54 47 43
'GAS2L2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S319.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
GAS2L2 MUTATED 1 0 1 1
GAS2L2 WILD-TYPE 46 14 33 20
'GAS2L2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S320.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
GAS2L2 MUTATED 1 0 2
GAS2L2 WILD-TYPE 48 24 41
'GAS2L2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S321.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
GAS2L2 MUTATED 1 1 1
GAS2L2 WILD-TYPE 67 39 38
'GAS2L2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.421 (Fisher's exact test), Q value = 1

Table S322.  Gene #34: 'GAS2L2 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
GAS2L2 MUTATED 1 0 0 1 1 0 0
GAS2L2 WILD-TYPE 41 26 12 23 7 23 12
'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S323.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
GAS2L2 MUTATED 1 1 1
GAS2L2 WILD-TYPE 50 55 39
'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S324.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
GAS2L2 MUTATED 1 1 1
GAS2L2 WILD-TYPE 67 37 40
'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S325.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
GAS2L2 MUTATED 1 1 1
GAS2L2 WILD-TYPE 66 35 43
'GAS2L2 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S326.  Gene #34: 'GAS2L2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
GAS2L2 MUTATED 1 0 1 1
GAS2L2 WILD-TYPE 35 32 37 40
'CDC27 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0335 (Fisher's exact test), Q value = 0.36

Table S327.  Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
CDC27 MUTATED 2 4 0
CDC27 WILD-TYPE 45 38 58

Figure S51.  Get High-res Image Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'CDC27 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S328.  Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
CDC27 MUTATED 3 1 2
CDC27 WILD-TYPE 51 47 43
'CDC27 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.189 (Fisher's exact test), Q value = 0.92

Table S329.  Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
CDC27 MUTATED 4 1 0 0
CDC27 WILD-TYPE 43 13 34 21
'CDC27 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.179 (Fisher's exact test), Q value = 0.92

Table S330.  Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
CDC27 MUTATED 4 1 0
CDC27 WILD-TYPE 45 23 43
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.169 (Fisher's exact test), Q value = 0.89

Table S331.  Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
CDC27 MUTATED 5 1 0
CDC27 WILD-TYPE 63 39 39
'CDC27 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0574 (Fisher's exact test), Q value = 0.51

Table S332.  Gene #35: '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 = 0.33 (Fisher's exact test), Q value = 1

Table S333.  Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
CDC27 MUTATED 3 3 0
CDC27 WILD-TYPE 48 53 40
'CDC27 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S334.  Gene #35: '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 = 0.169 (Fisher's exact test), Q value = 0.89

Table S335.  Gene #35: '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 = 0.0488 (Fisher's exact test), Q value = 0.48

Table S336.  Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
CDC27 MUTATED 1 4 1 0
CDC27 WILD-TYPE 35 28 37 41

Figure S52.  Get High-res Image Gene #35: 'CDC27 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'MUC2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.4 (Fisher's exact test), Q value = 1

Table S337.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
MUC2 MUTATED 4 7 5
MUC2 WILD-TYPE 43 35 53
'MUC2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.945 (Fisher's exact test), Q value = 1

Table S338.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
MUC2 MUTATED 5 6 5
MUC2 WILD-TYPE 49 42 40
'MUC2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.262 (Fisher's exact test), Q value = 1

Table S339.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
MUC2 MUTATED 4 0 6 1
MUC2 WILD-TYPE 43 14 28 20
'MUC2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S340.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
MUC2 MUTATED 4 4 3
MUC2 WILD-TYPE 45 20 40
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S341.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
MUC2 MUTATED 7 3 6
MUC2 WILD-TYPE 61 37 33
'MUC2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.985 (Fisher's exact test), Q value = 1

Table S342.  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 = 0.501 (Fisher's exact test), Q value = 1

Table S343.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
MUC2 MUTATED 7 4 5
MUC2 WILD-TYPE 44 52 35
'MUC2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.944 (Fisher's exact test), Q value = 1

Table S344.  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 = 0.792 (Fisher's exact test), Q value = 1

Table S345.  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 = 0.793 (Fisher's exact test), Q value = 1

Table S346.  Gene #36: 'MUC2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
MUC2 MUTATED 5 2 4 5
MUC2 WILD-TYPE 31 30 34 36
'TPTE2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.622 (Fisher's exact test), Q value = 1

Table S347.  Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
TPTE2 MUTATED 2 2 1
TPTE2 WILD-TYPE 45 40 57
'TPTE2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.232 (Fisher's exact test), Q value = 1

Table S348.  Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
TPTE2 MUTATED 2 0 3
TPTE2 WILD-TYPE 52 48 42
'TPTE2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S349.  Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
TPTE2 MUTATED 2 0 1 0
TPTE2 WILD-TYPE 45 14 33 21
'TPTE2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S350.  Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
TPTE2 MUTATED 2 0 1
TPTE2 WILD-TYPE 47 24 42
'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S351.  Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
TPTE2 MUTATED 4 0 1
TPTE2 WILD-TYPE 64 40 38
'TPTE2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S352.  Gene #37: '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 = 0.0505 (Fisher's exact test), Q value = 0.48

Table S353.  Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
TPTE2 MUTATED 4 0 1
TPTE2 WILD-TYPE 47 56 39
'TPTE2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S354.  Gene #37: '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 = 0.443 (Fisher's exact test), Q value = 1

Table S355.  Gene #37: '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 = 0.422 (Fisher's exact test), Q value = 1

Table S356.  Gene #37: 'TPTE2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
TPTE2 MUTATED 2 2 0 1
TPTE2 WILD-TYPE 34 30 38 40
'NAT10 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.387 (Fisher's exact test), Q value = 1

Table S357.  Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
NAT10 MUTATED 0 2 2
NAT10 WILD-TYPE 47 40 56
'NAT10 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S358.  Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
NAT10 MUTATED 2 1 1
NAT10 WILD-TYPE 52 47 44
'NAT10 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S359.  Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
NAT10 MUTATED 1 0 1 1
NAT10 WILD-TYPE 46 14 33 20
'NAT10 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S360.  Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
NAT10 MUTATED 1 0 2
NAT10 WILD-TYPE 48 24 41
'NAT10 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S361.  Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
NAT10 MUTATED 2 1 1
NAT10 WILD-TYPE 66 39 38
'NAT10 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.254 (Fisher's exact test), Q value = 1

Table S362.  Gene #38: '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 = 0.832 (Fisher's exact test), Q value = 1

Table S363.  Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
NAT10 MUTATED 2 1 1
NAT10 WILD-TYPE 49 55 39
'NAT10 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S364.  Gene #38: '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 S365.  Gene #38: '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 = 0.493 (Fisher's exact test), Q value = 1

Table S366.  Gene #38: 'NAT10 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
NAT10 MUTATED 0 2 1 1
NAT10 WILD-TYPE 36 30 37 40
'INTS4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S367.  Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
INTS4 MUTATED 1 1 1
INTS4 WILD-TYPE 46 41 57
'INTS4 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S368.  Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
INTS4 MUTATED 1 1 1
INTS4 WILD-TYPE 53 47 44
'INTS4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S369.  Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
INTS4 MUTATED 2 1 0
INTS4 WILD-TYPE 66 39 39
'INTS4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S370.  Gene #39: 'INTS4 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
INTS4 MUTATED 1 1 0 0 0 1 0
INTS4 WILD-TYPE 41 25 12 24 8 22 12
'INTS4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S371.  Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
INTS4 MUTATED 2 1 0
INTS4 WILD-TYPE 49 55 40
'INTS4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.614 (Fisher's exact test), Q value = 1

Table S372.  Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
INTS4 MUTATED 2 1 0
INTS4 WILD-TYPE 66 37 41
'INTS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S373.  Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
INTS4 MUTATED 2 1 0
INTS4 WILD-TYPE 65 35 44
'INTS4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.707 (Fisher's exact test), Q value = 1

Table S374.  Gene #39: 'INTS4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
INTS4 MUTATED 1 1 1 0
INTS4 WILD-TYPE 35 31 37 41
'TTC38 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S375.  Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
TTC38 MUTATED 0 2 2
TTC38 WILD-TYPE 47 40 56
'TTC38 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.114 (Fisher's exact test), Q value = 0.71

Table S376.  Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
TTC38 MUTATED 1 0 3
TTC38 WILD-TYPE 53 48 42
'TTC38 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.891 (Fisher's exact test), Q value = 1

Table S377.  Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
TTC38 MUTATED 2 0 2 0
TTC38 WILD-TYPE 45 14 32 21
'TTC38 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.197 (Fisher's exact test), Q value = 0.93

Table S378.  Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
TTC38 MUTATED 2 2 0
TTC38 WILD-TYPE 47 22 43
'TTC38 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.287 (Fisher's exact test), Q value = 1

Table S379.  Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
TTC38 MUTATED 2 0 2
TTC38 WILD-TYPE 66 40 37
'TTC38 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.817 (Fisher's exact test), Q value = 1

Table S380.  Gene #40: '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 = 0.193 (Fisher's exact test), Q value = 0.92

Table S381.  Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
TTC38 MUTATED 2 0 2
TTC38 WILD-TYPE 49 56 38
'TTC38 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.381 (Fisher's exact test), Q value = 1

Table S382.  Gene #40: '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 = 0.578 (Fisher's exact test), Q value = 1

Table S383.  Gene #40: '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 = 0.255 (Fisher's exact test), Q value = 1

Table S384.  Gene #40: 'TTC38 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
TTC38 MUTATED 0 2 0 2
TTC38 WILD-TYPE 36 30 38 39
'RBM3 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.374 (Fisher's exact test), Q value = 1

Table S385.  Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
RBM3 MUTATED 0 2 1
RBM3 WILD-TYPE 47 40 57
'RBM3 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S386.  Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
RBM3 MUTATED 2 1 0
RBM3 WILD-TYPE 52 47 45
'RBM3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S387.  Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
RBM3 MUTATED 2 1 0
RBM3 WILD-TYPE 66 39 39
'RBM3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S388.  Gene #41: '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 = 0.115 (Fisher's exact test), Q value = 0.71

Table S389.  Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
RBM3 MUTATED 0 3 0
RBM3 WILD-TYPE 51 53 40
'RBM3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S390.  Gene #41: '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 = 0.605 (Fisher's exact test), Q value = 1

Table S391.  Gene #41: '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 = 0.131 (Fisher's exact test), Q value = 0.79

Table S392.  Gene #41: 'RBM3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
RBM3 MUTATED 0 2 1 0
RBM3 WILD-TYPE 36 30 37 41
'TCHH MUTATION STATUS' versus 'CN_CNMF'

P value = 0.518 (Fisher's exact test), Q value = 1

Table S393.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
TCHH MUTATED 3 1 1
TCHH WILD-TYPE 44 41 57
'TCHH MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.131 (Fisher's exact test), Q value = 0.79

Table S394.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
TCHH MUTATED 4 1 0
TCHH WILD-TYPE 50 47 45
'TCHH MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0734 (Fisher's exact test), Q value = 0.59

Table S395.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
TCHH MUTATED 1 2 0 1
TCHH WILD-TYPE 46 12 34 20
'TCHH MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S396.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
TCHH MUTATED 3 0 1
TCHH WILD-TYPE 46 24 42
'TCHH MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S397.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
TCHH MUTATED 4 1 0
TCHH WILD-TYPE 64 39 39
'TCHH MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S398.  Gene #42: 'TCHH 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
TCHH MUTATED 3 1 0 0 0 1 0
TCHH WILD-TYPE 39 25 12 24 8 22 12
'TCHH MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.372 (Fisher's exact test), Q value = 1

Table S399.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
TCHH MUTATED 3 2 0
TCHH WILD-TYPE 48 54 40
'TCHH MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.322 (Fisher's exact test), Q value = 1

Table S400.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

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

P value = 0.209 (Fisher's exact test), Q value = 0.95

Table S401.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
TCHH MUTATED 4 1 0
TCHH WILD-TYPE 63 35 44
'TCHH MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.331 (Fisher's exact test), Q value = 1

Table S402.  Gene #42: 'TCHH MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
TCHH MUTATED 2 2 1 0
TCHH WILD-TYPE 34 30 37 41
'ZC3H11A MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0526 (Fisher's exact test), Q value = 0.49

Table S403.  Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
ZC3H11A MUTATED 3 0 0
ZC3H11A WILD-TYPE 44 42 58
'ZC3H11A MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S404.  Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
ZC3H11A MUTATED 2 1 0
ZC3H11A WILD-TYPE 52 47 45
'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S405.  Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
ZC3H11A MUTATED 2 0 1
ZC3H11A WILD-TYPE 66 40 38
'ZC3H11A MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.471 (Fisher's exact test), Q value = 1

Table S406.  Gene #43: 'ZC3H11A 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
ZC3H11A MUTATED 2 0 0 0 0 0 1
ZC3H11A WILD-TYPE 40 26 12 24 8 23 11
'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.373 (Fisher's exact test), Q value = 1

Table S407.  Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
ZC3H11A MUTATED 2 0 1
ZC3H11A WILD-TYPE 49 56 39
'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S408.  Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
ZC3H11A MUTATED 2 0 1
ZC3H11A WILD-TYPE 66 38 40
'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S409.  Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
ZC3H11A MUTATED 2 0 1
ZC3H11A WILD-TYPE 65 36 43
'ZC3H11A MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.397 (Fisher's exact test), Q value = 1

Table S410.  Gene #43: 'ZC3H11A MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
ZC3H11A MUTATED 2 0 0 1
ZC3H11A WILD-TYPE 34 32 38 40
'RAC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.384 (Fisher's exact test), Q value = 1

Table S411.  Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
RAC1 MUTATED 0 2 2
RAC1 WILD-TYPE 47 40 56
'RAC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.388 (Fisher's exact test), Q value = 1

Table S412.  Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
RAC1 MUTATED 3 1 0
RAC1 WILD-TYPE 51 47 45
'RAC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S413.  Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
RAC1 MUTATED 2 0 0 1
RAC1 WILD-TYPE 45 14 34 20
'RAC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S414.  Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
RAC1 MUTATED 2 0 1
RAC1 WILD-TYPE 47 24 42
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S415.  Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
RAC1 MUTATED 3 1 0
RAC1 WILD-TYPE 65 39 39
'RAC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.634 (Fisher's exact test), Q value = 1

Table S416.  Gene #44: '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 = 0.316 (Fisher's exact test), Q value = 1

Table S417.  Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
RAC1 MUTATED 3 1 0
RAC1 WILD-TYPE 48 55 40
'RAC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.481 (Fisher's exact test), Q value = 1

Table S418.  Gene #44: '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 = 0.366 (Fisher's exact test), Q value = 1

Table S419.  Gene #44: '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 = 0.0849 (Fisher's exact test), Q value = 0.63

Table S420.  Gene #44: 'RAC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
RAC1 MUTATED 3 0 1 0
RAC1 WILD-TYPE 33 32 37 41
'MTIF3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S421.  Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
MTIF3 MUTATED 1 1 1
MTIF3 WILD-TYPE 46 41 57
'MTIF3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.402 (Fisher's exact test), Q value = 1

Table S422.  Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
MTIF3 MUTATED 1 0 2
MTIF3 WILD-TYPE 53 48 43
'MTIF3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S423.  Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
MTIF3 MUTATED 2 0 1 0
MTIF3 WILD-TYPE 45 14 33 21
'MTIF3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S424.  Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
MTIF3 MUTATED 2 0 1
MTIF3 WILD-TYPE 47 24 42
'MTIF3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.621 (Fisher's exact test), Q value = 1

Table S425.  Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
MTIF3 MUTATED 2 0 1
MTIF3 WILD-TYPE 66 40 38
'MTIF3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S426.  Gene #45: '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 = 0.373 (Fisher's exact test), Q value = 1

Table S427.  Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
MTIF3 MUTATED 2 0 1
MTIF3 WILD-TYPE 49 56 39
'MTIF3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S428.  Gene #45: '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 = 0.793 (Fisher's exact test), Q value = 1

Table S429.  Gene #45: '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 = 0.797 (Fisher's exact test), Q value = 1

Table S430.  Gene #45: 'MTIF3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
MTIF3 MUTATED 1 1 0 1
MTIF3 WILD-TYPE 35 31 38 40
'MFF MUTATION STATUS' versus 'CN_CNMF'

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

Table S431.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
MFF MUTATED 1 1 1
MFF WILD-TYPE 46 41 57
'MFF MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S432.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
MFF MUTATED 2 1 0
MFF WILD-TYPE 52 47 45
'MFF MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S433.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
MFF MUTATED 2 0 0 1
MFF WILD-TYPE 45 14 34 20
'MFF MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S434.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
MFF MUTATED 2 0 1
MFF WILD-TYPE 47 24 42
'MFF MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S435.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
MFF MUTATED 2 1 0
MFF WILD-TYPE 66 39 39
'MFF MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.949 (Fisher's exact test), Q value = 1

Table S436.  Gene #46: 'MFF 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
MFF MUTATED 1 1 0 0 0 1 0
MFF WILD-TYPE 41 25 12 24 8 22 12
'MFF MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S437.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
MFF MUTATED 2 1 0
MFF WILD-TYPE 49 55 40
'MFF MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S438.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
MFF MUTATED 2 1 0
MFF WILD-TYPE 66 37 41
'MFF MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S439.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
MFF MUTATED 2 1 0
MFF WILD-TYPE 65 35 44
'MFF MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.704 (Fisher's exact test), Q value = 1

Table S440.  Gene #46: 'MFF MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
MFF MUTATED 1 1 1 0
MFF WILD-TYPE 35 31 37 41
'PABPC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S441.  Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
PABPC3 MUTATED 1 1 2
PABPC3 WILD-TYPE 46 41 56
'PABPC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.464 (Fisher's exact test), Q value = 1

Table S442.  Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
PABPC3 MUTATED 2 0 2
PABPC3 WILD-TYPE 52 48 43
'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.284 (Fisher's exact test), Q value = 1

Table S443.  Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
PABPC3 MUTATED 2 0 2
PABPC3 WILD-TYPE 66 40 37
'PABPC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S444.  Gene #47: '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 = 0.192 (Fisher's exact test), Q value = 0.92

Table S445.  Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
PABPC3 MUTATED 2 0 2
PABPC3 WILD-TYPE 49 56 38
'PABPC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.38 (Fisher's exact test), Q value = 1

Table S446.  Gene #47: '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 S447.  Gene #47: '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 = 0.305 (Fisher's exact test), Q value = 1

Table S448.  Gene #47: 'PABPC3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
PABPC3 MUTATED 2 0 0 2
PABPC3 WILD-TYPE 34 32 38 39
'CUX1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S449.  Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
CUX1 MUTATED 1 1 3
CUX1 WILD-TYPE 46 41 55
'CUX1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S450.  Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
CUX1 MUTATED 2 1 2
CUX1 WILD-TYPE 52 47 43
'CUX1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S451.  Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
CUX1 MUTATED 1 0 1 1
CUX1 WILD-TYPE 46 14 33 20
'CUX1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.602 (Fisher's exact test), Q value = 1

Table S452.  Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
CUX1 MUTATED 1 0 2
CUX1 WILD-TYPE 48 24 41
'CUX1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S453.  Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
CUX1 MUTATED 2 1 2
CUX1 WILD-TYPE 66 39 37
'CUX1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.962 (Fisher's exact test), Q value = 1

Table S454.  Gene #48: '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 = 0.635 (Fisher's exact test), Q value = 1

Table S455.  Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
CUX1 MUTATED 2 1 2
CUX1 WILD-TYPE 49 55 38
'CUX1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S456.  Gene #48: '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 = 0.858 (Fisher's exact test), Q value = 1

Table S457.  Gene #48: '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 = 0.72 (Fisher's exact test), Q value = 1

Table S458.  Gene #48: 'CUX1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
CUX1 MUTATED 2 0 1 2
CUX1 WILD-TYPE 34 32 37 39
'PCMTD1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0915 (Fisher's exact test), Q value = 0.64

Table S459.  Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
PCMTD1 MUTATED 2 3 0
PCMTD1 WILD-TYPE 45 39 58
'PCMTD1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S460.  Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
PCMTD1 MUTATED 3 1 1
PCMTD1 WILD-TYPE 51 47 44
'PCMTD1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S461.  Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
PCMTD1 MUTATED 3 0 0 1
PCMTD1 WILD-TYPE 44 14 34 20
'PCMTD1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.535 (Fisher's exact test), Q value = 1

Table S462.  Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
PCMTD1 MUTATED 3 0 1
PCMTD1 WILD-TYPE 46 24 42
'PCMTD1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.382 (Fisher's exact test), Q value = 1

Table S463.  Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
PCMTD1 MUTATED 4 1 0
PCMTD1 WILD-TYPE 64 39 39
'PCMTD1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S464.  Gene #49: '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 = 0.373 (Fisher's exact test), Q value = 1

Table S465.  Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
PCMTD1 MUTATED 3 2 0
PCMTD1 WILD-TYPE 48 54 40
'PCMTD1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.317 (Fisher's exact test), Q value = 1

Table S466.  Gene #49: '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 = 0.208 (Fisher's exact test), Q value = 0.95

Table S467.  Gene #49: '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 = 0.33 (Fisher's exact test), Q value = 1

Table S468.  Gene #49: 'PCMTD1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
PCMTD1 MUTATED 2 2 1 0
PCMTD1 WILD-TYPE 34 30 37 41
'EZH2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.826 (Fisher's exact test), Q value = 1

Table S469.  Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
EZH2 MUTATED 2 1 1
EZH2 WILD-TYPE 45 41 57
'EZH2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 1

Table S470.  Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
EZH2 MUTATED 2 2 0
EZH2 WILD-TYPE 52 46 45
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S471.  Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
EZH2 MUTATED 2 2 0
EZH2 WILD-TYPE 66 38 39
'EZH2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S472.  Gene #50: '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 = 0.56 (Fisher's exact test), Q value = 1

Table S473.  Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
EZH2 MUTATED 2 2 0
EZH2 WILD-TYPE 49 54 40
'EZH2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.278 (Fisher's exact test), Q value = 1

Table S474.  Gene #50: '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 = 0.275 (Fisher's exact test), Q value = 1

Table S475.  Gene #50: '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 = 0.279 (Fisher's exact test), Q value = 1

Table S476.  Gene #50: 'EZH2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
EZH2 MUTATED 2 0 2 0
EZH2 WILD-TYPE 34 32 36 41
'HTT MUTATION STATUS' versus 'CN_CNMF'

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

Table S477.  Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
HTT MUTATED 1 1 1
HTT WILD-TYPE 46 41 57
'HTT MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S478.  Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
HTT MUTATED 2 1 0
HTT WILD-TYPE 52 47 45
'HTT MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S479.  Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
HTT MUTATED 2 1 0
HTT WILD-TYPE 66 39 39
'HTT MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.682 (Fisher's exact test), Q value = 1

Table S480.  Gene #51: '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 = 0.628 (Fisher's exact test), Q value = 1

Table S481.  Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
HTT MUTATED 2 1 0
HTT WILD-TYPE 49 55 40
'HTT MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S482.  Gene #51: '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 = 0.606 (Fisher's exact test), Q value = 1

Table S483.  Gene #51: '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 = 0.705 (Fisher's exact test), Q value = 1

Table S484.  Gene #51: 'HTT MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
HTT MUTATED 1 1 1 0
HTT WILD-TYPE 35 31 37 41
'GSX2 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.31 (Fisher's exact test), Q value = 1

Table S485.  Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
GSX2 MUTATED 0 1 3
GSX2 WILD-TYPE 47 41 55
'GSX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S486.  Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
GSX2 MUTATED 0 2 2
GSX2 WILD-TYPE 54 46 43
'GSX2 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.324 (Fisher's exact test), Q value = 1

Table S487.  Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
GSX2 MUTATED 1 0 3 0
GSX2 WILD-TYPE 46 14 31 21
'GSX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0273 (Fisher's exact test), Q value = 0.31

Table S488.  Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
GSX2 MUTATED 1 3 0
GSX2 WILD-TYPE 48 21 43

Figure S53.  Get High-res Image Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'GSX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S489.  Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
GSX2 MUTATED 1 1 2
GSX2 WILD-TYPE 67 39 37
'GSX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.243 (Fisher's exact test), Q value = 1

Table S490.  Gene #52: '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 = 0.0666 (Fisher's exact test), Q value = 0.55

Table S491.  Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
GSX2 MUTATED 1 0 3
GSX2 WILD-TYPE 50 56 37
'GSX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.151 (Fisher's exact test), Q value = 0.83

Table S492.  Gene #52: '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 = 0.813 (Fisher's exact test), Q value = 1

Table S493.  Gene #52: '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 = 0.788 (Fisher's exact test), Q value = 1

Table S494.  Gene #52: 'GSX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
GSX2 MUTATED 0 1 1 2
GSX2 WILD-TYPE 36 31 37 39
'AHDC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.56 (Fisher's exact test), Q value = 1

Table S495.  Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
AHDC1 MUTATED 2 0 2
AHDC1 WILD-TYPE 45 42 56
'AHDC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00792 (Fisher's exact test), Q value = 0.19

Table S496.  Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
AHDC1 MUTATED 0 0 4
AHDC1 WILD-TYPE 54 48 41

Figure S54.  Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'AHDC1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.0619 (Fisher's exact test), Q value = 0.53

Table S497.  Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
AHDC1 MUTATED 0 1 3 0
AHDC1 WILD-TYPE 47 13 31 21
'AHDC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.108 (Fisher's exact test), Q value = 0.69

Table S498.  Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
AHDC1 MUTATED 0 2 2
AHDC1 WILD-TYPE 49 22 41
'AHDC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00412 (Fisher's exact test), Q value = 0.13

Table S499.  Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
AHDC1 MUTATED 0 0 4
AHDC1 WILD-TYPE 68 40 35

Figure S55.  Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'AHDC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0268 (Fisher's exact test), Q value = 0.31

Table S500.  Gene #53: '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 S56.  Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00496 (Fisher's exact test), Q value = 0.14

Table S501.  Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
AHDC1 MUTATED 0 0 4
AHDC1 WILD-TYPE 51 56 36

Figure S57.  Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00955 (Fisher's exact test), Q value = 0.19

Table S502.  Gene #53: '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 S58.  Get High-res Image Gene #53: '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 = 0.2

Table S503.  Gene #53: '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 S59.  Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'AHDC1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0143 (Fisher's exact test), Q value = 0.24

Table S504.  Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
AHDC1 MUTATED 0 0 0 4
AHDC1 WILD-TYPE 36 32 38 37

Figure S60.  Get High-res Image Gene #53: 'AHDC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'RFC3 MUTATION STATUS' versus 'CN_CNMF'

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

Table S505.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
RFC3 MUTATED 1 1 1
RFC3 WILD-TYPE 46 41 57
'RFC3 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.52 (Fisher's exact test), Q value = 1

Table S506.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
RFC3 MUTATED 1 2 0
RFC3 WILD-TYPE 53 46 45
'RFC3 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S507.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
RFC3 MUTATED 1 1 1 0
RFC3 WILD-TYPE 46 13 33 21
'RFC3 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.599 (Fisher's exact test), Q value = 1

Table S508.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
RFC3 MUTATED 1 0 2
RFC3 WILD-TYPE 48 24 41
'RFC3 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.451 (Fisher's exact test), Q value = 1

Table S509.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
RFC3 MUTATED 1 2 0
RFC3 WILD-TYPE 67 38 39
'RFC3 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.329 (Fisher's exact test), Q value = 1

Table S510.  Gene #54: 'RFC3 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
RFC3 MUTATED 0 1 1 0 0 1 0
RFC3 WILD-TYPE 42 25 11 24 8 22 12
'RFC3 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.779 (Fisher's exact test), Q value = 1

Table S511.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
RFC3 MUTATED 1 2 0
RFC3 WILD-TYPE 50 54 40
'RFC3 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.244 (Fisher's exact test), Q value = 1

Table S512.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
RFC3 MUTATED 1 2 0
RFC3 WILD-TYPE 67 36 41
'RFC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S513.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
RFC3 MUTATED 1 1 1
RFC3 WILD-TYPE 66 35 43
'RFC3 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.252 (Fisher's exact test), Q value = 1

Table S514.  Gene #54: 'RFC3 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
RFC3 MUTATED 0 1 2 0
RFC3 WILD-TYPE 36 31 36 41
'CHD4 MUTATION STATUS' versus 'CN_CNMF'

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

Table S515.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
CHD4 MUTATED 1 1 2
CHD4 WILD-TYPE 46 41 56
'CHD4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.69 (Fisher's exact test), Q value = 1

Table S516.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
CHD4 MUTATED 1 1 2
CHD4 WILD-TYPE 53 47 43
'CHD4 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S517.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
CHD4 MUTATED 2 0 1 1
CHD4 WILD-TYPE 45 14 33 20
'CHD4 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S518.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
CHD4 MUTATED 2 0 2
CHD4 WILD-TYPE 47 24 41
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S519.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
CHD4 MUTATED 2 1 1
CHD4 WILD-TYPE 66 39 38
'CHD4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.409 (Fisher's exact test), Q value = 1

Table S520.  Gene #55: 'CHD4 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
CHD4 MUTATED 1 1 1 0 0 0 1
CHD4 WILD-TYPE 41 25 11 24 8 23 11
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S521.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
CHD4 MUTATED 1 2 1
CHD4 WILD-TYPE 50 54 39
'CHD4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S522.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
CHD4 MUTATED 2 1 1
CHD4 WILD-TYPE 66 37 40
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S523.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
CHD4 MUTATED 2 0 2
CHD4 WILD-TYPE 65 36 42
'CHD4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

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

Table S524.  Gene #55: 'CHD4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
CHD4 MUTATED 1 1 1 1
CHD4 WILD-TYPE 35 31 37 40
'RUNX2 MUTATION STATUS' versus 'CN_CNMF'

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

Table S525.  Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
RUNX2 MUTATED 1 1 2
RUNX2 WILD-TYPE 46 41 56
'RUNX2 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S526.  Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
RUNX2 MUTATED 1 1 2
RUNX2 WILD-TYPE 53 47 43
'RUNX2 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S527.  Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
RUNX2 MUTATED 1 0 1 1
RUNX2 WILD-TYPE 46 14 33 20
'RUNX2 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.601 (Fisher's exact test), Q value = 1

Table S528.  Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
RUNX2 MUTATED 1 0 2
RUNX2 WILD-TYPE 48 24 41
'RUNX2 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S529.  Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
RUNX2 MUTATED 2 1 1
RUNX2 WILD-TYPE 66 39 38
'RUNX2 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S530.  Gene #56: '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 = 0.832 (Fisher's exact test), Q value = 1

Table S531.  Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
RUNX2 MUTATED 2 1 1
RUNX2 WILD-TYPE 49 55 39
'RUNX2 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S532.  Gene #56: '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 S533.  Gene #56: '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 = 0.495 (Fisher's exact test), Q value = 1

Table S534.  Gene #56: 'RUNX2 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
RUNX2 MUTATED 0 2 1 1
RUNX2 WILD-TYPE 36 30 37 40
'SP4 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.306 (Fisher's exact test), Q value = 1

Table S535.  Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
SP4 MUTATED 0 1 3
SP4 WILD-TYPE 47 41 55
'SP4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0184 (Fisher's exact test), Q value = 0.26

Table S536.  Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
SP4 MUTATED 0 4 0
SP4 WILD-TYPE 54 44 45

Figure S61.  Get High-res Image Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'SP4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0503 (Fisher's exact test), Q value = 0.48

Table S537.  Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
SP4 MUTATED 0 3 1
SP4 WILD-TYPE 68 37 38
'SP4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.112 (Fisher's exact test), Q value = 0.7

Table S538.  Gene #57: '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 = 0.252 (Fisher's exact test), Q value = 1

Table S539.  Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
SP4 MUTATED 0 3 1
SP4 WILD-TYPE 51 53 39
'SP4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0274 (Fisher's exact test), Q value = 0.31

Table S540.  Gene #57: '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 S62.  Get High-res Image Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'SP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0275 (Fisher's exact test), Q value = 0.31

Table S541.  Gene #57: '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 S63.  Get High-res Image Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'SP4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.173 (Fisher's exact test), Q value = 0.9

Table S542.  Gene #57: 'SP4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
SP4 MUTATED 0 0 3 1
SP4 WILD-TYPE 36 32 35 40
'DIAPH1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S543.  Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
DIAPH1 MUTATED 1 1 1
DIAPH1 WILD-TYPE 46 41 57
'DIAPH1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.644 (Fisher's exact test), Q value = 1

Table S544.  Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
DIAPH1 MUTATED 2 0 1
DIAPH1 WILD-TYPE 52 48 44
'DIAPH1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S545.  Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
DIAPH1 MUTATED 2 0 1
DIAPH1 WILD-TYPE 66 40 38
'DIAPH1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S546.  Gene #58: 'DIAPH1 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
DIAPH1 MUTATED 2 0 0 1 0 0 0
DIAPH1 WILD-TYPE 40 26 12 23 8 23 12
'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

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

Table S547.  Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
DIAPH1 MUTATED 1 1 1
DIAPH1 WILD-TYPE 50 55 39
'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S548.  Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
DIAPH1 MUTATED 2 0 1
DIAPH1 WILD-TYPE 66 38 40
'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S549.  Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
DIAPH1 MUTATED 2 0 1
DIAPH1 WILD-TYPE 65 36 43
'DIAPH1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.797 (Fisher's exact test), Q value = 1

Table S550.  Gene #58: 'DIAPH1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
DIAPH1 MUTATED 1 1 0 1
DIAPH1 WILD-TYPE 35 31 38 40
'PLEC MUTATION STATUS' versus 'CN_CNMF'

P value = 0.0498 (Fisher's exact test), Q value = 0.48

Table S551.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
PLEC MUTATED 6 0 4
PLEC WILD-TYPE 41 42 54

Figure S64.  Get High-res Image Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'PLEC MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.272 (Fisher's exact test), Q value = 1

Table S552.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
PLEC MUTATED 5 1 4
PLEC WILD-TYPE 49 47 41
'PLEC MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.379 (Fisher's exact test), Q value = 1

Table S553.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
PLEC MUTATED 2 2 4 1
PLEC WILD-TYPE 45 12 30 20
'PLEC MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.148 (Fisher's exact test), Q value = 0.83

Table S554.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
PLEC MUTATED 2 4 3
PLEC WILD-TYPE 47 20 40
'PLEC MUTATION STATUS' versus 'MRNASEQ_CNMF'

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

Table S555.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
PLEC MUTATED 4 2 4
PLEC WILD-TYPE 64 38 35
'PLEC MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.195 (Fisher's exact test), Q value = 0.92

Table S556.  Gene #59: 'PLEC 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
PLEC MUTATED 4 0 1 2 1 0 2
PLEC WILD-TYPE 38 26 11 22 7 23 10
'PLEC MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.425 (Fisher's exact test), Q value = 1

Table S557.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
PLEC MUTATED 4 2 4
PLEC WILD-TYPE 47 54 36
'PLEC MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.698 (Fisher's exact test), Q value = 1

Table S558.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
PLEC MUTATED 4 2 4
PLEC WILD-TYPE 64 36 37
'PLEC MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.336 (Fisher's exact test), Q value = 1

Table S559.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
PLEC MUTATED 4 1 5
PLEC WILD-TYPE 63 35 39
'PLEC MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.0854 (Fisher's exact test), Q value = 0.63

Table S560.  Gene #59: 'PLEC MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
PLEC MUTATED 4 0 1 5
PLEC WILD-TYPE 32 32 37 36
'NHS MUTATION STATUS' versus 'CN_CNMF'

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

Table S561.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
NHS MUTATED 1 0 2
NHS WILD-TYPE 46 42 56
'NHS MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S562.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
NHS MUTATED 2 1 0
NHS WILD-TYPE 52 47 45
'NHS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.318 (Fisher's exact test), Q value = 1

Table S563.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
NHS MUTATED 1 1 0 1
NHS WILD-TYPE 46 13 34 20
'NHS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S564.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
NHS MUTATED 2 0 1
NHS WILD-TYPE 47 24 42
'NHS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.794 (Fisher's exact test), Q value = 1

Table S565.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
NHS MUTATED 2 1 0
NHS WILD-TYPE 66 39 39
'NHS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

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

Table S566.  Gene #60: 'NHS 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
NHS MUTATED 2 0 0 0 0 1 0
NHS WILD-TYPE 40 26 12 24 8 22 12
'NHS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.627 (Fisher's exact test), Q value = 1

Table S567.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
NHS MUTATED 2 1 0
NHS WILD-TYPE 49 55 40
'NHS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S568.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 38 41
NHS MUTATED 2 1 0
NHS WILD-TYPE 66 37 41
'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

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

Table S569.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 67 36 44
NHS MUTATED 2 1 0
NHS WILD-TYPE 65 35 44
'NHS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.705 (Fisher's exact test), Q value = 1

Table S570.  Gene #60: 'NHS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
NHS MUTATED 1 1 1 0
NHS WILD-TYPE 35 31 37 41
'PIK3CD MUTATION STATUS' versus 'CN_CNMF'

P value = 0.24 (Fisher's exact test), Q value = 1

Table S571.  Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
PIK3CD MUTATED 3 0 1
PIK3CD WILD-TYPE 44 42 57
'PIK3CD MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.265 (Fisher's exact test), Q value = 1

Table S572.  Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
PIK3CD MUTATED 3 0 1
PIK3CD WILD-TYPE 51 48 44
'PIK3CD MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.483 (Fisher's exact test), Q value = 1

Table S573.  Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
PIK3CD MUTATED 3 0 1
PIK3CD WILD-TYPE 65 40 38
'PIK3CD MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.369 (Fisher's exact test), Q value = 1

Table S574.  Gene #61: '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 = 0.14 (Fisher's exact test), Q value = 0.81

Table S575.  Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
PIK3CD MUTATED 3 0 1
PIK3CD WILD-TYPE 48 56 39
'PIK3CD MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.699 (Fisher's exact test), Q value = 1

Table S576.  Gene #61: '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 S577.  Gene #61: '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 = 0.102 (Fisher's exact test), Q value = 0.67

Table S578.  Gene #61: 'PIK3CD MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
PIK3CD MUTATED 3 0 0 1
PIK3CD WILD-TYPE 33 32 38 40
'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

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

Table S579.  Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
EPAS1 MUTATED 2 0 3
EPAS1 WILD-TYPE 45 42 55
'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S580.  Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
EPAS1 MUTATED 2 1 2
EPAS1 WILD-TYPE 52 47 43
'EPAS1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S581.  Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
EPAS1 MUTATED 1 0 2 1
EPAS1 WILD-TYPE 46 14 32 20
'EPAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.83 (Fisher's exact test), Q value = 1

Table S582.  Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
EPAS1 MUTATED 1 1 2
EPAS1 WILD-TYPE 48 23 41
'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.724 (Fisher's exact test), Q value = 1

Table S583.  Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
EPAS1 MUTATED 2 1 2
EPAS1 WILD-TYPE 66 39 37
'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S584.  Gene #62: '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 = 0.633 (Fisher's exact test), Q value = 1

Table S585.  Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
EPAS1 MUTATED 2 1 2
EPAS1 WILD-TYPE 49 55 38
'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S586.  Gene #62: '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 = 0.858 (Fisher's exact test), Q value = 1

Table S587.  Gene #62: '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 = 0.719 (Fisher's exact test), Q value = 1

Table S588.  Gene #62: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
EPAS1 MUTATED 2 0 1 2
EPAS1 WILD-TYPE 34 32 37 39
'DLC1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.276 (Fisher's exact test), Q value = 1

Table S589.  Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 47 42 58
DLC1 MUTATED 2 1 0
DLC1 WILD-TYPE 45 41 58
'DLC1 MUTATION STATUS' versus 'METHLYATION_CNMF'

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

Table S590.  Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 54 48 45
DLC1 MUTATED 1 1 1
DLC1 WILD-TYPE 53 47 44
'DLC1 MUTATION STATUS' versus 'RPPA_CNMF'

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

Table S591.  Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 47 14 34 21
DLC1 MUTATED 2 0 0 1
DLC1 WILD-TYPE 45 14 34 20
'DLC1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

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

Table S592.  Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 49 24 43
DLC1 MUTATED 2 0 1
DLC1 WILD-TYPE 47 24 42
'DLC1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.796 (Fisher's exact test), Q value = 1

Table S593.  Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 68 40 39
DLC1 MUTATED 2 1 0
DLC1 WILD-TYPE 66 39 39
'DLC1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.95 (Fisher's exact test), Q value = 1

Table S594.  Gene #63: '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 = 0.629 (Fisher's exact test), Q value = 1

Table S595.  Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients CLUS_1 CLUS_2 CLUS_3
ALL 51 56 40
DLC1 MUTATED 2 1 0
DLC1 WILD-TYPE 49 55 40
'DLC1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

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

Table S596.  Gene #63: '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 = 0.608 (Fisher's exact test), Q value = 1

Table S597.  Gene #63: '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 = 0.702 (Fisher's exact test), Q value = 1

Table S598.  Gene #63: 'DLC1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients CLUS_1 CLUS_2 CLUS_3 CLUS_4
ALL 36 32 38 41
DLC1 MUTATED 1 1 1 0
DLC1 WILD-TYPE 35 31 37 41
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/15890416/transformed.cor.cli.txt

  • Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/TGCT-TP/15111345/TGCT-TP.transferedmergedcluster.txt

  • Number of patients = 147

  • Number of significantly mutated genes = 63

  • Number of Molecular subtypes = 10

  • Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)
[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)
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